Author: bugman
Date: Tue Feb 19 22:03:41 2013
New Revision: 18506
URL: http://svn.gna.org/viewcvs/relax?rev=18506&view=rev
Log:
Faster PDB parsing by the removal of the use of the re.search() function.
Now line slices are directly compared instead.
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=18506&r1=18505&r2=18506&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Tue Feb 19 22:03:41 2013
@@ -26,7 +26,6 @@
from numpy import array, dot, float64, linalg, zeros
import os
from os import F_OK, access
-from re import search
from string import digits
from warnings import warn
@@ -277,7 +276,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -303,18 +302,18 @@
# Loop over the data.
for i in range(len(lines)):
# A new model record.
- if search('^MODEL', lines[i]):
+ if lines[i][:5] == 'MODEL':
try:
model = int(lines[i].split()[1])
except:
raise RelaxError("The MODEL record " + repr(lines[i]) +
" is corrupt, cannot read the PDB file.")
# Skip all records prior to the first ATOM or HETATM record.
- if not (search('^ATOM', lines[i]) or search('^HETATM',
lines[i])) and not len(records):
+ if not (lines[i][:4] == 'ATOM' or lines[i][:6] == 'HETATM') and
not len(records):
continue
# End of the model.
- if search('^ENDMDL', lines[i]):
+ if lines[i][:6] == 'ENDMDL':
# Yield the info.
yield model, records
@@ -355,7 +354,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -382,7 +381,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -414,7 +413,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -443,7 +442,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -485,7 +484,7 @@
# 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:
+ if lines[i][:6] not in records:
break
# Return the remaining lines.
@@ -599,19 +598,19 @@
# Loop over the data.
for i in range(len(records)):
# A PDB termination record.
- if search('^END', records[i]):
+ if records[i][:3] == 'END':
break
# A model termination record.
- if search('^ENDMDL', records[i]):
+ if records[i][:6] == 'ENDMDL':
end = True
# A molecule termination record with no trailing HETATM.
- elif i < len(records)-1 and search('^TER', records[i]) and not
search('^HETATM', records[i+1]):
+ elif i < len(records)-1 and records[i][:3] == 'TER' and not
records[i+1][:6] == 'HETATM':
end = True
# A HETATM followed by an ATOM record.
- elif i < len(records)-1 and search('^HETATM', records[i]) and
search('^ATOM', records[i+1]):
+ elif i < len(records)-1 and records[i][:6] == 'HETATM' and
records[i+1][:4] == 'ATOM':
end = True
# End.
@@ -2187,11 +2186,11 @@
continue
# Add the atom.
- if search('^ATOM', record) or search('^HETATM', record):
+ if record[:4] == 'ATOM' or record[:6] == 'HETATM':
# Parse the record.
- if search('^ATOM', record):
+ if record[:4] == 'ATOM':
record_type, serial, name, alt_loc, res_name, chain_id,
res_seq, icode, x, y, z, occupancy, temp_factor, element, charge =
pdb_read.atom(record)
- if search('^HETATM', record):
+ if record[:6] == 'HETATM':
record_type, serial, name, alt_loc, res_name, chain_id,
res_seq, icode, x, y, z, occupancy, temp_factor, element, charge =
pdb_read.hetatm(record)
# Handle the alternate locations.
@@ -2212,7 +2211,7 @@
self.atom_add(pdb_record=record_type, atom_num=serial,
atom_name=name, res_name=res_name, chain_id=chain_id, res_num=res_seq,
pos=[x, y, z], element=element)
# Connect atoms.
- if search('^CONECT', record):
+ if record[:6] == 'CONECT':
# Parse the record.
record_type, serial, bonded1, bonded2, bonded3, bonded4 =
pdb_read.conect(record)
r18506 - /trunk/generic_fns/structure/internal.py