diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 661d6bbcd594376480886a1cda9a0379463ea16f..179808c8d6452832329617ac22f86678cf556fdd 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -357,105 +357,110 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
return atom_pos_wrong
chain_names='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz'
+ cur_chain_name = 0
+ water_chain = mol.ChainHandle()
+ ligand_chain = mol.ChainHandle()
+ a_pos_wrong = False
+ pdb_bu = mol.CreateEntity()
+ edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
+ chains = biounit.GetChainList()
+ c_intvls = biounit.GetChainIntervalList()
+ o_intvls = biounit.GetOperationsIntervalList()
# create list of operations
# for cartesian products, operations are stored in a list, multiplied with
# the next list of operations and re-stored... until all lists of operations
# are multiplied in an all-against-all manner.
operations = biounit.GetOperations()
- trans_matrices = list()
- if len(operations) > 0:
- for op in operations[0]:
- rot = geom.Mat4()
- rot.PasteRotation(op.rotation)
- trans = geom.Mat4()
- trans.PasteTranslation(op.translation)
- tr = geom.Mat4()
- tr = trans * rot
- trans_matrices.append(tr)
- for op_n in range(1, len(operations)):
- tmp_ops = list()
- for o in operations[op_n]:
+ for i in range(0,len(c_intvls)):
+ trans_matrices = list()
+ l_operations = operations[o_intvls[i][0]:o_intvls[i][1]]
+ if len(l_operations) > 0:
+ for op in l_operations[0]:
rot = geom.Mat4()
- rot.PasteRotation(o.rotation)
+ rot.PasteRotation(op.rotation)
trans = geom.Mat4()
- trans.PasteTranslation(o.translation)
+ trans.PasteTranslation(op.translation)
tr = geom.Mat4()
tr = trans * rot
- for t_o in trans_matrices:
- tp = t_o * tr
- tmp_ops.append(tp)
- trans_matrices = tmp_ops
- # select chains into a view as basis for each transformation
- assu = asu.Select('cname=' + ','.join(biounit.GetChainList()))
- # use each transformation on the view, store as entity and transform, PDBize
- # the result while adding everything to one large entity
- pdb_bu = mol.CreateEntity()
- edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
- cur_chain_name = 0
- water_chain = mol.ChainHandle()
- ligand_chain = mol.ChainHandle()
- a_pos_wrong = False
- for tr in trans_matrices:
- # do a PDBize, add each new entity to the end product
- for chain in assu.chains:
- residue_count = len(chain.residues)
- if seqres:
- seqres_chain = seqres.FindSequence(chain.name)
- if seqres_chain.IsValid():
- residue_count = len(seqres_chain)
- if chain.is_polymer and residue_count >= min_polymer_size:
- if len(chain_names) == cur_chain_name:
- raise RuntimeError('Running out of chain names')
- new_chain = edi.InsertChain(chain_names[cur_chain_name])
- cur_chain_name += 1
- edi.SetChainDescription(new_chain, chain.description)
- edi.SetChainType(new_chain, chain.type)
- new_chain.SetStringProp('original_name', chain.name)
- if chain.HasProp("pdb_auth_chain_name"):
- new_chain.SetStringProp("pdb_auth_chain_name",
- chain.GetStringProp("pdb_auth_chain_name"))
- for res in chain.residues:
- new_res = edi.AppendResidue(new_chain, res.name, res.number)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
- elif chain.type == mol.CHAINTYPE_WATER:
- if not water_chain.IsValid():
- # water gets '-' as name
- water_chain = edi.InsertChain('-')
- edi.SetChainDescription(water_chain, chain.description)
- edi.SetChainType(water_chain, chain.type)
- for res in chain.residues:
- new_res = edi.AppendResidue(water_chain, res.name)
- new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
- new_res.SetStringProp('description', chain.description)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
- else:
- if not ligand_chain.IsValid():
- # all ligands, put in one chain, are named '_'
- ligand_chain = edi.InsertChain('_')
- last_rnum = 0
- else:
- last_rnum = ligand_chain.residues[-1].number.num
- residues=chain.residues
- ins_code='\0'
- if len(residues)>1:
- ins_code='A'
- for res in chain.residues:
- new_res = edi.AppendResidue(ligand_chain, res.name,
