diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst index 87bd4d3c808e7f6e6a2e990d1353c859ed3684a8..d4c364c2ce328aedf03b35aa1ce16c115a3bc49e 100644 --- a/modules/io/doc/io.rst +++ b/modules/io/doc/io.rst @@ -78,12 +78,15 @@ behaviour. even if one is available in the IO Profile. :param pdb_string: A PDB file as a string. + :type pdb_str: :class:`str` :param profile: The IO Profile to read the entity with. For more information on the IO Profiles available, see :doc:`profile`. + :type profile: :class:`ost.io.IOProfile` :param process: If set to True, run the :class:`~ost.conop.Processor` contained in the IO Profile. + :type process: :class:`bool` :rtype: :class:`~ost.mol.EntityHandle`. @@ -92,11 +95,31 @@ behaviour. .. code-block:: python - with open('protein.pdb') as pdb_fd: - pdb_str = pdb.read() + with open('protein.pdb') as pdb_fh: + pdb_str = pdb_fh.read() ent = io.PDBStrToEntity(pdb_str, ost.io.profiles['DEFAULT'], True) +.. function:: MMCifStrToEntity(mmcif_str, profile=IOProfile(), process=False) + + Load entity from a string in mmCIF format. By default the entity is loaded with + an empty IO Profile and is not processed with the :class:`~ost.conop.Processor`, + even if one is available in the IO Profile. + + :param mmcif_str: mmCIF file as a string + :type mmcif_str: :class:`str` + + :param profile: The IO Profile to read the entity with. For more information + on the IO Profiles available, see :doc:`profile`. + :type profile: :class:`ost.io.IOProfile` + + :param process: If set to True, run the :class:`~ost.conop.Processor` + contained in the IO Profile. + :type process: :class:`bool` + + :rtype: :class:`~ost.mol.EntityHandle`. + + .. function:: LoadSDF(filename) Load an SDF file and return an entity.