def validate_apbs_exe(exe):
'''Get and validate apbs executable.
Raise CmdException if not found or broken.'''
import os, subprocess
if exe:
exe = cmd.exp_path(exe)
else:
try:
import freemol.apbs
exe = freemol.apbs.get_exe_path()
except:
pass
if not exe:
exe = cmd.exp_path('$SCHRODINGER/utilities/apbs')
if not os.path.exists(exe):
exe = "apbs"
try:
r = subprocess.call([exe, "--version"],
stdout=open(os.devnull, "w"),
stderr=subprocess.STDOUT)
if r < 0:
raise CmdException("Broken executable: " + exe)
except OSError:
raise CmdException("Cannot execute: " + exe)
return exe
def validate_apbs_exe(exe):
'''Get and validate apbs executable.
Raise CmdException if not found or broken.'''
import os, subprocess
if exe:
exe = cmd.exp_path(exe)
else:
try:
import freemol.apbs
exe = freemol.apbs.get_exe_path()
except:
pass
if not exe:
exe = cmd.exp_path('$SCHRODINGER/utilities/apbs')
if not os.path.exists(exe):
exe = "apbs"
try:
r = subprocess.call([exe, "--version"],
stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)
if r < 0:
raise CmdException("Broken executable: " + exe)
except OSError:
raise CmdException("Cannot execute: " + exe)
return exe
def loadall(pattern, group="", quiet=1, **kwargs):
"""
DESCRIPTION
Load all files matching given globbing pattern
"""
import glob, os
filenames = glob.glob(cmd.exp_path(pattern))
for filename in filenames:
if not quiet:
print " Loading", filename
cmd.load(filename, **kwargs)
if len(group):
if kwargs.get("object", "") != "":
print " Warning: group and object arguments given"
members = [kwargs["object"]]
else:
from pymol.cmd import file_ext_re, gz_ext_re, safe_oname_re
members = [
gz_ext_re.sub("", file_ext_re.sub("", safe_oname_re.sub("_", os.path.split(filename)[-1])))
for filename in filenames
]
cmd.group(group, " ".join(members))
def save_pdb_with_anisou(filename, selection='(all)', state=1, quiet=1):
'''
DESCRIPTION
Save in PDB format including ANISOU records.
SEE ALSO
save
'''
state, quiet = int(state), int(quiet)
pdbstr = cmd.get_pdbstr(selection, state)
atom_it = iter(cmd.get_model(selection, state).atom)
def mergeaniso():
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ['ATOM ', 'HETATM']:
u_str = ''.join('%7.0f' % (u * 1e4) for u in atom_it.next().u_aniso)
yield 'ANISOU' + line[6:28] + u_str + line[70:]
pdbstr = ''.join(mergeaniso())
filename = cmd.exp_path(filename)
f = open(filename, 'w')
f.write(pdbstr)
f.close()
if not quiet:
print(' Save with ANISOU: wrote "%s"' % (filename))
def get_sess(self,file):
from chempy import io
file = cmd.exp_path(file)
sess = io.pkl.fromFile(file)
del sess['wizard']
del sess['main']
return sess
def loadall(pattern, group='', quiet=1, **kwargs):
'''
DESCRIPTION
Load all files matching given globbing pattern
'''
import glob, os
filenames = glob.glob(cmd.exp_path(pattern))
for filename in filenames:
if not quiet:
print(' Loading ' + filename)
cmd.load(filename, **kwargs)
if len(group):
if kwargs.get('object', '') != '':
print(' Warning: group and object arguments given')
members = [kwargs['object']]
else:
from pymol.cmd import file_ext_re, gz_ext_re, safe_oname_re
members = [
gz_ext_re.sub(
'',
file_ext_re.sub(
'', safe_oname_re.sub('_',
os.path.split(filename)[-1])))
for filename in filenames
]
cmd.group(group, ' '.join(members))
def get_sess(self, file):
from chempy import io
file = cmd.exp_path(file)
sess = io.pkl.fromFile(file)
del sess['wizard']
del sess['main']
return sess
def save_pdb_with_anisou(filename, selection='(all)', state=1, quiet=1):
'''
DESCRIPTION
Save in PDB format including ANISOU records.
