Author: bugman
Date: Tue Jan 27 10:50:56 2015
New Revision: 27322
URL: http://svn.gna.org/viewcvs/relax?rev=27322&view=rev
Log:
Bug fix for the PDB secondary sheet handling when combining multiple PDB
structures.
The helix and sheet metadata now converts the original chain IDs into molecule
indices, shifted to
new values based on the currently loaded data, when the structure.read_pdb user
function is
executed. When the structure.write_pdb user function is executed, the molecule
indices are
converted into new chain IDs. This allows the chain IDs in the HELIX and SHEET
records to match
those of the ATOM and HETATOM records.
Modified:
trunk/lib/structure/internal/object.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27322&r1=27321&r2=27322&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Tue Jan 27 10:50:56 2015
@@ -487,6 +487,12 @@
'TURN '
]
+ # The number of pre-existing molecules.
+ if not len(self.structural_data):
+ mol_num = 0
+ else:
+ mol_num = len(self.structural_data[0].mol)
+
# Loop over the lines.
for i in range(len(lines)):
# No match, therefore assume to be out of the secondary structure
section.
@@ -498,34 +504,56 @@
# Parse the record.
record_type, ser_num, helix_id, init_res_name, init_chain_id,
init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode,
helix_class, comment, length = pdb_read.helix(lines[i])
+ # The molecule indices.
+ mol_init_index = self._pdb_chain_id_to_mol_index(init_chain_id)
+ mol_end_index = self._pdb_chain_id_to_mol_index(end_chain_id)
+
# Only load the desired molecule.
if read_mol != None:
- if self._pdb_chain_id_to_mol_index(init_chain_id)+1 not in
read_mol:
+ if mol_init_index + 1 not in read_mol:
continue
- if self._pdb_chain_id_to_mol_index(end_chain_id)+1 not in
read_mol:
+ if mol_end_index + 1 not in read_mol:
continue
+
+ # New molecule indices based on currently loaded data.
+ mol_init_index += mol_num
+ mol_end_index += mol_num
# Store the data.
if not hasattr(self, 'helices'):
self.helices = []
- self.helices.append([helix_id, init_chain_id, init_res_name,
init_seq_num, end_chain_id, end_res_name, end_seq_num, helix_class, length])
+ self.helices.append([helix_id, mol_init_index, init_res_name,
init_seq_num, mol_end_index, end_res_name, end_seq_num, helix_class, length])
# A sheet.
if lines[i][:5] == 'SHEET':
# Parse the record.
record_type, strand, sheet_id, num_strands, init_res_name,
init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id,
end_seq_num, end_icode, sense, cur_atom, cur_res_name, cur_chain_id,
cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id, prev_res_seq,
prev_icode = pdb_read.sheet(lines[i])
+ # The molecule indices.
+ mol_init_index = self._pdb_chain_id_to_mol_index(init_chain_id)
+ mol_end_index = self._pdb_chain_id_to_mol_index(end_chain_id)
+
# Only load the desired molecule.
if read_mol != None:
- if self._pdb_chain_id_to_mol_index(init_chain_id)+1 not in
read_mol:
+ if mol_init_index + 1 not in read_mol:
continue
- if self._pdb_chain_id_to_mol_index(end_chain_id)+1 not in
read_mol:
+ if mol_end_index + 1 not in read_mol:
continue
+
+ # New molecule indices based on currently loaded data.
+ mol_init_index += mol_num
+ mol_end_index += mol_num
+ mol_cur_index = None
+ if cur_chain_id:
+ mol_cur_index =
self._pdb_chain_id_to_mol_index(cur_chain_id) + mol_num
+ mol_prev_index = None
+ if prev_chain_id:
+ mol_prev_index =
self._pdb_chain_id_to_mol_index(prev_chain_id) + mol_num
# Store the data.
if not hasattr(self, 'sheets'):
self.sheets = []
- self.sheets.append([strand, sheet_id, num_strands,
init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name,
end_chain_id, end_seq_num, end_icode, sense, cur_atom, cur_res_name,
cur_chain_id, cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id,
prev_res_seq, prev_icode])
+ self.sheets.append([strand, sheet_id, num_strands,
init_res_name, mol_init_index, init_seq_num, init_icode, end_res_name,
mol_end_index, end_seq_num, end_icode, sense, cur_atom, cur_res_name,
mol_cur_index, cur_res_seq, cur_icode, prev_atom, prev_res_name,
mol_prev_index, prev_res_seq, prev_icode])
# Return the remaining lines.
return lines[i:]
@@ -2865,8 +2893,8 @@
# Loop over and unpack the helix data.
index = 1
- for helix_id, init_chain_id, init_res_name, init_seq_num,
end_chain_id, end_res_name, end_seq_num, helix_class, length in self.helices:
- pdb_write.helix(file, ser_num=index, helix_id=helix_id,
init_chain_id=init_chain_id, init_res_name=init_res_name,
init_seq_num=init_seq_num, end_chain_id=end_chain_id,
end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class,
length=length)
+ for helix_id, mol_init_index, init_res_name, init_seq_num,
mol_end_index, end_res_name, end_seq_num, helix_class, length in self.helices:
+ pdb_write.helix(file, ser_num=index, helix_id=helix_id,
init_chain_id=CHAIN_ID_LIST[mol_init_index], init_res_name=init_res_name,
init_seq_num=init_seq_num, end_chain_id=CHAIN_ID_LIST[mol_end_index],
end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class,
length=length)
index += 1
# The SHEET records.
@@ -2878,7 +2906,18 @@
# Loop over and unpack the helix data.
index = 1
- for strand, sheet_id, num_strands, init_res_name, init_chain_id,
init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode,
sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode, prev_atom,
prev_res_name, prev_chain_id, prev_res_seq, prev_icode in self.sheets:
+ for strand, sheet_id, num_strands, init_res_name, mol_init_index,
init_seq_num, init_icode, end_res_name, mol_end_index, end_seq_num, end_icode,
sense, cur_atom, cur_res_name, mol_cur_index, cur_res_seq, cur_icode,
prev_atom, prev_res_name, mol_prev_index, prev_res_seq, prev_icode in
self.sheets:
+ # Translate molecule indices to chain IDs.
+ init_chain_id = CHAIN_ID_LIST[mol_init_index]
+ end_chain_id = CHAIN_ID_LIST[mol_end_index]
+ cur_chain_id = None
+ if mol_cur_index != None:
+ cur_chain_id = CHAIN_ID_LIST[mol_cur_index]
+ prev_chain_id = None
+ if mol_prev_index != None:
+ prev_chain_id = CHAIN_ID_LIST[mol_prev_index]
+
+ # Write out.
pdb_write.sheet(file, strand=strand, sheet_id=sheet_id,
num_strands=num_strands, init_res_name=init_res_name,
init_chain_id=init_chain_id, init_seq_num=init_seq_num, init_icode=init_icode,
end_res_name=end_res_name, end_chain_id=end_chain_id, end_seq_num=end_seq_num,
end_icode=end_icode, sense=sense, cur_atom=cur_atom, cur_res_name=cur_res_name,
cur_chain_id=cur_chain_id, cur_res_seq=cur_res_seq, cur_icode=cur_icode,
prev_atom=prev_atom, prev_res_name=prev_res_name, prev_chain_id=prev_chain_id,
prev_res_seq=prev_res_seq, prev_icode=prev_icode)
index += 1
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