Hi Simon and Robert,
> It sounds like the file as it is read by the script is completely on one
> line. I wonder if this is the old UNIX vs MSDOS line ending problem.
yes, sounds like a linefeed problem. But actually python has universal
newline support. I made some changes to the script (quite a lot
changes, sorry ;-)) and now can read any of mac/unix/dos text files
using MacPyMol.
Cheers,
Thomas
--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
"""
Copyright (c) 2003 Robert L. Campbell
Copyright (c) 2010 Thomas Holder
Please read below for instructions
contains the functions
data2b_atom(mol='',data_file='')
data2b_res(mol='',data_file='')
data2q_atom(mol='',data_file='')
data2q_res(mol='',data_file='')
"""
import sys, re
comment = re.compile('^\s*$|^\s*#')
def atom_data_extract(data_file):
"""
Read the specified 'by-atom' data file and extract the data from it
and store it in parallel dictionaries specifying the data
and residue names (both with keys of chain and residue number and atom name).
The data file can contain comment lines starting with "#" (on lines by themselves).
These comment lines are ignored.
"""
bdat = {}
chain = ''
data_lines = file(data_file, 'rU')
for line in data_lines:
# ignore comment lines (beginning with a '#') or blank lines
if not comment.match(line):
words = line.split()
# check number of columns of data
if len(words) == 5:
chain = words[0]
resi = words[1]
resn = words[2]
name = words[3]
if chain == '-':
chain = ''
data = float(words[4])
elif len(words) == 4:
resi = words[0]
resn = words[1]
name = words[2]
data = float(words[3])
else:
sys.stderr.write("Error in reading data files -- check number of columns")
sys.exit(1)
bdat.setdefault(chain, {}).setdefault(resi, {})[name] = (data, resn)
return bdat
def residue_data_extract(data_file):
"""
Read the specified 'by-residue' data file and extract the data from it
and store it in parallel dictionaries specifying the data
and residue names (both with keys of chain and residue number).
The data file can contain comment lines starting with "#" (on lines by themselves).
These comment lines are ignored.
"""
bdat = {}
chain = ''
data_lines = file(data_file, 'rU')
for line in data_lines:
# ignore comment lines (beginning with a '#') or blank lines
if not comment.match(line):
words = line.split()
# check number of columns of data
if len(words) == 4:
chain = words[0]
resi = words[1]
resn = words[2]
if chain == '-':
chain = ''
data = float(words[3])
elif len(words) == 3:
resi = words[0]
resn = words[1]
data = float(words[2])
elif len(words) == 2:
resi = words[0]
data = float(words[1])
resn = ''
else:
sys.stderr.write("Error in reading data files -- check number of columns\n")
sys.exit(1)
bdat.setdefault(chain, {})[resi] = (data, resn)
return bdat
###########################################################################################
# for testing purposes:
# if calling this as a program on its own, read the pdb_file name from
# the command line and run residue_data_extract on it. (does not require
# importing cmd from pymol
if __name__ == '__main__':
pdb_file = sys.argv[1]
b_dict = residue_data_extract(pdb_file)
for chain in sorted(b_dict):
for resi in sorted(b_dict[chain]):
b, resn = b_dict[chain][resi]
print "b-factors %s %s %s %s new B='%s'" % (pdb_file, chain, resn, resi, b)
sys.exit()
###########################################################################################
# PyMOL stuff
from pymol import cmd
def data2b_atom(mol='', data_file='', prop='b'):
"""
DESCRIPTION
Alters the B-factor data by atom.
USAGE
data2b_atom <mol>, <data_file>
where <mol> is the molecular object whose B-factor data you wish to modify
and <data_file> is a file contain the data (one value for each atom)
The format of <data_file> should be:
chain resi resn name data
or
resi resn name data
(i.e. "chain" is optional if all atoms are in one chain).
Lines beginning with '#' are ignored as comments.
SEE ALSO
data2b_res, data2q_atom, data2q_res
"""
b_dict = atom_data_extract(data_file)
def b_lookup(chain, resi, name, b):
try:
return b_dict[chain][resi][name][0]
except KeyError:
return b
stored.b = b_lookup
cmd.alter(mol, '%s=stored.b(chain, resi, name, %s)' % (prop, prop))
cmd.rebuild()
def data2b_res(mol='', data_file='', prop='b'):
"""
DESCRIPTION
Alters the B-factor data by residue.
USAGE
data2b_res <mol>, <data_file>
where <mol> is the molecular object whose B-factor data you wish to modify
and <data_file> is a file contain the data (one value for each residue)
The format of <data_file> should be:
chain resi resn data
or
resi resn data
(i.e. "chain" is optional). Lines beginning with '#' are ignored as comments.
SEE ALSO
data2b_atom, data2q_atom, data2q_res
"""
b_dict = residue_data_extract(data_file)
def b_lookup(chain, resi, name, b):
try:
return b_dict[chain][resi][0]
except KeyError:
return b
stored.b = b_lookup
cmd.alter(mol, '%s=stored.b(chain, resi, name, %s)' % (prop, prop))
cmd.rebuild()
def data2q_atom(mol='',data_file=''):
"""
DESCRIPTION
Alters the occupancy data by atom.
USAGE
See data2b_atom
SEE ALSO
data2q_res, data2b_atom, data2b_res
"""
data2b_atom(mol, data_file, prop='q')
def data2q_res(mol='',data_file=''):
"""
DESCRIPTION
Alters the occupancy data by residue.
USAGE
See data2b_res
SEE ALSO
data2q_atom, data2b_atom, data2b_res
"""
data2b_res(mol, data_file, prop='q')
cmd.extend('data2b_res',data2b_res)
cmd.extend('data2b_atom',data2b_atom)
cmd.extend('data2q_res',data2q_res)
cmd.extend('data2q_atom',data2q_atom)
------------------------------------------------------------------------------
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