SEE ALSO
save
'''
state, quiet = int(state), int(quiet)
pdbstr = cmd.get_pdbstr(selection, state)
atom_it = iter(cmd.get_model(selection, state).atom)
def mergeaniso():
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ['ATOM ', 'HETATM']:
u_str = ''.join('%7.0f' % (u * 1e4)
for u in atom_it.next().u_aniso)
yield 'ANISOU' + line[6:28] + u_str + line[70:]
pdbstr = ''.join(mergeaniso())
filename = cmd.exp_path(filename)
f = open(filename, 'w')
f.write(pdbstr)
f.close()
if not quiet:
print(' Save with ANISOU: wrote "%s"' % (filename))
def pref_save(filename=PYMOLPLUGINSRC, quiet=1):
import pprint
repr = pprint.pformat
try:
f = open(cmd.exp_path(filename), 'w')
except IOError:
print(' Plugin-Error: Cannot write Plugins resource file to', filename)
return
print('# AUTOGENERATED FILE', file=f)
print('try:', file=f)
print(' import', __name__, file=f)
print(' ' + __name__ + '.autoload =', repr(autoload), file=f)
print(' ' + __name__ + '.preferences =', repr(preferences), file=f)
print(' ' + __name__ + '.set_startup_path(',
repr(get_startup_path(True)),
', False)',
file=f)
print('except:', file=f)
print(' import os', file=f)
print(' print("Error while loading " + os.path.abspath(__script__))',
file=f)
f.close()
if not int(quiet):
print(' Plugin settings saved!')
def intra_theseus(selection, state=1, cov=0, cycles=200,
exe='theseus', preserve=0, quiet=1, *, _self=cmd):
'''
DESCRIPTION
Fits all states of an object to an atom selection with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
selection = string: atoms to fit
state = integer: keep transformation of this state unchanged {default: 1}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
intra_fit, intra_rms_cur
'''
import tempfile, os
state, cov, cycles = int(state), int(cov), int(cycles)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
filename = os.path.join(tempdir, 'mobile.pdb')
_self.save(filename, selection, 0)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles, filename]
translations = []
rotations = []
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [-t[0]] + R[3:6] + [-t[1]] + R[6:9] + [-t[2], 0,0,0, 1]
for (R, t) in zip(rotations, translations)]
# intra fit states
obj_list = _self.get_object_list(selection)
for i, m in enumerate(matrices):
for obj in obj_list:
_self.transform_object(obj, m, i+1, transpose=1)
# fit back to given state
if 0 < state <= len(matrices):
m = list(matrices[state-1])
for i in [3,7,11]:
m[i] *= -1
for obj in obj_list:
_self.transform_object(obj, m, 0)
if not quiet:
print(' intra_theseus: %d states aligned' % (len(matrices)))
def intra_theseus(selection, state=1, cov=0, cycles=200,
exe='theseus', preserve=0, quiet=1):
'''
DESCRIPTION
Fits all states of an object to an atom selection with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
selection = string: atoms to fit
state = integer: keep transformation of this state unchanged {default: 1}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
intra_fit, intra_rms_cur
'''
import tempfile, os
state, cov, cycles = int(state), int(cov), int(cycles)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
filename = os.path.join(tempdir, 'mobile.pdb')
cmd.save(filename, selection, 0)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles, filename]
translations = []
rotations = []
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [-t[0]] + R[3:6] + [-t[1]] + R[6:9] + [-t[2], 0,0,0, 1]
for (R, t) in zip(rotations, translations)]
# intra fit states
obj_list = cmd.get_object_list('(' + selection + ')')
for i, m in enumerate(matrices):
for obj in obj_list:
cmd.transform_object(obj, m, i+1, transpose=1)
# fit back to given state
if 0 < state <= len(matrices):
m = list(matrices[state-1])
for i in [3,7,11]:
m[i] *= -1
for obj in obj_list:
cmd.transform_object(obj, m, 0)
if not quiet:
print(' intra_theseus: %d states aligned' % (len(matrices)))
def prosmart(mobile, target, mobile_state=1, target_state=1,
exe='prosmart', transform=1, object=None, quiet=0):
'''
DESCRIPTION
ProSMART wrapper.
