© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Mar 21, 2024. + Last updated on Apr 03, 2024.
#!/usr/bin/env python3
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
#
-# Copyright (c) 2021 Authors and contributors
+# Copyright (c) 2024 Authors and contributors
#
# Released under the GNU Public Licence, v2 or any higher version
# SPDX-License-Identifier: GPL-2.0-or-later
@@ -195,13 +195,20 @@ Source code for mdacli.cli
args = ap.parse_args()
+ # Set the logging level based on the verbose argument
+ # If verbose is not an argument, default to WARNING
+ if not hasattr(args, "verbose") or not args.verbose:
+ level = logging.WARNING
+ else:
+ level = logging.INFO
+
if args.debug:
- args.verbose = True
+ level = logging.DEBUG
else:
- # Ignore all warnings if not in debug mode
+ # Ignore all warnings if not in debug mode, because MDA is noisy
warnings.filterwarnings("ignore")
- with setup_logging(logger, logfile=args.logfile, debug=args.debug):
+ with setup_logging(logger, logfile=args.logfile, level=level):
# Execute the main client interface.
try:
analysis_callable = args.analysis_callable
@@ -240,7 +247,7 @@ Source code for mdacli.cli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/_modules/mdacli/colors.html b/0.1.29/_modules/mdacli/colors.html
index b86bfa9..b8e8167 100644
--- a/0.1.29/_modules/mdacli/colors.html
+++ b/0.1.29/_modules/mdacli/colors.html
@@ -314,7 +314,7 @@ Source code for mdacli.colors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/_modules/mdacli/libcli.html b/0.1.29/_modules/mdacli/libcli.html
index 4924c82..7c2a311 100644
--- a/0.1.29/_modules/mdacli/libcli.html
+++ b/0.1.29/_modules/mdacli/libcli.html
@@ -958,7 +958,7 @@ Source code for mdacli.libcli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/_modules/mdacli/logger.html b/0.1.29/_modules/mdacli/logger.html
index dd1ce0c..995bd83 100644
--- a/0.1.29/_modules/mdacli/logger.html
+++ b/0.1.29/_modules/mdacli/logger.html
@@ -106,7 +106,7 @@ Source code for mdacli.logger
[docs]
@contextlib.contextmanager
-def setup_logging(logobj, logfile=None, debug=False):
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
"""
Create a logging environment for a given logobj.
@@ -116,19 +116,20 @@ Source code for mdacli.logger
A logging instance
logfile : str
Name of the log file
- debug : bool
- If ``True`` detailed debug logs inludcing filename and function name
- are displayed. If ``False`` only the message logged from
- errors, warnings and infos will be displayed.
+ level : int
+ Set the root logger level to the specified level. If for example set
+ to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
+ function name are displayed. For :py:obj:`logging.INFO only the message
+ logged from errors, warnings and infos will be displayed.
"""
try:
- format = '{message}'
- if debug:
- format = "[{levelname}] {filename}:{name}:{funcName}:{lineno}: " \
- + format
- level = logging.DEBUG
+ if level == logging.DEBUG:
+ format = (
+ "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+ "{message}"
+ )
else:
- level = logging.INFO
+ format = "{message}"
logging.basicConfig(format=format,
handlers=[logging.StreamHandler(sys.stdout)],
@@ -164,7 +165,7 @@ Source code for mdacli.logger
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/_modules/mdacli/save.html b/0.1.29/_modules/mdacli/save.html
index 1081a1c..8a8f43c 100644
--- a/0.1.29/_modules/mdacli/save.html
+++ b/0.1.29/_modules/mdacli/save.html
@@ -553,7 +553,7 @@ Source code for mdacli.save
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/_modules/mdacli/utils.html b/0.1.29/_modules/mdacli/utils.html
index 08f9441..ddf5257 100644
--- a/0.1.29/_modules/mdacli/utils.html
+++ b/0.1.29/_modules/mdacli/utils.html
@@ -369,7 +369,7 @@ Source code for mdacli.utils
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api.html b/0.1.29/api.html
index 0d24cb9..89e0deb 100644
--- a/0.1.29/api.html
+++ b/0.1.29/api.html
@@ -127,7 +127,7 @@ API library documentation
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/cli.html b/0.1.29/api/cli.html
index 267c4f5..9341038 100644
--- a/0.1.29/api/cli.html
+++ b/0.1.29/api/cli.html
@@ -106,7 +106,7 @@
The toplevel command line interface.
-
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140119435511120'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140259180724288'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
Create the command-line interface.
This function creates a command line interface with a given name based
on a module list.
@@ -160,7 +160,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/colors.html b/0.1.29/api/colors.html
index b985b15..ab1fe25 100644
--- a/0.1.29/api/colors.html
+++ b/0.1.29/api/colors.html
@@ -330,7 +330,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/libcli.html b/0.1.29/api/libcli.html
index cd90878..41c9a92 100644
--- a/0.1.29/api/libcli.html
+++ b/0.1.29/api/libcli.html
@@ -427,7 +427,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/logger.html b/0.1.29/api/logger.html
index f364380..aa59fa4 100644
--- a/0.1.29/api/logger.html
+++ b/0.1.29/api/logger.html
@@ -106,16 +106,17 @@
Logging.
-
-mdacli.logger.setup_logging(logobj, logfile=None, debug=False)[source]
+mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
Create a logging environment for a given logobj.
- Parameters:
logobj (logging.Logger) – A logging instance
logfile (str) – Name of the log file
debug (bool) – If True detailed debug logs inludcing filename and function name
-are displayed. If False only the message logged from
-errors, warnings and infos will be displayed.
level (int) – Set the root logger level to the specified level. If for example set
+to logging.DEBUG detailed debug logs inludcing filename and
+function name are displayed. For :py:obj:`logging.INFO only the message
+logged from errors, warnings and infos will be displayed.
@@ -135,7 +136,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/save.html b/0.1.29/api/save.html
index e7bf0b4..6c71e13 100644
--- a/0.1.29/api/save.html
+++ b/0.1.29/api/save.html
@@ -344,7 +344,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/api/utils.html b/0.1.29/api/utils.html
index c200430..887f02b 100644
--- a/0.1.29/api/utils.html
+++ b/0.1.29/api/utils.html
@@ -204,7 +204,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/authors.html b/0.1.29/authors.html
index a5cdbb9..9564e22 100644
--- a/0.1.29/authors.html
+++ b/0.1.29/authors.html
@@ -110,7 +110,7 @@ Authors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/changelog.html b/0.1.29/changelog.html
index d62e70c..a80ece8 100644
--- a/0.1.29/changelog.html
+++ b/0.1.29/changelog.html
@@ -123,6 +123,10 @@
Changelog
+
+Replace Boolean debug option in setup_logging by more flexible integer
+level parameter.
