diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 8877bbc35b1d9802415281ab97ffe7d0dd6db6b2..078a66667edb73a815b9e0577182f22cc5733e29 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -80,7 +80,7 @@ of the annotation available.
.. attribute:: operations
Stores the operations needed to transform a crystal structure into a
- biounit.
+ bio unit.
Also available as :meth:`GetOperations`. May also be modified by
:meth:`AddOperation`.
@@ -115,9 +115,9 @@ of the annotation available.
.. method:: AddBioUnit(biounit)
- Add a biounit to the biounit list of an info object.
+ Add a bio unit to the bio unit list of an info object.
- :param biounit: Biounit to be added.
+ :param biounit: Bio unit to be added.
:type biounit: :class:`MMCifInfoBioUnit`
.. method:: GetBioUnits()
@@ -340,7 +340,7 @@ of the annotation available.
.. class:: MMCifInfoTransOperation
This stores operations needed to transform an
- :class:`entity <ost.mol.EntityHandle>` into a biounit.
+ :class:`entity <ost.mol.EntityHandle>` into a bio unit.
.. attribute:: id
@@ -403,7 +403,7 @@ of the annotation available.
.. class:: MMCifInfoBioUnit
This stores information how a structure is to be assembled to form the
- biounit.
+ bio unit.
.. attribute:: details
@@ -415,14 +415,14 @@ of the annotation available.
.. attribute:: chains
- Chains involved in this biounit. If not provided, resembles an empty list.
+ Chains involved in this bio unit. If not provided, resembles an empty list.
Also available as :meth:`GetChainList`. May also be modified by
:meth:`AddChain`.
.. attribute:: operations
- Translations and rotations needed to create the biounit. Filled with
+ Translations and rotations needed to create the bio unit. Filled with
objects of class :class:`MMCifInfoTransOperation`.
Also available as :meth:`GetOperations`. May be modified by
@@ -452,6 +452,39 @@ of the annotation available.
See :attr:`operations`
+ .. method:: PDBize(asu, seqres=None, min_polymer_size=10)
+
+ Returns the biological assembly (bio unit) for an entity. The new entity
+ created is well suited to be saved as a PDB file. Therefore the function
+ tries to meet the requirements of single-character chain names. The
+ following measures are taken.
+
+ - All ligands are put into one chain (_)
+ - Water is put into one chain (-)
+ - Each polymer gets its own chain, named A-Z 0-9 a-z.
+ - The description of non-polymer chains will be put into a generic string
+ property called description on the residue level.
+ - ligands which resemble a polymer but have less than min_polymer_size
+ residues are assigned the same numeric residue number. The residues are
+ distinguished by insertion code.
+
+ Since this function is at the moment mainly used to create biounits from
+ mmCIF files to be saved as PDBs, the function assumes that the
+ :ref:`ChainType` properties are set correctly. :func:`ost.conop.ConnectAll`
+ is used to derive connectivity.
+
+ :param asu: Asymmetric unit to work on. Should be created from a mmCIF
+ file.
+ :type asu: :class:`~ost.mol.EntityHandle>`
+ :param seqres: If set to a valid sequence list, the length of the seqres
+ records will be used to determine if a certain chain has the minimally
+ required length.
+ :type seqres: :class:'~ost.seq.SequenceList'
+ :param min_polymer_size: The minimal number of residues a polymer needs to
+ get its own chain. Everything below that number will be sorted into the
+ ligand chain.
+ :type min_polymer_size: int
+
.. class:: MMCifInfoStructDetails
Holds details about the structure.
@@ -642,3 +675,7 @@ of the annotation available.
.. method:: SetReplacedPDBID(descriptor)
See :attr:`replace_pdb_id`
+
+.. LocalWords: autofunction ChainTypes exptl attr pdbx oper conf spr biounits
+.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
+.. LocalWords: SPRSDE pdb func
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index e902903ea09b832b3ef13f2214816ed6931935a7..e22106b51fc4aba65bb38950d0709c631e020621 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -347,37 +347,9 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
# which is totally C++, but we want the method in Python... so we define it
# here (__init__) and add it as a member to the class. With this, the first
# arguement is the usual 'self'.
+# documentation for this function was moved to mmcif.rst,
+# MMCifInfoBioUnit.PDBize, since this function is not included in SPHINX.
def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
- """
- Returns the biological assembly (biounit) for an entity. The new entity
- created is well suited to be saved as a PDB file. Therefore the function
- tries to meet the requirements of single-character chain names. The following
- measures are taken.
-
- - All ligands are put into one chain (_)
- - Water is put into one chain (-)
- - Each polymer gets its own chain, named A-Z 0-9 a-z.
- - The description of non-polymer chains will be put into a generic string
- property called description on the residue level.
- - ligands which resemble a polymer but have less than min_polymer_size
- residues are assigned the same numeric residue number. The residues are
- distinguished by insertion code.
-
- Since this function is at the moment mainly used to create biounits from
- mmCIF files to be saved as PDBs, the function assumes that the ChainType
- properties are set correctly. conop.ConnectAll is used to derive connectivity.
-
- :param asu: Asymmetric unit to work on. Should be created from a mmCIF file.
- :type asu: :class:`~ost.mol.EntityHandle>`
- :param seqres: If set to a valid sequence list, the length of the seqres
- records will be used to determine if a certain chain has the minimally
- required length.
- :type seqres: :class:'~ost.seq.SequenceList'
- :param min_polymer_size: The minimal number of residues a polymer needs to
- get its own chain. Everything below that number will be sorted into the
- ligand chain.
- :type min_polymer_size: int
- """
def _CopyAtoms(src_res, dst_res, edi, trans=geom.Mat4()):
for atom in src_res.atoms:
tmp_pos = geom.Vec4(atom.pos)