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
'''
import subprocess, tempfile, os, shutil, glob
quiet = int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
cmd.save(mobile_filename, mobile, state=mobile_state)
cmd.save(target_filename, target, state=target_state)
exe = cmd.exp_path(exe)
args = [exe, '-p1', mobile_filename, '-p2', target_filename, '-a']
xglob = lambda x: glob.glob(os.path.join(tempdir, 'ProSMART_Output/Output_Files', x))
try:
subprocess.check_call(args, cwd=tempdir)
transfiles = xglob('Superposition/Transformations/*/*.txt')
with open(transfiles[0]) as f:
f = iter(f)
for line in f:
if line.startswith('ROTATION'):
matrix = [list(map(float, next(f).split())) + [0] for _ in range(3)]
elif line.startswith('TRANSLATION'):
matrix.append([-float(v) for v in next(f).split()] + [1])
break
if int(transform):
matrix = [v for m in matrix for v in m]
assert len(matrix) == 4*4
for model in cmd.get_object_list('(' + mobile + ')'):
cmd.transform_object(model, matrix, state=0)
if object:
from .importing import load_aln
alnfiles = xglob('Residue_Alignment_Scores/*/*.txt')
alnfiles = [x for x in alnfiles if not x.endswith('_clusters.txt')]
load_aln(alnfiles[0], object, mobile, target)
except OSError:
print(' Error: Cannot execute "%s", please provide full path to prosmart executable' % (exe))
raise CmdException
finally:
shutil.rmtree(tempdir)
if not quiet:
print(' prosmart: done')
def prosmart(mobile, target, mobile_state=1, target_state=1,
exe='prosmart', transform=1, object=None, quiet=0):
'''
DESCRIPTION
ProSMART wrapper.
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
'''
import subprocess, tempfile, os, shutil, glob
quiet = int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
cmd.save(mobile_filename, mobile, state=mobile_state)
cmd.save(target_filename, target, state=target_state)
exe = cmd.exp_path(exe)
args = [exe, '-p1', mobile_filename, '-p2', target_filename, '-a']
xglob = lambda x: glob.glob(os.path.join(tempdir, 'ProSMART_Output/Output_Files', x))
try:
subprocess.check_call(args, cwd=tempdir)
transfiles = xglob('Superposition/Transformations/*/*.txt')
with open(transfiles[0]) as f:
f = iter(f)
for line in f:
if line.startswith('ROTATION'):
matrix = [list(map(float, next(f).split())) + [0] for _ in range(3)]
elif line.startswith('TRANSLATION'):
matrix.append([-float(v) for v in next(f).split()] + [1])
break
if int(transform):
matrix = [v for m in matrix for v in m]
assert len(matrix) == 4*4
for model in cmd.get_object_list('(' + mobile + ')'):
cmd.transform_object(model, matrix, state=0)
if object:
from .importing import load_aln
alnfiles = xglob('Residue_Alignment_Scores/*/*.txt')
alnfiles = [x for x in alnfiles if not x.endswith('_clusters.txt')]
load_aln(alnfiles[0], object, mobile, target)
except OSError:
print(' Error: Cannot execute "%s", please provide full path to prosmart executable' % (exe))
raise CmdException
finally:
shutil.rmtree(tempdir)
if not quiet:
print(' prosmart: done')
def run_testfiles(filenames='all', verbosity=2, out=sys.stderr, **kwargs):
'''
DESCRIPTION
Run one or multiple unit test files as a test suite.