v0.1.29 (2024-03-21)
@@ -335,7 +339,7 @@ v0.1.0 (2021-11-18)
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/contributing.html b/0.1.29/contributing.html
index 5320737..53fdc27 100644
--- a/0.1.29/contributing.html
+++ b/0.1.29/contributing.html
@@ -251,7 +251,7 @@ Pull Request
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/genindex.html b/0.1.29/genindex.html
index b846e75..c9dbdd9 100644
--- a/0.1.29/genindex.html
+++ b/0.1.29/genindex.html
@@ -437,7 +437,7 @@ Y
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/index.html b/0.1.29/index.html
index df15d26..a912a76 100644
--- a/0.1.29/index.html
+++ b/0.1.29/index.html
@@ -198,7 +198,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/installation.html b/0.1.29/installation.html
index a12b511..295016b 100644
--- a/0.1.29/installation.html
+++ b/0.1.29/installation.html
@@ -143,7 +143,7 @@ conda
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/philosophy.html b/0.1.29/philosophy.html
index e9d5184..aea4d9e 100644
--- a/0.1.29/philosophy.html
+++ b/0.1.29/philosophy.html
@@ -155,7 +155,7 @@ Philosophy and approach
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/py-modindex.html b/0.1.29/py-modindex.html
index d8b98d1..0fb5f60 100644
--- a/0.1.29/py-modindex.html
+++ b/0.1.29/py-modindex.html
@@ -146,7 +146,7 @@ Python Module Index
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/readme.html b/0.1.29/readme.html
index d249539..c0da8c6 100644
--- a/0.1.29/readme.html
+++ b/0.1.29/readme.html
@@ -193,7 +193,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/search.html b/0.1.29/search.html
index ea80f97..058aa80 100644
--- a/0.1.29/search.html
+++ b/0.1.29/search.html
@@ -109,7 +109,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/0.1.29/searchindex.js b/0.1.29/searchindex.js
index 17a0bd3..49a88df 100644
--- a/0.1.29/searchindex.js
+++ b/0.1.29/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": 0, "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140119435511120": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3, 4], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 4, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 4, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": 4, "logobj": 4, "environ": [4, 9, 11], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "int": 6, "integ": 6, "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "py": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "more": [8, 10, 12, 13, 14], "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "For": [9, 10, 13, 14], "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "specifi": [10, 13], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": [0, 4, 8], "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140259180724288": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 4, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 8, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 4, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": [4, 8], "logobj": 4, "30": 4, "environ": [4, 9, 11], "int": [4, 6], "root": 4, "specifi": [4, 10, 13], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "For": [4, 9, 10, 13, 14], "py": [4, 8, 9, 11], "obj": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "integ": [6, 8], "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "replac": 8, "boolean": 8, "more": [8, 10, 12, 13, 14], "flexibl": 8, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
diff --git a/0.1.29/usage.html b/0.1.29/usage.html
index 3532f22..86f8784 100644
--- a/0.1.29/usage.html
+++ b/0.1.29/usage.html
@@ -151,7 +151,7 @@ Usage
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/index.html b/dev/_modules/index.html
index 7e4b86e..64d1a7f 100644
--- a/dev/_modules/index.html
+++ b/dev/_modules/index.html
@@ -102,7 +102,7 @@ All modules for which code is available
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/cli.html b/dev/_modules/mdacli/cli.html
index be43b73..020edf4 100644
--- a/dev/_modules/mdacli/cli.html
+++ b/dev/_modules/mdacli/cli.html
@@ -90,7 +90,7 @@ Source code for mdacli.cli
#!/usr/bin/env python3
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
#
-# Copyright (c) 2021 Authors and contributors
+# Copyright (c) 2024 Authors and contributors
#
# Released under the GNU Public Licence, v2 or any higher version
# SPDX-License-Identifier: GPL-2.0-or-later
@@ -195,13 +195,20 @@ Source code for mdacli.cli
args = ap.parse_args()
+ # Set the logging level based on the verbose argument
+ # If verbose is not an argument, default to WARNING
+ if not hasattr(args, "verbose") or not args.verbose:
+ level = logging.WARNING
+ else:
+ level = logging.INFO
+
if args.debug:
- args.verbose = True
+ level = logging.DEBUG
else:
- # Ignore all warnings if not in debug mode
+ # Ignore all warnings if not in debug mode, because MDA is noisy
warnings.filterwarnings("ignore")
- with setup_logging(logger, logfile=args.logfile, debug=args.debug):
+ with setup_logging(logger, logfile=args.logfile, level=level):
# Execute the main client interface.
try:
analysis_callable = args.analysis_callable
@@ -240,7 +247,7 @@ Source code for mdacli.cli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/colors.html b/dev/_modules/mdacli/colors.html
index b86bfa9..b8e8167 100644
--- a/dev/_modules/mdacli/colors.html
+++ b/dev/_modules/mdacli/colors.html
@@ -314,7 +314,7 @@ Source code for mdacli.colors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/libcli.html b/dev/_modules/mdacli/libcli.html
index 4924c82..7c2a311 100644
--- a/dev/_modules/mdacli/libcli.html
+++ b/dev/_modules/mdacli/libcli.html
@@ -958,7 +958,7 @@ Source code for mdacli.libcli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/logger.html b/dev/_modules/mdacli/logger.html
index dd1ce0c..995bd83 100644
--- a/dev/_modules/mdacli/logger.html
+++ b/dev/_modules/mdacli/logger.html
@@ -106,7 +106,7 @@ Source code for mdacli.logger
[docs]
@contextlib.contextmanager
-def setup_logging(logobj, logfile=None, debug=False):
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
"""
Create a logging environment for a given logobj.
@@ -116,19 +116,20 @@ Source code for mdacli.logger
A logging instance
logfile : str
Name of the log file
- debug : bool
- If ``True`` detailed debug logs inludcing filename and function name
- are displayed. If ``False`` only the message logged from
- errors, warnings and infos will be displayed.
+ level : int
+ Set the root logger level to the specified level. If for example set
+ to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
+ function name are displayed. For :py:obj:`logging.INFO only the message
+ logged from errors, warnings and infos will be displayed.
"""
try:
- format = '{message}'
- if debug:
- format = "[{levelname}] {filename}:{name}:{funcName}:{lineno}: " \
- + format
- level = logging.DEBUG
+ if level == logging.DEBUG:
+ format = (
+ "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+ "{message}"
+ )
else:
- level = logging.INFO
+ format = "{message}"
logging.basicConfig(format=format,
handlers=[logging.StreamHandler(sys.stdout)],
@@ -164,7 +165,7 @@ Source code for mdacli.logger
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/save.html b/dev/_modules/mdacli/save.html
index 1081a1c..8a8f43c 100644
--- a/dev/_modules/mdacli/save.html
+++ b/dev/_modules/mdacli/save.html
@@ -553,7 +553,7 @@ Source code for mdacli.save
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/_modules/mdacli/utils.html b/dev/_modules/mdacli/utils.html
index 08f9441..ddf5257 100644
--- a/dev/_modules/mdacli/utils.html
+++ b/dev/_modules/mdacli/utils.html
@@ -369,7 +369,7 @@ Source code for mdacli.utils
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api.html b/dev/api.html
index 0d24cb9..89e0deb 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -127,7 +127,7 @@ API library documentation
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/cli.html b/dev/api/cli.html
index 267c4f5..9341038 100644
--- a/dev/api/cli.html
+++ b/dev/api/cli.html
@@ -106,7 +106,7 @@
The toplevel command line interface.
-
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140119435511120'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140259180724288'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
Create the command-line interface.
This function creates a command line interface with a given name based
on a module list.
@@ -160,7 +160,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/colors.html b/dev/api/colors.html
index b985b15..ab1fe25 100644
--- a/dev/api/colors.html
+++ b/dev/api/colors.html
@@ -330,7 +330,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/libcli.html b/dev/api/libcli.html
index cd90878..41c9a92 100644
--- a/dev/api/libcli.html
+++ b/dev/api/libcli.html
@@ -427,7 +427,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/logger.html b/dev/api/logger.html
index f364380..aa59fa4 100644
--- a/dev/api/logger.html
+++ b/dev/api/logger.html
@@ -106,16 +106,17 @@
Logging.
