Author: bugman
Date: Tue Feb 19 21:54:11 2013
New Revision: 18505
URL: http://svn.gna.org/viewcvs/relax?rev=18505&view=rev
Log:
Added a series of _parse_pdb_*() methods to the internal structural object.
These correspond to each section of the PDB format version 3.30
http://www.wwpdb.org/documentation/format33/v3.3.html. The currently loop
over the records of their
section, returning the remaining PDB records. The aim is for fast parsing
and breaking into
sections.
Modified:
trunk/generic_fns/structure/internal.py
Modified: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18505&r1=18504&r2=18505&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Tue Feb 19 21:54:11 2013
@@ -255,8 +255,40 @@
return 'Average vector'
+ def _parse_pdb_connectivity_annotation(self, lines):
+ """Loop over and parse the PDB connectivity annotation records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect6.html}
+
+
+ @param lines: The lines of the PDB file excluding the sections
prior to the connectivity annotation section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the connectivity
annotation records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the connectivity annotation
section.
+ records = [
+ 'SSBOND',
+ 'LINK ',
+ 'CISPEP'
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the connectivity
annotation section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
def _parse_pdb_coord(self, lines):
"""Generator function for looping over the models in the PDB file.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect9.html}.
+
@param lines: The lines of the coordinate section.
@type lines: list of str
@@ -298,6 +330,196 @@
# If records is not empty then there are no models, so yield the lot.
if len(records):
yield model, records
+
+
+ def _parse_pdb_hetrogen(self, lines):
+ """Loop over and parse the PDB hetrogen records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect4.html}.
+
+
+ @param lines: The lines of the PDB file excluding the sections
prior to the hetrogen section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the hetrogen
records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the hetrogen section.
+ records = [
+ 'HET ',
+ 'FORMUL',
+ 'HETNAM',
+ 'HETSYN'
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the hetrogen section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
+ def _parse_pdb_misc(self, lines):
+ """Loop over and parse the PDB miscellaneous records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect7.html}.
+
+
+ @param lines: The lines of the PDB file excluding the sections
prior to the miscellaneous section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the miscellaneous
records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the miscellaneous section.
+ records = [
+ 'SITE '
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the miscellaneous
section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
+ def _parse_pdb_prim_struct(self, lines):
+ """Loop over and parse the PDB primary structure records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect3.html}.
+
+
+ @param lines: The lines of the PDB file excluding the title
section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the primary
structure records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the primary structure section.
+ records = [
+ 'DBREF ',
+ 'DBREF1',
+ 'DBREF2',
+ 'SEQADV',
+ 'SEQRES',
+ 'MODRES'
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the primary structure
section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
+ def _parse_pdb_ss(self, lines):
+ """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}.
+
+
+ @param lines: The lines of the PDB file excluding the sections
prior to the secondary structure section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the secondary
structure records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the secondary structure
section (the depreciated TURN record is also included to handle old PDB
files).
+ records = [
+ 'HELIX ',
+ 'SHEET ',
+ 'TURN '
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the secondary
structure section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
+ def _parse_pdb_title(self, lines):
+ """Loop over and parse the PDB title records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect2.html}.
+
+
+ @param lines: All lines of the PDB file.
+ @type lines: list of str
+ @return: The remaining PDB lines with the title records
stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of (sometimes truncated) record names in the
title section.
+ records = [
+ 'HEADER',
+ 'OBSLTE',
+ 'TITLE ',
+ 'SPLT ',
+ 'CAVEAT',
+ 'COMPND',
+ 'SOURCE',
+ 'KEYWDS',
+ 'EXPDTA',
+ 'NUMMDL',
+ 'MDLTYP',
+ 'AUTHOR',
+ 'REVDAT',
+ 'SPRSDE',
+ 'JRNL ',
+ 'REMARK'
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the title section.
+ if lines[i][0: 6] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
+
+
+ def _parse_pdb_transform(self, lines):
+ """Loop over and parse the PDB transform records.
+
+ These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect8.html}.
+
+
+ @param lines: The lines of the PDB file excluding the sections
prior to the transform section.
+ @type lines: list of str
+ @return: The remaining PDB lines with the transform
records stripped.
+ @rtype: list of str
+ """
+
+ # The ordered list of record names in the transform section.
+ records = [
+ 'CRYST',
+ 'MTRIX',
+ 'ORIGX',
+ 'SCALE',
+ ]
+
+ # Loop over the lines.
+ for i in range(len(lines)):
+ # No match, therefore assume to be out of the transform section.
+ if lines[i][0: 5] not in records:
+ break
+
+ # Return the remaining lines.
+ return lines[i:]
def _parse_models_xyz(self, file_path):
@@ -1059,6 +1281,15 @@
if pdb_lines == []:
raise RelaxError("The PDB file is empty.")
+ # Process the different sections.
+ 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_connectivity_annotation(pdb_lines)
+ pdb_lines = self._parse_pdb_misc(pdb_lines)
+ pdb_lines = self._parse_pdb_transform(pdb_lines)
+
# Loop over all models in the PDB file.
model_index = 0
orig_model_num = []
r18505 - /trunk/generic_fns/structure/internal.py