From c7f3da8a19671dbdd4621079622633c7b30cfb15 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 24 Jan 2024 08:43:21 +0100
Subject: [PATCH] mmcif writer: allow to pre-define entities in io.SaveMMCIF
---
modules/io/doc/mmcif.rst | 6 ++++--
modules/io/pymod/__init__.py | 9 +++++++--
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index fefd64b7b..0a648960c 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -1956,7 +1956,9 @@ To see it all in action:
(:class:`ost.StringList`) Asym chain names that are assigned to this entity
+.. class:: MMCifWriterEntityList
+ A list for :class:`MMCifWriterEntity`
.. class:: MMCifWriter
@@ -1979,11 +1981,11 @@ To see it all in action:
starting point, i.e. chains in *ent* are matched to
entities in *entity_info*. In case of no match, this
list gets extended. Starts from empty list if not given.
- :type entity_info: :class:`list` of :class:`MMCifWriterEntity`
+ :type entity_info: :class:`MMCifWriterEntityList`
.. method:: GetEntities()
- Returns :class:`list` of :class:`MMCifWriterEntity`. Useful to check after
+ Returns :class:`MMCifWriterEntityList`. Useful to check after
:func:`SetStructure` has been called. Order in this list defines entity
ids in written mmCIF file with zero based indexing.
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index caec78dae..5f011e997 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -457,7 +457,8 @@ def LoadMMCIF(filename, fault_tolerant=None, calpha_only=None,
raise
-def SaveMMCIF(ent, filename, data_name="OST_structure", mmcif_conform = True):
+def SaveMMCIF(ent, filename, data_name="OST_structure", mmcif_conform = True,
+ entity_info = MMCifWriterEntityList()):
"""
Save OpenStructure entity in mmCIF format
@@ -477,12 +478,16 @@ def SaveMMCIF(ent, filename, data_name="OST_structure", mmcif_conform = True):
to identify and separate mmCIF entities based on
:class:`ost.mol.ChemClass` of the residues in a chain.
:type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+ :param entity_info: Advanced usage - passed as *entity_info* parameter to
+ :func:`MMCifWriter.SetStructure`
:type filename: :class:`str`
:type data_name: :class:`str`
:type mmcif_conform: :class:`bool`
+ :type entity_info: :class:`MMCifWriterEntityList`
"""
writer = MMCifWriter()
- writer.SetStructure(ent, mmcif_conform = mmcif_conform)
+ writer.SetStructure(ent, mmcif_conform = mmcif_conform,
+ entity_info = entity_info)
writer.Write(data_name, filename)
--
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