-
-mdacli.logger.setup_logging(logobj, logfile=None, debug=False)[source]
+mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
Create a logging environment for a given logobj.
- Parameters:
logobj (logging.Logger) – A logging instance
logfile (str) – Name of the log file
debug (bool) – If True detailed debug logs inludcing filename and function name
-are displayed. If False only the message logged from
-errors, warnings and infos will be displayed.
level (int) – Set the root logger level to the specified level. If for example set
+to logging.DEBUG detailed debug logs inludcing filename and
+function name are displayed. For :py:obj:`logging.INFO only the message
+logged from errors, warnings and infos will be displayed.
@@ -135,7 +136,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/save.html b/dev/api/save.html
index e7bf0b4..6c71e13 100644
--- a/dev/api/save.html
+++ b/dev/api/save.html
@@ -344,7 +344,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/api/utils.html b/dev/api/utils.html
index c200430..887f02b 100644
--- a/dev/api/utils.html
+++ b/dev/api/utils.html
@@ -204,7 +204,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/authors.html b/dev/authors.html
index a5cdbb9..9564e22 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -110,7 +110,7 @@ Authors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/changelog.html b/dev/changelog.html
index d62e70c..a80ece8 100644
--- a/dev/changelog.html
+++ b/dev/changelog.html
@@ -123,6 +123,10 @@
Changelog
+
+Replace Boolean debug option in setup_logging by more flexible integer
+level parameter.
v0.1.29 (2024-03-21)
@@ -335,7 +339,7 @@ v0.1.0 (2021-11-18)
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/contributing.html b/dev/contributing.html
index 5320737..53fdc27 100644
--- a/dev/contributing.html
+++ b/dev/contributing.html
@@ -251,7 +251,7 @@ Pull Request
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/genindex.html b/dev/genindex.html
index b846e75..c9dbdd9 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -437,7 +437,7 @@ Y
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/index.html b/dev/index.html
index df15d26..a912a76 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -198,7 +198,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/installation.html b/dev/installation.html
index a12b511..295016b 100644
--- a/dev/installation.html
+++ b/dev/installation.html
@@ -143,7 +143,7 @@ conda
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/philosophy.html b/dev/philosophy.html
index e9d5184..aea4d9e 100644
--- a/dev/philosophy.html
+++ b/dev/philosophy.html
@@ -155,7 +155,7 @@ Philosophy and approach
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/py-modindex.html b/dev/py-modindex.html
index d8b98d1..0fb5f60 100644
--- a/dev/py-modindex.html
+++ b/dev/py-modindex.html
@@ -146,7 +146,7 @@ Python Module Index
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/readme.html b/dev/readme.html
index d249539..c0da8c6 100644
--- a/dev/readme.html
+++ b/dev/readme.html
@@ -193,7 +193,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/search.html b/dev/search.html
index ea80f97..058aa80 100644
--- a/dev/search.html
+++ b/dev/search.html
@@ -109,7 +109,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 17a0bd3..49a88df 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": 0, "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140119435511120": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3, 4], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 4, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 4, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": 4, "logobj": 4, "environ": [4, 9, 11], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "int": 6, "integ": 6, "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "py": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "more": [8, 10, 12, 13, 14], "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "For": [9, 10, 13, 14], "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "specifi": [10, 13], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": [0, 4, 8], "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140259180724288": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 4, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 8, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 4, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": [4, 8], "logobj": 4, "30": 4, "environ": [4, 9, 11], "int": [4, 6], "root": 4, "specifi": [4, 10, 13], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "For": [4, 9, 10, 13, 14], "py": [4, 8, 9, 11], "obj": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "integ": [6, 8], "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "replac": 8, "boolean": 8, "more": [8, 10, 12, 13, 14], "flexibl": 8, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
diff --git a/dev/usage.html b/dev/usage.html
index 3532f22..86f8784 100644
--- a/dev/usage.html
+++ b/dev/usage.html
@@ -151,7 +151,7 @@ Usage
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/index.html b/stable/_modules/index.html
index 7e4b86e..64d1a7f 100644
--- a/stable/_modules/index.html
+++ b/stable/_modules/index.html
@@ -102,7 +102,7 @@ All modules for which code is available
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/cli.html b/stable/_modules/mdacli/cli.html
index be43b73..020edf4 100644
--- a/stable/_modules/mdacli/cli.html
+++ b/stable/_modules/mdacli/cli.html
@@ -90,7 +90,7 @@ Source code for mdacli.cli
#!/usr/bin/env python3
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
#
-# Copyright (c) 2021 Authors and contributors
+# Copyright (c) 2024 Authors and contributors
#
# Released under the GNU Public Licence, v2 or any higher version
# SPDX-License-Identifier: GPL-2.0-or-later
@@ -195,13 +195,20 @@ Source code for mdacli.cli
args = ap.parse_args()
+ # Set the logging level based on the verbose argument
+ # If verbose is not an argument, default to WARNING
+ if not hasattr(args, "verbose") or not args.verbose:
+ level = logging.WARNING
+ else:
+ level = logging.INFO
+
if args.debug:
- args.verbose = True
+ level = logging.DEBUG
else:
- # Ignore all warnings if not in debug mode
+ # Ignore all warnings if not in debug mode, because MDA is noisy
warnings.filterwarnings("ignore")
- with setup_logging(logger, logfile=args.logfile, debug=args.debug):
+ with setup_logging(logger, logfile=args.logfile, level=level):
# Execute the main client interface.
try:
analysis_callable = args.analysis_callable
@@ -240,7 +247,7 @@ Source code for mdacli.cli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/colors.html b/stable/_modules/mdacli/colors.html
index b86bfa9..b8e8167 100644
--- a/stable/_modules/mdacli/colors.html
+++ b/stable/_modules/mdacli/colors.html
@@ -314,7 +314,7 @@ Source code for mdacli.colors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/libcli.html b/stable/_modules/mdacli/libcli.html
index 4924c82..7c2a311 100644
--- a/stable/_modules/mdacli/libcli.html
+++ b/stable/_modules/mdacli/libcli.html
@@ -958,7 +958,7 @@ Source code for mdacli.libcli
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/logger.html b/stable/_modules/mdacli/logger.html
index dd1ce0c..995bd83 100644
--- a/stable/_modules/mdacli/logger.html
+++ b/stable/_modules/mdacli/logger.html
@@ -106,7 +106,7 @@ Source code for mdacli.logger
[docs]
@contextlib.contextmanager
-def setup_logging(logobj, logfile=None, debug=False):
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
"""
Create a logging environment for a given logobj.
@@ -116,19 +116,20 @@ Source code for mdacli.logger
A logging instance
logfile : str
Name of the log file
- debug : bool
- If ``True`` detailed debug logs inludcing filename and function name
- are displayed. If ``False`` only the message logged from
- errors, warnings and infos will be displayed.
+ level : int
+ Set the root logger level to the specified level. If for example set
+ to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
+ function name are displayed. For :py:obj:`logging.INFO only the message
+ logged from errors, warnings and infos will be displayed.
