Release 2.0.0

.gitignore

@@ -54,3 +54,9 @@ Wired*
 *.wt
 *.tar.gz
 *.bson
+
+#cache files
+.chemoton*.pickle
+.chemoton*.pkl
+.iterable_edit_widget_copy.pkl
+test/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "dev"]
+	path = dev
+	url = https://github.com/qcscine/development-utils.git

CHANGELOG.rst

@@ -1,6 +1,60 @@
 Changelog
 =========
 
+Release 2.0.0
+-------------
+New features:
+  - Add SCINE Chemoton tab to run explorations from within Heron
+  - Add tab to run the Chemoton Steering Wheel
+  - Add SCINE ReaDuct tab to carry out any ReaDuct task (e.g., structure optimizations)
+  - Modify Interactive to run with any SCINE backend calculator
+  - Add QM/MM capabilities, SFAM parametrization, and automated QM region selection to Interactive including database support
+  - Add option to construct Chemoton aggregate and reactive site filters
+  - Add option to store and generate reaction templates for SCINE Art
+  - Add possibility to slice trajectories
+  - Select and move multiple atoms in Interactive
+  - Add activate/deactive buttons to compounds in network view for rudimentary exploration control
+  - Allow direct connection to a database at start-up from the command line
+  - Introduce binary and human readable save formats for some tabs
+  - Added package variants for easier installation of optional requirements
+  - Generate graph of the entire CRN or import graph of the CRN for efficient processing purposes
+  - Introduced cache for every local CRN around a centroid; once built, it can be easily accessed again
+  - Enable fast filtering on barriers, flux, or date created (can be easily expanded to other filters)
+  - Reactions trajectory consistently extends from the center to the outer node
+  - Highlighting connected nodes when clicking on them
+  - Add new color style, `legacy`, based on Chemoton 1.0 colors
+  - Carry out steering wheel preview in background with progress bar with time estimate. The preview query can be aborted should it take too long
+  - Format reaction equation in path energy level widget
+  - Add timeout option for shortest path search, allowing users to easily interrupt lengthy searches if needed
+  - Add support for StructureFilter
+  - Add support for changed GearOptions
+  - Add AggregateFilter to database viewer tab
+
+Changes:
+  - Extend graph building capabilities
+  - Improve visualization of (shortest) path searches
+  - Improve error messaging
+  - Moved database queries to the SCINE Database module
+  - Rename 'Molecular Viewer' to 'Interactive'
+  - Node positions are now efficiently determined by algorithms implemented in Networkx
+  - Status bar in graph traversal is now identical to the main status bar
+  - Implement new caching logic for shortest paths, storing paths with and without two reactions in a path
+  - Add support for `ElementaryStepFilter` and `ReactionFilter` required by Chemoton 4.0.0.
+
+Bugfixes:
+  - Handle the case of loading a completely empty database
+  - Prevent overlapping nodes in reactions
+  - Implement plateaus in spline representation to enhance visualization
+  - Being capable of representing local CRNs with more than 100 nodes
+
+Technical:
+  - Removed complicated code for positioning compound and reaction nodes, improving code readability and maintainability
+  - Functionalized individual parts to render and position nodes
+  - Functionalized reaction profile and cleaned up redundant code
+  - Employed energy diagram class for plateaus in reaction profile
+  - Removed substep_callback in Worker
+  - Update address in license
+
 Release 1.0.0
 -------------
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

MANIFEST.in

@@ -9,4 +9,4 @@ recursive-exclude * *.py[co]
 include scine_heron/_version.py
 
 # If including data files in the package, add them like:
-include scine_heron/resources
+recursive-include scine_heron/resources *

README.rst

@@ -0,0 +1 @@
+docs/source/readme.rst

conanfile.txt

@@ -1,15 +1,22 @@
-
 [requires]
-scine_utilities/[>=4.0.0]@
-scine_sparrow/[>=3.0.0]@
-scine_database/[>=1.0.0]@
-scine_molassembler/[>=1.2.0]@
+scine_utilities/10.0.0@
+scine_sparrow/5.1.0@
+scine_database/1.4.0@
+scine_molassembler/3.0.0@
+scine_readuct/6.0.0@
+scine_serenity_wrapper/3.1.0@
+scine_swoose/2.1.0@
+scine_xtb_wrapper/3.0.1@
 
 [options]
 scine_utilities:python=True
 scine_sparrow:python=True
 scine_database:python=True
 scine_molassembler:python=True
+scine_readuct:python=True
+scine_serenity_wrapper:python=True
+scine_swoose:python=True
+scine_xtb_wrapper:python=True
 
 [generators]
 virtualenv_python

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    = "-W"  # This flag turns warnings into errors.
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = PackagingScientificPython
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/citing.rst

@@ -0,0 +1,35 @@
+Futher Citations
+----------------
+
+Specific features which are implemented in or accessible via Heron are described in their
+own papers. We kindly ask you to cite these papers when appropriate:
+
+  - | If you are applying SCINE Chemoton:
+    | J. P. Unsleber, S. A. Grimmel, M. Reiher, "Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks", J. Chem. Theory Comput., 2022, 18, 5393.
+
+  - | If you are applying SCINE Pathfinder in your exploration or analysis:
+    | P. L. Türtscher, M. Reiher, "Pathfinder - Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach", J. Chem. Inf. Model., 2023, 63, 147.
+
+  - | If you are applying kinetic modeling in your exploration or analysis:
+    | J. Proppe, M. Reiher, "Mechanism Deduction from Noisy Chemical Reaction Networks", J. Chem. Theory Comput., 2019, 15, 357.
+    | M. Bensberg, M. Reiher, "Concentration-Flux-Steered Mechanism Exploration with an Organocatalysis Application", Isr. J. Chem., 2023, 63, 147.
+
+  - | If you are applying the Steering Wheel in your exploration:
+    | M. Steiner, M. Reiher, "A human-machine interface for automatic exploration of chemical reaction networks", Nat. Commun., 2024, 15, 3680.
+
+  - | If you are construct hybrid models or run them in an interactive setting:
+    | K.-S. Csizi, M. Steiner, M. Reiher, "Nanoscale chemical reaction exploration with a quantum magnifying glass", Nat. Commun., 2024, 15, 5320.
+
+  - | If you construct a system-focused atomistic model:
+    | C. Brunken, M. Reiher, "Self-parametrizing system-focused atomistic models", J. Chem. Theory Comput., 2020, 16, 1646.
+
+  - | If you determine the QM region of your hybrid model automatically:
+    | C. Brunken, M. Reiher, "Automated construction of quantum–classical hybrid models", J. Chem. Theory Comput., 2021, 17, 3797.
+
+  - | If you carry out calculations with ReaDuct:
+    | A. C. Vaucher, M. Reiher, "Minimum Energy Paths and Transition States by Curve Optimization", J. Chem. Theory Comput., 2018, 14, 3091.
+
+  - | If you are applying interactive calculations in real-time:
+    | M. P. Haag, M. Reiher, "Real-Time Quantum Chemistry", Int. J. Quantum Chem. 2013, 113, 8.
+    | M. P. Haag, M. Reiher, "Studying chemical reactivity in a virtual environment", Faraday Discuss. 2014, 169, 89.
+    | M. P. Haag, A. C. Vaucher, M. Bosson, S. Redon, M. Reiher, "Interactive Chemical Reactivity Exploration", ChemPhysChem, 2014, 15, 3301.