USAGE
run_testfiles file1 file2 ... [, verbosity [, out ]]
'''
import glob
if filenames in ('all', ['all']):
global run_all
run_all = True
filenames = os.path.join(pymol_test_dir, 'tests', '*', '*.py')
if isinstance(filenames, basestring):
filenames = [filename
for pattern in filenames.split()
for filename in glob.glob(cmd.exp_path(pattern))]
suite = unittest.TestSuite()
for filename in filenames:
if os.path.isdir(filename):
filenames.extend(glob.glob(os.path.join(filename, '*.py')))
continue
mod = import_from_file(filename)
# hacky: register working directory with test cases
dirname = os.path.abspath(os.path.dirname(filename))
PyMOLTestCase.moddirs[mod.__name__] = dirname
suite.addTest(unittest.defaultTestLoader
.loadTestsFromModule(mod))
if not 'xml' in kwargs:
kwargs['xml'] = False
if kwargs['xml']:
import xmlrunner
testresult = xmlrunner.XMLTestRunner(output=out, verbosity=int(verbosity)).run(suite)
else:
if isinstance(out, str):
out = open(out, 'w')
testresult = unittest.TextTestRunner(stream=out,
resultclass=PyMOLTestResult, verbosity=int(verbosity)).run(suite)
while deferred_unlink:
os.unlink(deferred_unlink.pop())
while deferred_rmtree:
import subprocess
subprocess.call(['rd', '/s', '/q', deferred_rmtree.pop()], shell=True)
return len(testresult.errors) + len(testresult.failures)
def theseus(mobile, target, match='align', cov=0, cycles=200,
mobile_state=1, target_state=1, exe='theseus', preserve=0, quiet=1,
*, _self=cmd):
'''
DESCRIPTION
Structural superposition of two molecules with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
match = string: in, like, align, none or the name of an alignment object
(see "local_rms" help for details) {default: align}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
align, super, cealign
'''
import tempfile, os
cov, cycles = int(cov), int(cycles)
mobile_state, target_state = int(mobile_state), int(target_state)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
mm = MatchMaker(mobile, target, match, _self=_self)
_self.save(mobile_filename, mm.mobile, mobile_state)
_self.save(target_filename, mm.target, target_state)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles,
mobile_filename, target_filename]
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [i*t[0]] + R[3:6] + [i*t[1]] + R[6:9] + [i*t[2], 0,0,0, 1]
for (R, t, i) in zip(rotations, translations, [-1,1])]
obj_list = _self.get_object_list(mobile)
for obj in obj_list:
_self.transform_object(obj, matrices[0], 0, transpose=1)
_self.transform_object(obj, matrices[1], 0)
if not quiet:
print(' theseus: done')
def dss_promotif(selection="all", exe="", raw="", state=-1, quiet=1):
"""
DESCRIPTION
Secondary structure assignment with PROMOTIF.
http://www.rubic.rdg.ac.uk/~gail/#Software
SEE ALSO
dss, dssp, stride
"""
from subprocess import Popen, PIPE
import tempfile, os, shutil
state, quiet = int(state), int(quiet)
ss_map = {"B": "S", "E": "S", "H": "H", "G": "H"}
exe = cmd.exp_path(exe)
if not exe:
from . import which
motifdir = os.environ.get("motifdir")
exe = which("p_sstruc3", "p_sstruc2", "promotif.scr", path=[motifdir] if motifdir else None)
tmpdir = tempfile.mkdtemp()
tmpfilepdb = os.path.join(tmpdir, "xxxx.pdb")
tmpfilesst = os.path.join(tmpdir, "xxxx.sst")
ss_dict = dict()
try:
for model in cmd.get_object_list("(" + selection + ")"):
cmd.save(tmpfilepdb, "model %s and (%s)" % (model, selection), state)
process = Popen([exe, tmpfilepdb], cwd=tmpdir, stdin=PIPE)
process.communicate(tmpfilepdb + os.linesep)
with open(tmpfilesst) as handle:
for line in handle:
if line.startswith(" num seq.no"):
break
for line in handle:
if not line.strip():
break
chain = line[6].strip("-")
resi = line[7:12].strip()
ss = line[23]
ss_dict[model, chain, resi] = ss
os.remove(tmpfilesst)
except OSError:
print " Error: Cannot execute exe=" + exe
raise CmdException
finally:
shutil.rmtree(tmpdir)
_common_ss_alter(selection, ss_dict, ss_map, raw)
def theseus(mobile, target, match='align', cov=0, cycles=200,
mobile_state=1, target_state=1, exe='theseus', preserve=0, quiet=1):
'''
DESCRIPTION
Structural superposition of two molecules with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
match = string: in, like, align, none or the name of an alignment object
(see "local_rms" help for details) {default: align}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
align, super, cealign
'''
import tempfile, os
cov, cycles = int(cov), int(cycles)
mobile_state, target_state = int(mobile_state), int(target_state)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
mm = MatchMaker(mobile, target, match)
cmd.save(mobile_filename, mm.mobile, mobile_state)
cmd.save(target_filename, mm.target, target_state)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles,
mobile_filename, target_filename]
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [i*t[0]] + R[3:6] + [i*t[1]] + R[6:9] + [i*t[2], 0,0,0, 1]
for (R, t, i) in zip(rotations, translations, [-1,1])]
obj_list = cmd.get_object_list('(' + mobile + ')')
for obj in obj_list:
cmd.transform_object(obj, matrices[0], 0, transpose=1)
cmd.transform_object(obj, matrices[1], 0)
if not quiet:
print(' theseus: done')
def get_sess(self,file):
from chempy import io
try:
file = cmd.exp_path(file)
sess = io.pkl.fromFile(file)
del sess['wizard']
del sess['main']
return sess
except:
traceback.print_exc()
return None
def run(filename, namespace='global', _spawn=0, _self=None):
'''
DESCRIPTION
"run" executes an external Python script in a local name space,
the main Python namespace, the global PyMOL namespace, or in its
own namespace (as a module).
USAGE
run file [, namespace ]
ARGUMENTS
file = string: a Python program, typically ending in .py or .pym.
namespace = local, global, module, main, or private {default: global}
NOTES
Due to an idiosyncracy in Pickle, you can not pickle objects
directly created at the main level in a script run as "module",
(because the pickled object becomes dependent on that module).
Workaround: delegate construction to an imported module.
SEE ALSO
spawn
'''
from __main__ import __dict__ as ns_main
from pymol import __dict__ as ns_pymol
if not _self:
from pymol import cmd as _self
if filename.endswith('.pml'):
return _self.load(filename)
path = _self.exp_path(filename)
spawn = int(_spawn)
run_ = spawn_file if spawn else run_file
if namespace == 'global':
run_(path, ns_pymol, ns_pymol)
elif namespace == 'local':
run_(path, ns_pymol, {})
elif namespace == 'main':
run_(path, ns_main, ns_main)
elif namespace == 'private':
run_(path, ns_main, {})
elif namespace == 'module':
run_file_as_module(path, spawn=spawn)
else:
raise ValueError('invalid namespace "%s"' % namespace)
def get_sess(self,file):
from chempy import io
try:
file = cmd.exp_path(file)
sess = io.pkl.fromFile(file)
del sess['wizard']
del sess['main']
return sess
except:
traceback.print_exc()
return None
def run(filename, namespace='global', _spawn=0, _self=None):
'''
DESCRIPTION
"run" executes an external Python script in a local name space,
the main Python namespace, the global PyMOL namespace, or in its
own namespace (as a module).
USAGE
run file [, namespace ]
ARGUMENTS
file = string: a Python program, typically ending in .py or .pym.
namespace = local, global, module, main, or private {default: global}
NOTES
Due to an idiosyncracy in Pickle, you can not pickle objects
directly created at the main level in a script run as "module",
(because the pickled object becomes dependent on that module).
Workaround: delegate construction to an imported module.
SEE ALSO
spawn
'''
from __main__ import __dict__ as ns_main
from pymol import __dict__ as ns_pymol
if not _self:
from pymol import cmd as _self
if filename.endswith('.pml'):
return _self.load(filename)
path = _self.exp_path(filename)
spawn = int(_spawn)
run_ = spawn_file if spawn else run_file
if namespace == 'global':
run_(path, ns_pymol, ns_pymol)
elif namespace == 'local':
run_(path, ns_pymol, {})
elif namespace == 'main':
run_(path, ns_main, ns_main)
elif namespace == 'private':
run_(path, ns_main, {})
elif namespace == 'module':
run_file_as_module(path, spawn=spawn)
else:
raise ValueError('invalid namespace "%s"' % namespace)
def find_apbs_exe():
try:
import freemol.apbs
exe = freemol.apbs.get_exe_path()
except:
exe = ''
if not exe:
exe = cmd.exp_path('$SCHRODINGER/utilities/apbs')
if not os.path.exists(exe):
from distutils import spawn
exe = spawn.find_executable('apbs')
return exe
def save(self):
# write compounds to a file
if self.object==None:
print " Filter-Error: please choose an object first"
else:
self.check_object_dict()
fname = self.object+".txt"
try:
f=open(fname,'w')
f.close()
except:
print " Filter-Warning: '"+fname+"' in current directory is not writable."
print " Filter-Warning: attempting to write in home directory."
fname = cmd.exp_path(os.path.join('~', fname))
try:
f=open(fname,'w')
sd = self.state_dict
sdo = self.dict[self.object]
f.write('Object\t"%s"\n'%(self.object))
f.write('Total\t%d\nAccepted\t%d\nRejected\t%d\nDeferred\t%d\nRemaining\t%d\n\n'%(
self.tota,
self.acce,
self.reje,
self.defe,
self.togo))
# sort output in order of states
lst = []
for a in sd.keys():
lst.append((sd[a],a))
lst.sort()
# write list with decisions
for a in lst:
if sdo.has_key(a[1]):
f.write('%d\t"%s"\t"%s"\n'%(a[0],a[1],sdo[a[1]]))
else:
f.write('%d\t"%s"\t"?"\n'%(a[0],a[1]))
f.close()
print " Filter: Wrote '%s'."%fname
except:
traceback.print_exc()
print " Filter-Error: Unable to write '%s'."%fname
def save(self):
# write compounds to a file
if self.object is None:
print(" Filter-Error: please choose an object first")
else:
self.check_object_dict()
fname = self.object+".txt"
try:
f=open(fname,'w')
f.close()
except:
print(" Filter-Warning: '"+fname+"' in current directory is not writable.")
print(" Filter-Warning: attempting to write in home directory.")
fname = cmd.exp_path(os.path.join('~', fname))
try:
f=open(fname,'w')
sd = self.state_dict
sdo = self.dict[self.object]
f.write('Object\t"%s"\n'%(self.object))
f.write('Total\t%d\nAccepted\t%d\nRejected\t%d\nDeferred\t%d\nRemaining\t%d\n\n'%(
self.tota,
self.acce,
self.reje,
self.defe,
self.togo))
# sort output in order of states
lst = []
for a in sd.keys():
lst.append((sd[a],a))
lst.sort()
# write list with decisions
for a in lst:
if a[1] in sdo:
f.write('%d\t"%s"\t"%s"\n'%(a[0],a[1],sdo[a[1]]))
else:
f.write('%d\t"%s"\t"?"\n'%(a[0],a[1]))
f.close()
print(" Filter: Wrote '%s'."%fname)
except:
traceback.print_exc()
print(" Filter-Error: Unable to write '%s'."%fname)
def validate_apbs_exe(exe):
'''Get and validate apbs executable.
Raise CmdException if not found or broken.'''
import subprocess
if exe:
exe = cmd.exp_path(exe)
else:
exe = find_apbs_exe() or 'apbs'
try:
r = subprocess.call([exe, "--version"],
stdin=subprocess.PIPE, # Windows pythonw fix
stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)
if r < 0:
raise CmdException("Broken executable: " + exe)
except OSError as e:
print(e)
raise CmdException("Cannot execute: " + exe)
return exe
def loadall(pattern, group='', quiet=1, **kwargs):
'''
DESCRIPTION
Load all files matching given globbing pattern
'''
import glob, os
filenames = glob.glob(cmd.exp_path(pattern))
for filename in filenames:
if not quiet:
print ' Loading', filename
cmd.load(filename, **kwargs)
if len(group):
if kwargs.get('object', '') != '':
print ' Warning: group and object arguments given'
members = [kwargs['object']]
else:
from pymol.cmd import file_ext_re, gz_ext_re, safe_oname_re
members = [gz_ext_re.sub('', file_ext_re.sub('',
safe_oname_re.sub('_', os.path.split(filename)[-1])))
for filename in filenames]
cmd.group(group, ' '.join(members))
def pref_save(filename='~/.pymolrc_plugins.py', quiet=1):
import pprint
repr = pprint.pformat
try:
f = open(cmd.exp_path(filename), 'w')
except IOError:
print ' Plugin-Error: Cannot write Plugins resource file to', filename
return
print >> f, '# AUTOGENERATED FILE'
print >> f, 'try:'
print >> f, ' import', __name__
print >> f, ' ' + __name__ + '.autoload =', repr(autoload)
print >> f, ' ' + __name__ + '.preferences =', repr(preferences)
print >> f, ' ' + __name__ + '.set_startup_path(', repr(get_startup_path()), ', False)'
print >> f, 'except:'
print >> f, ' import os'
print >> f, ' print "Error while loading " + os.path.abspath(__script__)'
f.close()
if not int(quiet):
print ' Plugin settings saved!'
def pref_save(filename=PYMOLPLUGINSRC, quiet=1):
import pprint
repr = pprint.pformat
try:
f = open(cmd.exp_path(filename), 'w')
except IOError:
print(' Plugin-Error: Cannot write Plugins resource file to', filename)
return
print('# AUTOGENERATED FILE', file=f)
print('try:', file=f)
print(' import', __name__, file=f)
print(' ' + __name__ + '.autoload =', repr(autoload), file=f)
print(' ' + __name__ + '.preferences =', repr(preferences), file=f)
print(' ' + __name__ + '.set_startup_path(', repr(get_startup_path(True)), ', False)', file=f)
print('except:', file=f)
print(' import os', file=f)
print(' print("Error while loading " + os.path.abspath(__script__))', file=f)
f.close()
if not int(quiet):
print(' Plugin settings saved!')
def save_settings(filename='~/.pymolrc-settings.py', quiet=1):
'''
DESCRIPTION
Dumps all settings with non-default values to ~/.pymolrc-settings.py
Feature Request: Save settings for later use - ID: 1009951
https://sourceforge.net/tracker/?func=detail&aid=1009951&group_id=4546&atid=354546
'''
from pymol.setting import get_name_list
quiet = int(quiet)
if not filename.endswith('.py'):
print('Warning: filename should end with ".py"')
# temporatily load default settings and remember them
cmd.reinitialize('store_defaults')
cmd.reinitialize('original_settings')
original = [(name, cmd.get(name)) for name in get_name_list()]
cmd.reinitialize('settings')
# dump to file
filename = cmd.exp_path(filename)
f = open(filename, 'w')
print('# AUTOGENERATED FILE', file=f)
print('from pymol import cmd, invocation', file=f)
print('if invocation.options.show_splash:', end=' ', file=f) # no newline
print(' print "Loading settings from",', repr(filename), file=f)
count = 0
for name, o_value in original:
value = cmd.get(name)
if value != o_value:
print('cmd.set("%s", %s)' % (name, repr(value)), file=f)
if not quiet:
print('set %s, %s # default: %s' % (name, value, o_value))
count += 1
f.close()
if not quiet:
print('Dumped %d settings to %s' % (count, filename))
def load_aln(filename, object=None, mobile=None, target=None, mobile_id=None,
target_id=None, format='', transform=0, quiet=1):
'''
DESCRIPTION
Load an alignment from file and apply it to already loaded structures.