"""
try:
- format = '{message}'
- if debug:
- format = "[{levelname}] {filename}:{name}:{funcName}:{lineno}: " \
- + format
- level = logging.DEBUG
+ if level == logging.DEBUG:
+ format = (
+ "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+ "{message}"
+ )
else:
- level = logging.INFO
+ format = "{message}"
logging.basicConfig(format=format,
handlers=[logging.StreamHandler(sys.stdout)],
@@ -164,7 +165,7 @@ Source code for mdacli.logger
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/save.html b/stable/_modules/mdacli/save.html
index 1081a1c..8a8f43c 100644
--- a/stable/_modules/mdacli/save.html
+++ b/stable/_modules/mdacli/save.html
@@ -553,7 +553,7 @@ Source code for mdacli.save
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/_modules/mdacli/utils.html b/stable/_modules/mdacli/utils.html
index 08f9441..ddf5257 100644
--- a/stable/_modules/mdacli/utils.html
+++ b/stable/_modules/mdacli/utils.html
@@ -369,7 +369,7 @@ Source code for mdacli.utils
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api.html b/stable/api.html
index 0d24cb9..89e0deb 100644
--- a/stable/api.html
+++ b/stable/api.html
@@ -127,7 +127,7 @@ API library documentation
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/cli.html b/stable/api/cli.html
index 267c4f5..9341038 100644
--- a/stable/api/cli.html
+++ b/stable/api/cli.html
@@ -106,7 +106,7 @@
The toplevel command line interface.
-
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140119435511120'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140259180724288'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
Create the command-line interface.
This function creates a command line interface with a given name based
on a module list.
@@ -160,7 +160,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/colors.html b/stable/api/colors.html
index b985b15..ab1fe25 100644
--- a/stable/api/colors.html
+++ b/stable/api/colors.html
@@ -330,7 +330,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/libcli.html b/stable/api/libcli.html
index cd90878..41c9a92 100644
--- a/stable/api/libcli.html
+++ b/stable/api/libcli.html
@@ -427,7 +427,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/logger.html b/stable/api/logger.html
index f364380..aa59fa4 100644
--- a/stable/api/logger.html
+++ b/stable/api/logger.html
@@ -106,16 +106,17 @@
Logging.
-
-mdacli.logger.setup_logging(logobj, logfile=None, debug=False)[source]
+mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
Create a logging environment for a given logobj.
- Parameters:
logobj (logging.Logger) – A logging instance
logfile (str) – Name of the log file
debug (bool) – If True detailed debug logs inludcing filename and function name
-are displayed. If False only the message logged from
-errors, warnings and infos will be displayed.
level (int) – Set the root logger level to the specified level. If for example set
+to logging.DEBUG detailed debug logs inludcing filename and
+function name are displayed. For :py:obj:`logging.INFO only the message
+logged from errors, warnings and infos will be displayed.
@@ -135,7 +136,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/save.html b/stable/api/save.html
index e7bf0b4..6c71e13 100644
--- a/stable/api/save.html
+++ b/stable/api/save.html
@@ -344,7 +344,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/api/utils.html b/stable/api/utils.html
index c200430..887f02b 100644
--- a/stable/api/utils.html
+++ b/stable/api/utils.html
@@ -204,7 +204,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/authors.html b/stable/authors.html
index a5cdbb9..9564e22 100644
--- a/stable/authors.html
+++ b/stable/authors.html
@@ -110,7 +110,7 @@ Authors
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/changelog.html b/stable/changelog.html
index d62e70c..a80ece8 100644
--- a/stable/changelog.html
+++ b/stable/changelog.html
@@ -123,6 +123,10 @@
Changelog
+
+Replace Boolean debug option in setup_logging by more flexible integer
+level parameter.
v0.1.29 (2024-03-21)
@@ -335,7 +339,7 @@ v0.1.0 (2021-11-18)
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/contributing.html b/stable/contributing.html
index 5320737..53fdc27 100644
--- a/stable/contributing.html
+++ b/stable/contributing.html
@@ -251,7 +251,7 @@ Pull Request
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/genindex.html b/stable/genindex.html
index b846e75..c9dbdd9 100644
--- a/stable/genindex.html
+++ b/stable/genindex.html
@@ -437,7 +437,7 @@ Y
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/index.html b/stable/index.html
index df15d26..a912a76 100644
--- a/stable/index.html
+++ b/stable/index.html
@@ -198,7 +198,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/installation.html b/stable/installation.html
index a12b511..295016b 100644
--- a/stable/installation.html
+++ b/stable/installation.html
@@ -143,7 +143,7 @@ conda
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/philosophy.html b/stable/philosophy.html
index e9d5184..aea4d9e 100644
--- a/stable/philosophy.html
+++ b/stable/philosophy.html
@@ -155,7 +155,7 @@ Philosophy and approach
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/py-modindex.html b/stable/py-modindex.html
index d8b98d1..0fb5f60 100644
--- a/stable/py-modindex.html
+++ b/stable/py-modindex.html
@@ -146,7 +146,7 @@ Python Module Index
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/readme.html b/stable/readme.html
index d249539..c0da8c6 100644
--- a/stable/readme.html
+++ b/stable/readme.html
@@ -193,7 +193,7 @@ Available modules
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/search.html b/stable/search.html
index ea80f97..058aa80 100644
--- a/stable/search.html
+++ b/stable/search.html
@@ -109,7 +109,7 @@
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.
diff --git a/stable/searchindex.js b/stable/searchindex.js
index 17a0bd3..49a88df 100644
--- a/stable/searchindex.js
