Write mmcif header

prody/proteins/ciffile.py

@@ -15,7 +15,7 @@
 from prody import LOGGER, SETTINGS
 
 from .localpdb import fetchPDB
-from .starfile import parseSTARSection
+from .starfile import parseSTARSection, writeSTARStream
 from .cifheader import getCIFHeaderDict
 from .header import buildBiomolecules, assignSecstr
 
@@ -600,8 +600,16 @@ def writeMMCIF(filename, atoms, csets=None, autoext=True, **kwargs):
     if autoext and not filename.lower().endswith('.cif'):
         filename += '.cif'
 
-    structure = atoms.toBioPythonStructure(header=header, csets=csets)
+    structure = atoms.toBioPythonStructure(csets=csets)
+
+    filehandle = open(filename, 'w')
+    writeSTARStream(filehandle, header['starDict1'], prog='mmcif')
     io=MMCIFIO()
     io.set_structure(structure)
-    io.save(filename)
+    io.save(filehandle, preserve_atom_numbering=True)
+    if header['starDict2'][0].numEntries() > 0:
+        writeSTARStream(filehandle, header['starDict2'],
+                        writeDataBlockTitle=False, prog='mmcif')
+    filehandle.close()
+
     return filename

prody/proteins/cifheader.py

@@ -13,7 +13,7 @@
 from .header import (Chemical, Polymer, DBRef, _PDB_DBREF,
                      cleanString)
 
-from .starfile import parseSTARSection
+from .starfile import parseSTARSection, parseSTARLines, StarDict
 
 __all__ = ['parseCIFHeader', 'getCIFHeaderDict']
 
@@ -167,6 +167,21 @@ def getCIFHeaderDict(stream, *keys):
         for poly in header.get('polymers', []):
             poly.pdbentry = pdbid
             header[poly.chid] = poly
+
+        filename = stream.name if hasattr(stream, 'name') else ''
+
+        parsingDict1, prog = parseSTARLines(lines, shlex=True,
+            stop_field='_atom_site.group_PDB')
+        header['starDict1'] = StarDict(
+            parsingDict1, prog, filename)
+
+        parsingDict2, prog = parseSTARLines(lines, shlex=True,
+            start_field='_atom_site.group_PDB')
+        starDict2 = StarDict(
+            parsingDict2, prog, filename)
+        starDict2[0].pop(0)
+        header['starDict2'] = starDict2
+
         return header