From 5c37a72b5a701e0c489d0d2c5fe5601698d5f272 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 8 Jan 2025 17:35:52 -0700 Subject: [PATCH 1/3] Updated CHANGELOG for 1.2.0 --- docs/CHANGELOG.rst | 12 ++++++++++++ news/add-protocol-errors.rst | 23 ----------------------- news/added_LigandNetwork_reduce_graph.rst | 23 ----------------------- news/pickle-explicitmoleculecomponent.rst | 23 ----------------------- news/zstd_compression.rst | 23 ----------------------- 5 files changed, 12 insertions(+), 92 deletions(-) delete mode 100644 news/add-protocol-errors.rst delete mode 100644 news/added_LigandNetwork_reduce_graph.rst delete mode 100644 news/pickle-explicitmoleculecomponent.rst delete mode 100644 news/zstd_compression.rst diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 2659e23d..a78b8975 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,6 +4,18 @@ gufe Change Log .. current developments +v1.2.0 +==================== + +**Added:** + +* Added `Protocol` errors hierarchy +* added LigandNetwork.trim_graph +* Added warning when pickling an ``ExplicitMoleculeComponent`` that RDKit mol properties not preserved by default. +* JSON encoder now uses `zstandard compression `_ . + + + v1.1.0 ==================== diff --git a/news/add-protocol-errors.rst b/news/add-protocol-errors.rst deleted file mode 100644 index 979f1c1f..00000000 --- a/news/add-protocol-errors.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Added `Protocol` errors hierarchy - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/added_LigandNetwork_reduce_graph.rst b/news/added_LigandNetwork_reduce_graph.rst deleted file mode 100644 index fd0eb4c7..00000000 --- a/news/added_LigandNetwork_reduce_graph.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* added LigandNetwork.trim_graph - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/pickle-explicitmoleculecomponent.rst b/news/pickle-explicitmoleculecomponent.rst deleted file mode 100644 index 85109017..00000000 --- a/news/pickle-explicitmoleculecomponent.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* Added warning when pickling an ``ExplicitMoleculeComponent`` that RDKit mol properties not preserved by default. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/zstd_compression.rst b/news/zstd_compression.rst deleted file mode 100644 index d9971daf..00000000 --- a/news/zstd_compression.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* JSON encoder now uses `zstandard compression `_ . - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* From 2a9ffb6bded7ff79f57180f4432573e448c500f4 Mon Sep 17 00:00:00 2001 From: David Dotson Date: Wed, 8 Jan 2025 17:37:56 -0700 Subject: [PATCH 2/3] Fixes to changelog --- docs/CHANGELOG.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index a78b8975..edd1b182 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -10,7 +10,8 @@ v1.2.0 **Added:** * Added `Protocol` errors hierarchy -* added LigandNetwork.trim_graph +* Added `AtomMappingError` +* Added LigandNetwork.trim_graph * Added warning when pickling an ``ExplicitMoleculeComponent`` that RDKit mol properties not preserved by default. * JSON encoder now uses `zstandard compression `_ . @@ -21,7 +22,7 @@ v1.1.0 **Added:** -* use rever to manage changelog +* Use rever to manage changelog * KeyedChain GufeTokenizable representation was added, allowing GUFE objects to be deduplicated when serializing GufeTokenizables (PR #286). From 8634cda33448d67a69058ff08e320e96e134840e Mon Sep 17 00:00:00 2001 From: David Dotson Date: Thu, 9 Jan 2025 09:25:55 -0700 Subject: [PATCH 3/3] Seeded an approach to capturing explicit solvent, membranes, etc. in a ChemicalSystem --- gufe/components/explictsolventcomponent.py | 25 ++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 gufe/components/explictsolventcomponent.py diff --git a/gufe/components/explictsolventcomponent.py b/gufe/components/explictsolventcomponent.py new file mode 100644 index 00000000..9ca55d4c --- /dev/null +++ b/gufe/components/explictsolventcomponent.py @@ -0,0 +1,25 @@ +from .explicitmoleculecomponent import ExplicitMoleculeComponent + + + +class ExplicitRepeatedComponent(ExplicitMoleculeComponent): + + + def __init__(self): + """An explicit molecule that is repeated many times, with coordinates + specified for each instance. + + """ + ... + + +class ExplicitSolventCompoent(ExplicitRepeatedComponent): + ... + + +class MembraneComponent(ExplicitRepeatedComponent): + ... + + +class IonsComponent(ExplicitRepeatedComponent): + ...