+++ b/stable/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": 0, "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140119435511120": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3, 4], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 4, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 4, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": 4, "logobj": 4, "environ": [4, 9, 11], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "int": 6, "integ": 6, "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "py": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "more": [8, 10, 12, 13, 14], "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "For": [9, 10, 13, 14], "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "specifi": [10, 13], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["api", "api/cli", "api/colors", "api/libcli", "api/logger", "api/save", "api/utils", "authors", "changelog", "contributing", "index", "installation", "philosophy", "readme", "usage"], "filenames": ["api.rst", "api/cli.rst", "api/colors.rst", "api/libcli.rst", "api/logger.rst", "api/save.rst", "api/utils.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "installation.rst", "philosophy.rst", "readme.rst", "usage.rst"], "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "terms": {"The": [0, 1, 2, 3, 5, 6, 9, 12, 14], "refer": [0, 3, 8, 9, 10, 13], "intern": 0, "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "onli": [0, 3, 4, 9, 10, 13], "advanc": 0, "user": [0, 12], "veri": [0, 9, 12], "specif": [0, 9], "develop": [0, 10, 11, 12, 13], "goal": 0, "might": 0, "need": [0, 3, 8, 9], "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "interfac": [0, 1, 3, 12], "A": [0, 3, 4, 5, 6, 10, 12, 13, 14], "regular": 0, "want": [0, 11], "from": [0, 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14], "command": [0, 1, 3, 5, 9, 12, 14], "line": [0, 1, 3, 5, 6, 12, 14], "doe": [0, 3, 6], "page": [0, 8, 10, 13, 14], "usag": 0, "instead": 0, "high": [0, 12], "level": [0, 4, 8], "support": [0, 8, 10, 13], "function": [0, 1, 4, 5, 6, 9, 10, 13, 14], "cli": [0, 1, 6, 8, 10, 12, 13], "result": [0, 12, 14], "save": [0, 3, 8, 12, 14], "color": 0, "log": [0, 3, 14], "util": 0, "toplevel": 1, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "module_list": 1, "base_class": 1, "mock": 1, "analysisbas": [1, 3, 12], "id": 1, "140259180724288": 1, "version": [1, 3, 9], "descript": [1, 3, 6, 8, 10, 13], "skip_modul": 1, "none": [1, 3, 4, 5, 8], "ignore_warn": [1, 3], "fals": [1, 3], "sourc": [1, 2, 3, 4, 5, 6], "creat": [1, 3, 4, 5, 12], "thi": [1, 2, 3, 6, 10, 12, 13, 14], "given": [1, 3, 4, 6, 10, 13], "base": [1, 3, 5, 6, 8, 9, 10, 12, 13], "modul": [1, 3, 8, 14], "list": [1, 3, 5, 8, 9, 14], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "str": [1, 2, 3, 4, 5, 6], "which": [1, 3, 5, 6, 11, 12], "i": [1, 2, 3, 5, 6, 9, 10, 11, 12, 13, 14], "build": [1, 9, 12], "up": [1, 3, 9, 12], "cl": [1, 3], "class": [1, 2, 3, 6, 8, 10, 12, 13, 14], "anaylsi": 1, "belong": [1, 3], "string": [1, 2, 3, 5, 6, 14], "contain": [1, 3, 5, 6, 12, 14], "should": [1, 3, 9, 11], "ommit": 1, "bool": [1, 3, 5], "ignor": [1, 3, 5, 9], "warn": [1, 2, 3, 4, 14], "when": [1, 6, 9], "import": [1, 3, 9], "exampl": [1, 2, 4, 9, 14], "code": [1, 9, 12], "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "analysi": [1, 3, 5, 8, 10, 12, 13, 14], "__all__": 1, "skip_mod": 1, "analysisfromfunct": 1, "hydrogenbondanalysi": 1, "waterbridgeanalysi": 1, "contact": [1, 10, 11, 13], "dihedr": [1, 8, 10, 13], "persistencelength": 1, "interrdf_": 1, "f": [1, 12, 14], "m": [1, 7, 9], "__version__": 1, "__doc__": 1, "true": [1, 5], "emphais": 2, "etc": [2, 14], "taken": [2, 5], "http": [2, 3, 6, 8, 9, 11], "gist": 2, "github": [2, 7, 8, 9, 11], "com": [2, 3, 6, 9, 11], "tuvokki": 2, "14deb97bef6df9bc6553": 2, "emphasis": 2, "variabl": [2, 12], "bold": 2, "attribut": [2, 5], "underlin": 2, "grai": 2, "red": 2, "green": 2, "yellow": 2, "blue": 2, "pink": 2, "turquois": 2, "x1b": 2, "94m": 2, "1m": 2, "static": 2, "debug": [2, 3, 4, 8, 14], "messag": [2, 4, 9, 10, 13], "return": [2, 3, 5, 6], "decorated_messag": 2, "decor": 2, "print": [2, 3], "bcolor": 2, "1": [2, 3, 5], "style": [2, 8, 9], "desir": 2, "could": [2, 3, 6, 12], "see": [2, 3, 6, 9, 14], "avail": [2, 3, 14], "my": [2, 9], "error": [2, 4], "potenti": 2, "danger": 2, "90m": 2, "92m": 2, "header": [2, 5, 14], "great": 2, "info": [2, 4, 5], "yai": 2, "ok": 2, "95m": 2, "91m": 2, "96m": 2, "4m": 2, "93m": 2, "creation": [3, 6, 8], "libcli": [3, 8], "kwargsdict": 3, "option_str": 3, "dest": 3, "narg": 3, "const": 3, "default": [3, 5, 14], "type": [3, 5, 6, 8, 12], "choic": [3, 8], "requir": [3, 6, 8, 14], "help": [3, 8, 10, 12, 13, 14], "metavar": 3, "convert": [3, 6, 8], "input": [3, 5, 6], "dictionari": [3, 5, 6, 12], "If": [3, 4, 5, 6, 9, 11, 12], "point": 3, "json": [3, 5, 12, 14], "file": [3, 4, 5, 8, 9, 10, 12, 13, 14], "read": [3, 9], "els": [3, 5], "attempt": 3, "load": 3, "add_cli_univers": 3, "parser": [3, 6, 12], "add": [3, 5, 8], "univers": [3, 12], "an": [3, 6, 9, 10, 12, 13, 14], "argpars": [3, 10, 12, 13], "argumentpars": 3, "instanc": [3, 4, 5], "topologi": [3, 12], "topology_format": 3, "atom_styl": 3, "coordin": [3, 10, 13], "trajectory_format": 3, "ar": [3, 4, 5, 6, 9, 10, 11, 12, 13, 14], "ad": [3, 6, 8, 12], "pars": [3, 6, 8], "analysis_class_pars": 3, "argumentspars": 3, "run": [3, 6, 8, 10, 13, 14], "grorup": 3, "suffix": 3, "argument": [3, 8, 12], "add_output_group": 3, "output": [3, 14], "group": [3, 10, 13, 14], "output_prefix": 3, "output_directori": 3, "add_run_group": 3, "start": [3, 6, 8, 12], "stop": [3, 8], "step": [3, 6, 9], "verbos": [3, 14], "convert_analysis_paramet": 3, "analysis_cal": 3, "analysis_paramet": 3, "reference_univers": 3, "suitabl": 3, "anlysi": 3, "special": 3, "e": [3, 9, 12, 14], "atomgroup": [3, 