diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index 2659e23d2..edd1b1825 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -4,12 +4,25 @@ gufe Change Log .. current developments +v1.2.0 +==================== + +**Added:** + +* Added `Protocol` errors hierarchy +* 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 `_ . + + + 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). diff --git a/gufe/components/explictsolventcomponent.py b/gufe/components/explictsolventcomponent.py new file mode 100644 index 000000000..9ca55d4cb --- /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): + ... diff --git a/news/add-protocol-errors.rst b/news/add-protocol-errors.rst deleted file mode 100644 index 979f1c1f5..000000000 --- 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 fd0eb4c7d..000000000 --- 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 85109017c..000000000 --- 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 d9971daff..000000000 --- a/news/zstd_compression.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* JSON encoder now uses `zstandard compression `_ . - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -*