def run_pymol_script(pml, width=500, height=500):
is_quit = 'quit' in util.words_in_file(pml)
if is_quit:
pymol_batch = data.binary("pymol_batch")
cmd = pymol_batch + ' -c '
else:
pymol = data.binary("pymol")
cmd = pymol + " -q " # no splash screen
cmd += " -W %d -H %d " % (width, height)
cmd += pml
util.run_with_output(cmd)
def convert_crd_to_trj_frame(crd):
vals = [float(word) for word in util.words_in_file(crd)[1:]]
lines = []
line = ''
for i in range(0, len(vals)):
line += "%8.3f" % vals[i]
if (i % 10) == 9:
lines.append(line)
line = ''
if line:
lines.append(line)
return '\n'.join(lines) + '\n'
def convert_crd_to_trj_frame(crd):
"""
Returns a string that corresponds to a frame in a .trj from a
.crd file. This is for writing to .trj files.
"""
vals = [float(word) for word in util.words_in_file(crd)[1:]]
lines = []
line = ''
for i in range(0, len(vals)):
line += "%8.3f" % vals[i]
if (i % 10) == 9:
lines.append(line)
line = ''
if line:
lines.append(line)
return '\n'.join(lines) + '\n'
def convert_crd_to_trj_frame(crd):
"""
Returns a string that corresponds to a frame in a .trj from a
.crd file. This is for writing to .trj files.
"""
vals = [float(word) for word in util.words_in_file(crd)[1:]]
lines = []
line = ''
for i in range(0, len(vals)):
line += "%8.3f" % vals[i]
if (i % 10) == 9:
lines.append(line)
line = ''
if line:
lines.append(line)
return '\n'.join(lines) + '\n'
def expand_pdbs(*pdbs):
"""
Returns a cleaned-up list of PDB codes given a mixed list
of pdb codes, pdb filenames, and text files containing such.
"""
results = []
for pdb in pdbs:
if os.path.isfile(pdb):
print "Reading PDB codes from", pdb
new_pdbs = expand_pdbs(*util.words_in_file(pdb))
results.extend(new_pdbs)
else:
pdb = pdb.lower()
if pdb.endswith('.pdb'):
pdb = pdb[:-4]
if len(pdb) != 4:
raise Exception("PDB code is not 4 letters long")
results.append(pdb)
return results
def expand_pdbs(*pdbs):
"""
Returns a cleaned-up list of PDB codes given a mixed list
of pdb codes, pdb filenames, and text files containing such.
"""
results = []
for pdb in pdbs:
if os.path.isfile(pdb):
print "Reading PDB codes from", pdb
new_pdbs = expand_pdbs(*util.words_in_file(pdb))
results.extend(new_pdbs)
else:
pdb = pdb.lower()
if pdb.endswith('.pdb'):
pdb = pdb[:-4]
if len(pdb) != 4:
raise Exception("PDB code is not 4 letters long")
results.append(pdb)
return results