8, 10, 13, 14], "correct": [3, 8, 9], "format": [3, 6], "chang": [3, 8, 14], "inplac": 3, "note": [3, 5], "kei": [3, 5, 6], "new": [3, 8, 12], "present": [3, 6, 9], "doc": [3, 8, 9], "dict": [3, 5, 6], "select": [3, 10, 12, 13, 14], "sinc": [3, 9, 12], "follow": [3, 6, 9, 10, 13], "atom": [3, 10, 13, 14], "select_atom": 3, "everi": 3, "element": 3, "perform": [3, 9, 10, 13], "process": [3, 9, 12], "done": 3, "anaylysi": 3, "ine": 3, "rais": [3, 6], "valueerror": [3, 6], "ani": [3, 6, 9, 11, 12], "create_cli": [3, 8], "sub_pars": 3, "interface_nam": 3, "subpars": 3, "cli_pars": 3, "divid": 3, "categori": 3, "time": [3, 6, 8, 9], "frame": [3, 6, 8, 10, 12, 13], "begin": 3, "end": 3, "vebos": 3, "mandatori": 3, "defin": [3, 5], "per": 3, "design": 3, "option": [3, 5, 8, 14], "exist": [3, 12], "all": [3, 5, 9, 12, 14], "": [3, 6, 9, 12, 14], "sub": 3, "where": [3, 5, 6], "fill": 3, "create_univers": 3, "dimens": [3, 5, 8], "initil": 3, "stream": 3, "core": [3, 12], "np": [3, 5], "ndarrai": [3, 5], "charmm": 3, "xplor": 3, "psf": 3, "pdb": 3, "gromac": [3, 12, 14], "gro": 3, "includ": 3, "bond": 3, "inform": [3, 6, 10, 13, 14], "partial": 3, "charg": 3, "mass": 3, "data": [3, 5, 12, 14], "altern": 3, "mai": [3, 9], "numpi": [3, 5], "empti": 3, "can": [3, 6, 9, 11, 12, 14], "provid": [3, 12, 14], "singl": [3, 5, 8], "eg": 3, "crd": 3, "trajectori": [3, 8, 10, 12, 13, 14], "namd": 3, "lammp": 3, "dcd": 3, "xtc": 3, "trr": [3, 14], "gener": [3, 8, 12], "xyz": 3, "must": 3, "order": 3, "same": [3, 5, 9, 11, 12], "wai": [3, 9, 12], "tabl": [3, 5], "what": 3, "guess": 3, "extens": [3, 5], "also": [3, 9, 11, 12, 14], "pass": [3, 9], "subclass": 3, "topologyreaderbas": 3, "custom": 3, "reader": 3, "object": [3, 5, 6, 12], "keyword": 3, "ha": [3, 5, 6], "effect": 3, "suppli": 3, "becaus": [3, 9], "chain": 3, "each": [3, 5, 10, 12, 13, 14], "individu": [3, 9], "member": 3, "protoread": 3, "customis": 3, "work": [3, 10, 13], "iter": 3, "float": [3, 6], "vector": 3, "unit": [3, 6], "cell": 3, "length": [3, 5], "probabl": 3, "angl": [3, 10, 13], "expect": 3, "shape": 3, "either": [3, 12], "6": 3, "0": 3, "3": [3, 5], "set": [3, 4, 8, 9, 14], "90": 3, "degre": 3, "indexerror": [3, 6], "dimes": 3, "find_classes_in_modul": 3, "module_nam": 3, "find": 3, "seri": 3, "parent": [3, 12], "search": 3, "absolut": 3, "rel": 3, "term": 3, "g": 3, "pkg": 3, "mod": 3, "found": [3, 6], "find_cls_memb": 3, "certain": [3, 5], "flag": [3, 9, 12, 14], "init_base_argpars": 3, "basic": [3, 10, 13], "mode": 3, "logfil": [3, 4, 14], "funtion": 3, "logic": [3, 8], "actual": [3, 12, 14], "nor": 3, "how": [3, 9, 12, 14], "store": [3, 5, 12, 14], "program": [3, 10, 13], "run_analysi": [3, 8], "mandatory_analysis_paramet": 3, "optional_analysis_paramet": 3, "reference_universe_paramet": 3, "run_paramet": 3, "output_paramet": 3, "main": [3, 6], "client": [3, 14], "execut": [3, 5], "after": [3, 9, 14], "setup_cli": 3, "ap": 3, "titl": [3, 9], "split_argparse_into_group": 3, "namespac": 3, "split": [3, 5, 6], "popul": 3, "stackoverflow": 3, "question": 3, "31519997": 3, "possibl": 3, "one": [3, 5], "arg_grouped_dict": 3, "accord": 3, "logger": 4, "setup_log": [4, 8], "logobj": 4, "30": 4, "environ": [4, 9, 11], "int": [4, 6], "root": 4, "specifi": [4, 10, 13], "detail": [4, 6, 14], "inludc": 4, "filenam": 4, "displai": 4, "For": [4, 9, 10, 13, 14], "py": [4, 8, 9, 11], "obj": 4, "manag": 5, "get_1d_arrai": 5, "get": 5, "item": 5, "correspond": [5, 14], "dim": 5, "get_cli_input": 5, "proper": 5, "fomat": 5, "is_1d_arrai": 5, "arr": 5, "ndim": 5, "assert": 5, "valu": [5, 6, 8], "arrai": [5, 12, 14], "is_2d_arrai": 5, "2": [5, 6], "is_3d_arrai": 5, "is_dimension_arrai": 5, "is_higher_dimension_arrai": 5, "is_serializ": 5, "serializ": 5, "remove_fil": 5, "remov": [5, 8], "disk": 5, "return_with_remov": 5, "ddict": 5, "serv": 5, "subset": 5, "origin": 5, "fprefix": 5, "mdacli_result": 5, "1d": [5, 12], "2d": [5, 12], "3d": 5, "csv": [5, 12, 14], "vertic": 5, "stack": 5, "directli": [5, 11, 14], "along": 5, "shortest": 5, "togeth": [5, 11, 14], "zip": [5, 12, 14], "higher": [5, 12, 14], "dimension": [5, 12, 14], "we": [5, 9, 12], "try": 5, "everyth": [5, 11], "non": 5, "prefix": [5, 14], "save_1d_arrai": 5, "1darrai": 5, "like": [5, 9], "map": 5, "save_2d_arrai": 5, "2darr": 5, "save_3d_array_to_2d_csv": 5, "arr_nam": 5, "zipit": 5, "save_3d_arrai": 5, "3darr": 5, "save_results_object": 5, "thei": [5, 12], "save_files_to_zip": 5, "zipnam": 5, "thezip": 5, "compress": 5, "archiv": 5, "without": [5, 12], "save_higher_dim_arrai": 5, "xdarr": 5, "min_ndim": 5, "4": [5, 14], "multidimension": 5, "save_json_serializ": 5, "jsonarg": 5, "save_result_arrai": 5, "accor": 5, "num": 5, "save_to_json": 5, "json_dict": 5, "fname": 5, "jdict": 5, "indent": 5, "sort_kei": 5, "savetxt_w_command": 5, "x": [5, 6, 9], "fsuffix": 5, "kwarg": 5, "about": [5, 10, 13, 14], "check": 5, "doubl": 5, "filesuffix": 5, "stack_1d_arrays_list": 5, "list_1d": 5, "extra_list": 5, "got": 5, "number": [5, 6, 8, 14], "row": [5, 14], "addit": [5, 9, 14], "oper": 5, "out_list": 5, "organ": 5, "out_extra": 5, "appli": [5, 9, 12], "try_to_squeeze_m": 5, "squeez": 5, "helper": 6, "convert_str_tim": 6, "dt": 6, "its": [6, 12, 14], "assum": 6, "alreadi": [6, 9, 11], "split_time_unit": 6, "p": 6, "integ": [6, 8], "parse_callable_signatur": 6, "callable_obj": 6, "callabl": 6, "signatur": 6, "conveni": 6, "combin": [6, 12], "docstr": [6, 8, 12], "inspect": [6, 12], "storage_dict": 6, "parse_doc": 6, "klass": 6, "numpydocstr": 6, "yet": 6, "so": [6, 9, 11, 12, 14], "strict": 6, "__init__": 6, "method": [6, 9], "extract": 6, "tupl": 6, "One": 6, "summari": 6, "extend": 6, "subdictinari": 6, "desc": 6, "regex": [6, 8], "regex101": 6, "r": 6, "lzabil": 6, "happen": [6, 14], "philip": 7, "loch": 7, "joao": 7, "c": [7, 9, 11], "teixeira": 7, "webpag": 