r27106 - /trunk/lib/structure/internal/object.py -- December 12, 2014 - 12:08

Author: bugman
Date: Fri Dec 12 12:08:20 2014
New Revision: 27106

URL: http://svn.gna.org/viewcvs/relax?rev=27106&view=rev
Log:
Improvement for the structure.read_pdb user function.

The helix and sheet secondary structure reading now takes the real_mol 
argument into account to
avoid reading in too much information.


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=27106&r1=27105&r2=27106&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py      (original)
+++ trunk/lib/structure/internal/object.py      Fri Dec 12 12:08:20 2014
@@ -465,7 +465,7 @@
         return lines[i:]
 
 
-    def _parse_pdb_ss(self, lines):
+    def _parse_pdb_ss(self, lines, read_mol=None):
         """Loop over and parse the PDB secondary structure records.
 
         These are the records identified in the PDB version 3.30 
documentation at U{http://www.wwpdb.org/documentation/format33/sect5.html}.
@@ -473,6 +473,8 @@
 
         @param lines:       The lines of the PDB file excluding the sections 
prior to the secondary structure section.
         @type lines:        list of str
+        @keyword read_mol:  The molecule(s) to read from the file, 
independent of model.  The molecules are determined differently by the 
different parsers, but are numbered consecutively from 1.  If set to None, 
then all molecules will be loaded.
+        @type read_mol:     None, int, or list of int
         @return:            The remaining PDB lines with the secondary 
structure records stripped.
         @rtype:             list of str
         """
@@ -495,6 +497,13 @@
                 # 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])
 
+                # Only load the desired molecule.
+                if read_mol != None:
+                    if self._pdb_chain_id_to_mol_index(init_chain_id) not in 
read_mol:
+                        continue
+                    if self._pdb_chain_id_to_mol_index(end_chain_id) not in 
read_mol:
+                        continue
+
                 # Store the data.
                 if not hasattr(self, 'helices'):
                     self.helices = []
@@ -504,6 +513,13 @@
             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])
+
+                # Only load the desired molecule.
+                if read_mol != None:
+                    if self._pdb_chain_id_to_mol_index(init_chain_id) not in 
read_mol:
+                        continue
+                    if self._pdb_chain_id_to_mol_index(end_chain_id) not in 
read_mol:
+                        continue
 
                 # Store the data.
                 if not hasattr(self, 'sheets'):
@@ -1951,7 +1967,7 @@
         pdb_lines = self._parse_pdb_title(pdb_lines)
         pdb_lines = self._parse_pdb_prim_struct(pdb_lines)
         pdb_lines = self._parse_pdb_hetrogen(pdb_lines)
-        pdb_lines = self._parse_pdb_ss(pdb_lines)
+        pdb_lines = self._parse_pdb_ss(pdb_lines, read_mol=read_mol)
         pdb_lines = self._parse_pdb_connectivity_annotation(pdb_lines)
         pdb_lines = self._parse_pdb_misc(pdb_lines)
         pdb_lines = self._parse_pdb_transform(pdb_lines)