- mol.ResNum(last_rnum+1, ins_code))
- new_res.SetStringProp('description', chain.description)
- new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
- new_res.SetStringProp("original_name", chain.name)
+ trans_matrices.append(tr)
+ for op_n in range(1, len(l_operations)):
+ tmp_ops = list()
+ for o in l_operations[op_n]:
+ rot = geom.Mat4()
+ rot.PasteRotation(o.rotation)
+ trans = geom.Mat4()
+ trans.PasteTranslation(o.translation)
+ tr = geom.Mat4()
+ tr = trans * rot
+ for t_o in trans_matrices:
+ tp = t_o * tr
+ tmp_ops.append(tp)
+ trans_matrices = tmp_ops
+ # select chains into a view as basis for each transformation
+ assu = asu.Select('cname='+','.join(chains[c_intvls[i][0]:c_intvls[i][1]]))
+ # use each transformation on the view, store as entity and transform, PDBize
+ # the result while adding everything to one large entity
+ for tr in trans_matrices:
+ # do a PDBize, add each new entity to the end product
+ for chain in assu.chains:
+ residue_count = len(chain.residues)
+ if seqres:
+ seqres_chain = seqres.FindSequence(chain.name)
+ if seqres_chain.IsValid():
+ residue_count = len(seqres_chain)
+ if chain.is_polymer and residue_count >= min_polymer_size:
+ if len(chain_names) == cur_chain_name:
+ raise RuntimeError('Running out of chain names')
+ new_chain = edi.InsertChain(chain_names[cur_chain_name])
+ cur_chain_name += 1
+ edi.SetChainDescription(new_chain, chain.description)
+ edi.SetChainType(new_chain, chain.type)
+ new_chain.SetStringProp('original_name', chain.name)
if chain.HasProp("pdb_auth_chain_name"):
- new_res.SetStringProp("pdb_auth_chain_name",
- chain.GetStringProp("pdb_auth_chain_name"))
- ins_code = chr(ord(ins_code)+1)
- a_b = _CopyAtoms(res, new_res, edi, tr)
- if not a_pos_wrong:
- a_pos_wrong = a_b
+ new_chain.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
+ for res in chain.residues:
+ new_res = edi.AppendResidue(new_chain, res.name, res.number)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
+ elif chain.type == mol.CHAINTYPE_WATER:
+ if not water_chain.IsValid():
+ # water gets '-' as name
+ water_chain = edi.InsertChain('-')
+ edi.SetChainDescription(water_chain, chain.description)
+ edi.SetChainType(water_chain, chain.type)
+ for res in chain.residues:
+ new_res = edi.AppendResidue(water_chain, res.name)
+ new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp('description', chain.description)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
+ else:
+ if not ligand_chain.IsValid():
+ # all ligands, put in one chain, are named '_'
+ ligand_chain = edi.InsertChain('_')
+ last_rnum = 0
+ else:
+ last_rnum = ligand_chain.residues[-1].number.num
+ residues=chain.residues
+ ins_code='\0'
+ if len(residues)>1:
+ ins_code='A'
+ for res in chain.residues:
+ new_res = edi.AppendResidue(ligand_chain, res.name,
+ mol.ResNum(last_rnum+1, ins_code))
+ new_res.SetStringProp('description', chain.description)
+ new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
+ new_res.SetStringProp("original_name", chain.name)
+ if chain.HasProp("pdb_auth_chain_name"):
+ new_res.SetStringProp("pdb_auth_chain_name",
+ chain.GetStringProp("pdb_auth_chain_name"))
+ ins_code = chr(ord(ins_code)+1)
+ a_b = _CopyAtoms(res, new_res, edi, tr)
+ if not a_pos_wrong:
+ a_pos_wrong = a_b
move_to_origin = None
if a_pos_wrong:
start = pdb_bu.bounds.min
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index ff46a796cc43ccfd018b534590c0c8c0113a69f6..313235d791e1921bf1bdb8d7b9d1756f33512425 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -201,7 +201,7 @@ class TestMMCifInfo(unittest.TestCase):
pdb_ent, t = info.GetBioUnits()[0].PDBize(ent, transformation=True)
self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[0], -915.8, 1)
self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[1], -952.345, 2)
- self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.74, 2)
+ self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.75, 2)
self.assertEquals(geom.Equal(t,
geom.Mat4(1,0,0,-920.462,
0,1,0,-966.654,