diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst index 33aa310fee90640e8ee9f3fdcf560ca58c04223d..a2111f546d866d16bd91b9374b62538a23a192c8 100644 --- a/modules/io/doc/mmcif.rst +++ b/modules/io/doc/mmcif.rst @@ -1203,15 +1203,83 @@ of the annotation available. See :attr:`first_release` +.. class:: MMCifInfoEntityBranchLink + + Data from ``pdbx_entity_branch``, most specifically + ``pdbx_entity_branch_link``. That is connectivity information for branched + entities, e.g. carbohydrates/ oligosaccharides. + :class:`Conop Processors <ost.conop.Processor>` can not easily connect them so + we use this information in :meth:`LoadMMCIF` to do that. + + .. attribute:: atom1 + + The first atom of the bond. Corresponds to ``entity_branch_link.atom_id_1``, + ``entity_branch_link.comp_id_1`` and + ``entity_branch_link.entity_branch_list_num_1``. Also available via + :meth:`GetAtom1` and :meth:`SetAtom1`. + + :type: :class:`~ost.mol.AtomHandle` + + .. attribute:: atom2 + + The second atom of the bond. Corresponds to ``entity_branch_link.atom_id_2``, + ``entity_branch_link.comp_id_2`` and + ``entity_branch_link.entity_branch_list_num_2``. Also available via + :meth:`GetAtom2` and :meth:`SetAtom2`. + + :type: :class:`~ost.mol.AtomHandle` + + .. attribute:: bond_order + + Order of a bond (e.g. 1=single, 2=double, 3=triple). Corresponds to + ``entity_branch_link.value_order``. Also available via :meth:`GetBondOrder` + and :meth:`SetBondOrder`. + + :type: :class:`int` + + .. method:: ConnectBranchLink(editor) + + Establish a bond between :attr:`atom1` and :attr:`atom2` of a + :class:`MMCifInfoEntityBranchLink`. + + :param editor: The editor instance to call for connecting the atoms. + :type editor: :class:`~ost.mol.XCSEditor` + :returns: Nothing + + .. method:: GetAtom1 + + See :attr:`atom1` + + .. method:: GetAtom2 + + See :attr:`atom2` + + .. method:: GetBondOrder + + See :attr:`bond_order` + + .. method:: SetAtom1 + + See :attr:`atom1` + + .. method:: SetAtom2 + + See :attr:`atom2` + + .. method:: SetBondOrder + + See :attr:`bond_order` + .. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE .. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif .. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym .. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr .. LocalWords: GetRevisions AddRevision SetRevisionsDateOriginal GetSize .. LocalWords: GetNum num GetStatus GetLastDate GetFirstRelease storable -.. LocalWords: cas isbn pubmed asu seqres conop casp COMPND OBSLTE +.. LocalWords: cas isbn pubmed asu seqres conop casp COMPND OBSLTE LoadMMCIF .. LocalWords: SetChainList MMCifInfoTransOp ChainTypes MMCifInfoStructRef .. LocalWords: MMCifInfoRevisions bool difs MMCifInfoStructRefSeqDif rnum .. LocalWords: SetDateOriginal GetDateOriginal yyyy operationsintervalls -.. LocalWords: chainintervalls GetChainIntervalList GetMethodDetails -.. LocalWords: GetOperationsIntervalList SetMethodDetails +.. LocalWords: chainintervalls GetChainIntervalList GetMethodDetails GetAtom +.. LocalWords: GetOperationsIntervalList SetMethodDetails oligosaccharides +.. LocalWords: SetAtom GetBondOrder SetBondOrder MMCifInfoEntityBranchLink diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh index 15237188546fe36add5a81a786d8ac72c96e9ed0..76d418147a5e5a173f7d5913160793f8489c4432 100644 --- a/modules/io/src/mol/mmcif_info.hh +++ b/modules/io/src/mol/mmcif_info.hh @@ -919,7 +919,7 @@ private: String details_; }; -/// \brief Store information on brnached structures (oligosaccharides) +/// \brief Store information on branched structures (oligosaccharides) /// class DLLEXPORT_OST_IO MMCifInfoEntityBranchLink { public: