From 6a8f4a3a2614243015c26b9dd8c497d55753c242 Mon Sep 17 00:00:00 2001
From: B13nch3n <stefan.bienert@me.com>
Date: Fri, 17 Jul 2020 14:56:50 +0200
Subject: [PATCH] SCHWED-4850: Essential documentation
---
modules/io/doc/mmcif.rst | 74 ++++++++++++++++++++++++++++++--
modules/io/src/mol/mmcif_info.hh | 2 +-
2 files changed, 72 insertions(+), 4 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 33aa310fe..a2111f546 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 152371885..76d418147 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:
--
GitLab