From a5c5c72269d6fcc29c64e09f14230b605589115e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 21 Jan 2024 22:09:50 +0100
Subject: [PATCH] mmcif writer: docu update
---
modules/io/doc/mmcif.rst | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 2791add55..b05225f2e 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -1794,6 +1794,45 @@ The special cases listed above (_atom_site.auth_asym_id,
_pdbx_poly_seq_scheme.pdb_strand_id, _atom_site.auth_seq_id etc.) are
treated the same as if *mmcif_conform* was true.
+To see it all in action:
+
+.. code-block:: python
+
+ from ost import io
+
+ ent = io.LoadMMCIF("1a0s", remote=True)
+
+ writer = io.MMCifWriter()
+
+ # The MMCifWriter is still object of type StarWriter
+ # I can decorate my mmCIF file with any data I want
+ val = io.StarWriterValue.FromInt(42)
+ data_item = io.StarWriterDataItem("_the", "answer", val)
+ writer.Push(data_item)
+
+ # pre-define mmCIF entity which is total nonsense
+ entity_info = io.MMCifWriterEntityList()
+ mon_ids = ost.StringList()
+ mon_ids.append("ALA")
+ mon_ids.append("GLU")
+ mon_ids.append("ALA")
+ lib = conop.GetDefaultLib()
+ mmcif_ent = io.MMCifWriterEntity.FromPolymer("polypeptide(L)",
+ mon_ids, lib)
+ entity_info.append(mmcif_ent)
+
+ # The actual relevant part... mmcif_conform can be set to
+ # True, as we loaded from mmCIF file
+ writer.SetStructure(ent, mmcif_conform = True,
+ entity_info = entity_info)
+
+ # And write...
+ writer.Write("1a0s", "1a0s.cif.gz")
+
+ # The written mmCIF file will contain _the.answer and
+ # writes out the mmCIF entity we defined above in
+ # _entity_poly. However, nothing matches that entity...
+
.. class:: MMCifWriterEntity
Defines mmCIF entity which will be written in :class:`MMCifWriter`
--
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