7, "oliv": 7, "beckstein": 7, "lili": 7, "wang": 7, "henrik": 7, "j\u00e4ger": 7, "replac": 8, "boolean": 8, "more": [8, 10, 12, 13, 14], "flexibl": 8, "handl": 8, "lowercas": 8, "make": [8, 9, 12], "parsabl": 8, "114": 8, "reenabl": 8, "org": 8, "canon": 8, "mda": [8, 10, 12, 13, 14], "integr": [8, 9], "test": 8, "complet": 8, "renam": 8, "run_analsi": 8, "move": 8, "nt": 8, "arg": 8, "fix": 8, "109": 8, "long": 8, "py3": 8, "codecov": 8, "upload": 8, "translat": 8, "setup": [8, 9, 11], "pyproject": 8, "toml": 8, "classifi": 8, "cfg": 8, "disabl": 8, "deploi": 8, "python": [8, 9, 11, 12], "ci": [8, 9], "matrix": 8, "limit": [8, 12], "thread": 8, "allow": 8, "isort": 8, "depend": [8, 11], "introduc": 8, "updat": [8, 11], "__authors__": 8, "readm": 8, "rst": [8, 9], "typo": 8, "do": [8, 9], "posit": 8, "bump2vers": 8, "conda": [8, 9], "packag": [8, 9], "instal": [8, 10, 13, 14], "instruct": [8, 14], "88": 8, "82": 8, "simplifi": 8, "add_argu": 8, "detect": [8, 12], "save_result": 8, "improv": 8, "83": 8, "tox": 8, "86": 8, "banner": 8, "85": 8, "action": [8, 9], "68": 8, "permiss": 8, "maco": 8, "fail": [8, 9], "window": 8, "81": 8, "url": 8, "80": 8, "deploy": 8, "78": 8, "link": 8, "75": 8, "document": [8, 9, 10, 13, 14], "70": 8, "manual": 8, "box": 8, "65": 8, "bumpvers": 8, "contribut": [8, 10, 13], "accordingli": 8, "initi": [8, 12], "releas": 8, "easi": 9, "have": [9, 11, 14], "power": 9, "relax": 9, "guid": 9, "you": [9, 11, 14], "alwai": 9, "welcom": [9, 10, 13], "Not": 9, "form": 9, "via": 9, "issu": [9, 11], "especi": 9, "earli": [9, 10, 13], "phase": 9, "interact": 9, "u": [9, 11], "account": 9, "final": 9, "review": 9, "next": 9, "guidelin": 9, "git": 9, "pro": 9, "wish": 9, "own": [9, 14], "safe": 9, "our": [9, 12], "befor": 9, "local": 9, "machin": 9, "cd": 9, "t": [9, 11], "no_entry_sign": 9, "smile": 9, "first": [9, 11], "previou": 9, "checkout": 9, "myfork": 9, "usernam": 9, "fetch": 9, "now": 9, "b": 9, "nice": 9, "commit": 9, "encapsul": 9, "That": 9, "finish": 9, "some": [9, 12, 14], "task": 9, "good": 9, "push": 9, "onc": 9, "give": 9, "feedback": 9, "hopefulli": 9, "accept": 9, "howev": [9, 12], "pr": 9, "continu": 9, "madcli": 9, "most": 9, "contributor": 9, "v2": 9, "insid": [9, 12], "dep": [9, 11], "It": 9, "reflect": 9, "real": 9, "avoid": 9, "twice": 9, "don": [9, 11], "did": 9, "place": 9, "pleas": [9, 11], "whole": 9, "pipelin": 9, "tox_": 9, "friend": 9, "smile_cat": 9, "pip": 9, "forg": [9, 11], "certifi": 9, "correctli": 9, "These": 9, "exactli": 9, "onlin": [9, 14], "workflow": 9, "possibli": 9, "interpret": 9, "lint": 9, "under": 9, "explanatori": 9, "bullet": 9, "bellow": 9, "right": 9, "last": 9, "subtitl": 9, "here": 9, "goe": 9, "explain": [9, 14], "them": [9, 12], "shortli": 9, "well": 9, "vx": 9, "1900": 9, "01": 9, "author": 9, "engag": 9, "commun": 9, "pullrequest": 9, "open": [9, 14], "submit": 9, "verifi": 9, "describ": 9, "implement": 9, "case": 9, "upstream": 9, "incompat": 9, "merg": 9, "ff": 9, "conflict": 9, "appear": 9, "go": 9, "simpl": [10, 12, 13, 14], "project": [10, 12, 13], "stage": [10, 13], "progress": [10, 13], "To": [10, 11, 13, 14], "h": [10, 13, 14], "overview": [10, 13], "current": [10, 13, 14], "aligntraj": [10, 13], "rm": [10, 13], "align": [10, 13], "structur": [10, 12, 13], "averagestructur": [10, 13], "calcul": [10, 13, 14], "averag": [10, 13], "observ": [10, 13], "densityanalysi": [10, 13], "volumetr": [10, 13], "densiti": [10, 13], "distancematrix": [10, 13], "pairwis": [10, 13], "distanc": [10, 13], "between": [10, 13, 14], "janin": [10, 13], "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "ramachandran": [10, 13], "\u03d5": [10, 13], "\u03c8": [10, 13], "dielectricconst": [10, 13], "comput": [10, 13], "dipol": [10, 13], "moment": [10, 13], "gnmanalysi": [10, 13], "tool": [10, 11, 13], "gnm": [10, 13], "closecontactgnmanalysi": [10, 13], "close": [10, 13], "helan": [10, 13], "helix": [10, 13], "your": [10, 11, 13, 14], "holeanalysi": [10, 13], "hole": [10, 13], "lineardens": [10, 13], "linear": [10, 13], "profil": [10, 13], "einsteinmsd": [10, 13], "mean": [10, 13], "squar": [10, 13], "displac": [10, 13], "einstein": [10, 13], "relat": [10, 13], "pca": [10, 13], "princip": [10, 13], "compon": [10, 13], "md": [10, 13], "interrdf": [10, 13, 14], "intermolecular": [10, 13], "pair": [10, 13], "distribut": [10, 13, 14], "rmsd": [10, 13], "rmsf": [10, 13], "across": [10, 13], "through": [10, 12, 13], "pluge": 11, "slightli": 11, "top": 11, "activ": 11, "just": [11, 12], "upgrad": 11, "Or": 11, "expert": 11, "clone": 11, "repositori": 11, "automat": [11, 12], "later": 11, "doubt": 11, "evolv": 12, "experi": 12, "taurenmd": 12, "maico": 12, "both": 12, "fly": 12, "were": 12, "face": 12, "problem": 12, "lab": 12, "regularli": 12, "student": 12, "scientist": 12, "write": 12, "script": 12, "challeng": 12, "loop": 12, "copi": 12, "mani": 12, "analyz": 12, "sever": 12, "simul": 12, "clever": 12, "solv": 12, "sometim": 12, "direct": 12, "dai": 12, "wrapper": 12, "therefor": 12, "peopl": 12, "least": 12, "effort": 12, "With": 12, "easier": 12, "stai": 12, "within": 12, "known": 12, "framework": 12, "attract": 12, "locat": 12, "around": 12, "downstream": 12, "codebas": 12, "show": 12, "adjust": 12, "itself": 12, "librari": 12, "syntax": 12, "inspir": 12, "routin": 12, "dump": [12, 14], "termin": 14, "ask": 14, "emul": 14, "two": 14, "other": 14, "radial": 14, "rdf": 14, "sampl": 14, "water": 14, "rigid": 14, "spc": 14, "topol": 14, "tpr": 14, "topolgi": 14, "traj": 14, "oxygen": 14, "g1": 14, "ow": 14, "g2": 14, "achiev": 14, "v": 14, "even": 14, "directori": 14, "o": 14, "pre": 14, "2nd": 14, "3rd": 14, "column": 14, "interrdf_count_bins_rdf": 14, "bare": 14, "complex": 14, "bunch": 14, "similar": 14, "procedur": 14}, "objects": {"mdacli": [[1, 0, 0, "-", "cli"], [2, 0, 0, "-", "colors"], [3, 0, 