diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 5469a7d4..011c0036 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -7,6 +7,17 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 `_: New PDB class that allows to handle an input PDB file with multiple molecules. + +Tests added +""""""""""" +- `PR #137 `_: Adds tests to validate the new PDB class that allows to handle an input PDB file with multiple molecules. + 1.2.1 - API Documentation and improvements ------------------------------------------ diff --git a/docs/usage.rst b/docs/usage.rst index 51141c4b..c4639bf3 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -104,6 +104,7 @@ arguments. To obtain the full list of flags you can type: The name of the method to use to compute charges --charges_from_file PATH The path to the file with charges + --chain CHAIN Chain of the molecule to parameterize --include_terminal_rotamers Not exclude terminal rotamers when building the rotamer library @@ -221,6 +222,18 @@ It sets the method to load external partial charges. $ python -m peleffy.main path/to/my_ligand.pdb --charges_from_file path/to/my_ligand.mae +Chain +----- +It defines the chain of the molecule to parameterize from the input PDB file. + +- Flag: ``--chain`` +- Default: ``None`` +- Example: the code below will parameterize the hetero molecule in the chain L of the input file + + .. code-block:: bash + + $ python -m peleffy.main path/to/my_system.pdb --chain L + Include terminal rotamers ------------------------- It always includes terminal rotamers, even if they belong to a terminal methyl group whose rotation is trivial in PELE.