swap asym ids and fix downstream

jamesmkrieger · Oct 12, 2023 · 1005eb5 · 1005eb5
1 parent cd3e513
commit 1005eb5
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Showing 3 changed files with 25 additions and 7 deletions.
diff --git a/prody/proteins/ciffile.py b/prody/proteins/ciffile.py
@@ -19,7 +19,7 @@
 from .cifheader import getCIFHeaderDict
 from .header import buildBiomolecules, assignSecstr, isHelix, isSheet
 
-__all__ = ['parseMMCIFStream', 'parseMMCIF']
+__all__ = ['parseMMCIFStream', 'parseMMCIF', 'parseCIF']
 
 
 class MMCIFParseError(Exception):
@@ -122,9 +122,27 @@ def parseMMCIF(pdb, **kwargs):
     result = parseMMCIFStream(cif, chain=chain, **kwargs)
     cif.close()
     if unite_chains:
-        result.setSegnames(result.getChids())
+        if isinstance(result, AtomGroup):
+            result.setChids(result.getSegnames())
+
+        elif isinstance(result, list):
+            # e.g. multiple biomol assemblies
+            [r.setChids(r.getSegnames()) for r in result if isinstance(r, AtomGroup)]
+
+        elif isinstance(result, tuple):
+            # atoms, header
+            if isinstance(result[0], AtomGroup):
+                result[0].setChids(result[0].getSegnames())
+
+            elif isinstance(result[0], list):
+                # e.g. multiple biomol assemblies
+                [r.setChids(r.getSegnames()) for r in result[0] if isinstance(r, AtomGroup)]
+
+        else:
+            raise TypeError('result from parseMMCIFStream should be a tuple, AtomGroup or list')
     return result
 
+parseCIF = parseMMCIF
 
 def parseMMCIFStream(stream, **kwargs):
     """Returns an :class:`.AtomGroup` and/or a class:`.StarDict` 
@@ -375,14 +393,14 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
             if not (atomname in subset and resname in protein_resnames):
                 continue
 
-        chID = line.split()[fields['auth_asym_id']]
+        chID = line.split()[fields['label_asym_id']]
         if chain is not None:
             if isinstance(chain, str):
                 chain = chain.split(',')
             if not chID in chain:
                 continue
 
-        segID = line.split()[fields['label_asym_id']]
+        segID = line.split()[fields['auth_asym_id']]
 
         alt = line.split()[fields['label_alt_id']]
         if alt not in which_altlocs and which_altlocs != 'all':

diff --git a/prody/proteins/cifheader.py b/prody/proteins/cifheader.py
@@ -185,7 +185,7 @@ def _getBiomoltrans(lines):
         currentBiomolecule = item1["_pdbx_struct_assembly_gen.assembly_id"]
         applyToChains = []
 
-        chains = item1["_pdbx_struct_assembly_gen.asym_id_list"].split(',')
+        chains = item1["_pdbx_struct_assembly_gen.asym_id_list"].replace(';','').strip().split(',')
         applyToChains.extend(chains)
 
         biomt = biomolecule[currentBiomolecule]

diff --git a/prody/proteins/header.py b/prody/proteins/header.py
@@ -1111,10 +1111,10 @@ def buildBiomolecules(header, atoms, biomol=None):
             translation[2] = line2[3]
             t = Transformation(rotation, translation)
 
-            newag = atoms.select('chain ' + ' or chain '.join(mt[times*4+0])).copy()
+            newag = atoms.select('chain ' + ' or chain '.join(mt[times*4+0]))
             if newag is None:
                 continue
-            newag.all.setSegnames(decToHybrid36(times+1,resnum=True))
+            newag = newag.copy()
             for acsi in range(newag.numCoordsets()):
                 newag.setACSIndex(acsi)
                 newag = t.apply(newag)