0, "-", "libcli"], [4, 0, 0, "-", "logger"], [5, 0, 0, "-", "save"], [6, 0, 0, "-", "utils"]], "mdacli.cli": [[1, 1, 1, "", "cli"]], "mdacli.colors": [[2, 2, 1, "", "Emphasise"]], "mdacli.colors.Emphasise": [[2, 3, 1, "", "blue"], [2, 3, 1, "", "bold"], [2, 4, 1, "", "debug"], [2, 4, 1, "", "emphasise"], [2, 4, 1, "", "error"], [2, 3, 1, "", "gray"], [2, 3, 1, "", "green"], [2, 4, 1, "", "header"], [2, 4, 1, "", "info"], [2, 4, 1, "", "ok"], [2, 3, 1, "", "pink"], [2, 3, 1, "", "red"], [2, 3, 1, "", "turquoise"], [2, 3, 1, "", "underline"], [2, 4, 1, "", "warning"], [2, 3, 1, "", "yellow"]], "mdacli.libcli": [[3, 2, 1, "", "KwargsDict"], [3, 1, 1, "", "add_cli_universe"], [3, 1, 1, "", "add_output_group"], [3, 1, 1, "", "add_run_group"], [3, 1, 1, "", "convert_analysis_parameters"], [3, 1, 1, "", "create_cli"], [3, 1, 1, "", "create_universe"], [3, 1, 1, "", "find_classes_in_modules"], [3, 1, 1, "", "find_cls_members"], [3, 1, 1, "", "init_base_argparse"], [3, 1, 1, "", "run_analysis"], [3, 1, 1, "", "setup_clients"], [3, 1, 1, "", "split_argparse_into_groups"]], "mdacli.logger": [[4, 1, 1, "", "setup_logging"]], "mdacli.save": [[5, 1, 1, "", "get_1D_arrays"], [5, 1, 1, "", "get_cli_input"], [5, 1, 1, "", "is_1d_array"], [5, 1, 1, "", "is_2d_array"], [5, 1, 1, "", "is_3d_array"], [5, 1, 1, "", "is_dimension_array"], [5, 1, 1, "", "is_higher_dimension_array"], [5, 1, 1, "", "is_serializable"], [5, 1, 1, "", "remove_files"], [5, 1, 1, "", "return_with_remove"], [5, 1, 1, "", "save"], [5, 1, 1, "", "save_1D_arrays"], [5, 1, 1, "", "save_2D_arrays"], [5, 1, 1, "", "save_3D_array_to_2D_csv"], [5, 1, 1, "", "save_3D_arrays"], [5, 1, 1, "", "save_Results_object"], [5, 1, 1, "", "save_files_to_zip"], [5, 1, 1, "", "save_higher_dim_arrays"], [5, 1, 1, "", "save_json_serializables"], [5, 1, 1, "", "save_result_array"], [5, 1, 1, "", "save_to_json"], [5, 1, 1, "", "savetxt_w_command"], [5, 1, 1, "", "stack_1d_arrays_list"], [5, 1, 1, "", "try_to_squeeze_me"]], "mdacli.utils": [[6, 1, 1, "", "convert_str_time"], [6, 1, 1, "", "parse_callable_signature"], [6, 1, 1, "", "parse_docs"], [6, 1, 1, "", "split_time_unit"]]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"]}, "titleterms": {"api": [0, 1], "librari": 0, "document": 0, "high": 1, "level": 1, "color": 2, "support": 3, "function": 3, "cli": 3, "log": 4, "result": 5, "save": 5, "util": 6, "author": 7, "changelog": [8, 9], "v0": 8, "1": 8, "29": 8, "2024": 8, "03": 8, "21": 8, "28": 8, "2023": 8, "09": 8, "27": 8, "08": 8, "25": 8, "26": 8, "06": 8, "02": 8, "24": 8, "01": 8, "23": 8, "22": 8, "2022": 8, "04": 8, "20": 8, "13": 8, "19": 8, "12": 8, "18": 8, "17": 8, "07": 8, "16": 8, "15": 8, "14": 8, "11": 8, "10": 8, "9": 8, "8": 8, "7": 8, "2021": 8, "6": 8, "5": 8, "4": 8, "3": 8, "2": 8, "0": 8, "contribut": 9, "fork": 9, "thi": 9, "repositori": 9, "clone": 9, "main": 9, "project": 9, "your": 9, "comput": 9, "add": 9, "remot": 9, "creat": 9, "new": 9, "branch": 9, "start": 9, "develop": 9, "pull": 9, "request": 9, "chang": 9, "instal": [9, 11], "run": 9, "test": 9, "tox": 9, "updat": 9, "mdanalysi": [10, 13], "command": [10, 13], "line": [10, 13], "interfac": [10, 13], "avail": [10, 13], "modul": [10, 13], "pip": 11, "conda": 11, "philosophi": 12, "approach": 12, "usag": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"API library documentation": [[0, "api-library-documentation"]], "High-Level API": [[1, "module-mdacli.cli"]], "Coloring": [[2, "module-mdacli.colors"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Logging": [[4, "module-mdacli.logger"]], "Results Saving": [[5, "module-mdacli.save"]], "Utilities": [[6, "module-mdacli.utils"]], "Authors": [[7, "authors"]], "Changelog": [[8, "changelog"]], "v0.1.29 (2024-03-21)": [[8, "v0-1-29-2024-03-21"]], "v0.1.28 (2023-09-29)": [[8, "v0-1-28-2023-09-29"]], "v0.1.27 (2023-08-25)": [[8, "v0-1-27-2023-08-25"]], "v0.1.26 (2023-06-27)": [[8, "v0-1-26-2023-06-27"]], "v0.1.25 (2023-02-21)": [[8, "v0-1-25-2023-02-21"]], "v0.1.24 (2023-01-27)": [[8, "v0-1-24-2023-01-27"]], "v0.1.23 (2023-01-27)": [[8, "v0-1-23-2023-01-27"]], "v0.1.22 (2023-01-27)": [[8, "v0-1-22-2023-01-27"]], "v0.1.21 (2022-04-22)": [[8, "v0-1-21-2022-04-22"]], "v0.1.20 (2022-04-13)": [[8, "v0-1-20-2022-04-13"]], "v0.1.19 (2022-04-12)": [[8, "v0-1-19-2022-04-12"]], "v0.1.18 (2022-04-12)": [[8, "v0-1-18-2022-04-12"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.9 (2022-01-16)": [[8, "v0-1-9-2022-01-16"]], "v0.1.8 (2022-01-16)": [[8, "v0-1-8-2022-01-16"]], "v0.1.7 (2021-12-18)": [[8, "v0-1-7-2021-12-18"]], "v0.1.6 (2021-12-01)": [[8, "v0-1-6-2021-12-01"]], "v0.1.5 (2021-12-01)": [[8, "v0-1-5-2021-12-01"]], "v0.1.4 (2021-11-24)": [[8, "v0-1-4-2021-11-24"]], "v0.1.3 (2021-11-24)": [[8, "v0-1-3-2021-11-24"]], "v0.1.2 (2021-11-18)": [[8, "v0-1-2-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "Contributing": [[9, "contributing"]], "Fork this repository": [[9, "fork-this-repository"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Install for developers": [[9, "install-for-developers"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Update CHANGELOG": [[9, "update-changelog"]], "Pull Request": [[9, "pull-request"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Installation": [[11, "installation"]], "pip": [[11, "pip"]], "conda": [[11, "conda"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Usage": [[14, "usage"]]}, "indexentries": {"cli() (in module mdacli.cli)": [[1, "mdacli.cli.cli"]], "mdacli.cli": [[1, "module-mdacli.cli"]], "module": [[1, "module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
diff --git a/stable/usage.html b/stable/usage.html
index 3532f22..86f8784 100644
--- a/stable/usage.html
+++ b/stable/usage.html
@@ -151,7 +151,7 @@ Usage
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
- Last updated on Mar 21, 2024.
+ Last updated on Apr 03, 2024.