USAGE
load_aln filename [, object [, mobile [, target [, mobile_id [, target_id [, format ]]]]]]
ARGUMENTS
filename = string: alignment file
object = string: name of the object {default: filename prefix}
mobile, target = string: atom selections {default: ids from alignment file}
mobile_id, target_id = string: ids from alignment file {default: first two}
format = string: file format, see http://biopython.org/wiki/AlignIO
{default: guess from first line in file}
EXAMPLE
fetch 1bz4 1cpr, async=0
super 1bz4 and guide, 1cpr and guide, object=aln1, window=5
save /tmp/super.aln, aln1
delete aln1
load_aln /tmp/super.aln, aln2, format=clustal
'''
from . import one_letter
from .seqalign import needle_alignment, alignment_mapping, aln_magic_read
quiet = int(quiet)
if object is None:
object = os.path.basename(filename).rsplit('.', 1)[0]
# load alignment file
alignment = aln_magic_read(cmd.exp_path(filename), format)
aln_dict = dict((record.id, record) for record in alignment)
mobile_record = alignment[0] if mobile_id is None else aln_dict[mobile_id]
target_record = alignment[1] if target_id is None else aln_dict[target_id]
# guess selections from sequence identifiers (if not given)
if mobile is None: mobile = mobile_record.id
if target is None: target = target_record.id
try:
mobile_obj = cmd.get_object_list('(' + mobile + ')')[0]
target_obj = cmd.get_object_list('(' + target + ')')[0]
except:
print ' Error: selection "%s" or "%s" does not exist' % (mobile, target)
raise CmdException
# get structure models and sequences
mobile_model = cmd.get_model('(%s) and guide' % mobile)
target_model = cmd.get_model('(%s) and guide' % target)
mobile_sequence = ''.join(one_letter.get(a.resn, 'X') for a in mobile_model.atom)
target_sequence = ''.join(one_letter.get(a.resn, 'X') for a in target_model.atom)
# align sequences from file to structures
mobile_aln = needle_alignment(str(mobile_record.seq), mobile_sequence)
target_aln = needle_alignment(str(target_record.seq), target_sequence)
# get index mappings
mobile_aln_i2j = dict(alignment_mapping(*mobile_aln))
target_aln_i2j = dict(alignment_mapping(*target_aln))
record_i2j = alignment_mapping(mobile_record, target_record)
# build alignment list
r = []
for i, j, in record_i2j:
if i in mobile_aln_i2j and j in target_aln_i2j:
i = mobile_aln_i2j[i]
j = target_aln_i2j[j]
r.append({
mobile_obj: mobile_model.atom[i].index,
target_obj: target_model.atom[j].index,
})
set_raw_alignment(object, r, int(transform))
return r
def tmalign(mobile,
target,
args='',
exe='TMalign',
ter=0,
transform=1,
object=None,
quiet=0):
"""
DESCRIPTION
TMalign wrapper
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
USAGE
tmalign mobile, target [, args [, exe ]]
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign executable {default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
SEE ALSO
tmscore, mmalign
"""
import subprocess
import tempfile
import os
import re
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
matrix_filename = tempfile.mktemp('.txt', 'matrix')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % mobile
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % target
if ter:
save = cmd.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele)
save(target_filename, target_ca_sele)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename, '-m', matrix_filename
] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
lines = process.stdout.readlines()
except OSError:
print('Cannot execute "%s", please provide full path to TMscore or '
'TMalign executable' % exe)
raise CmdException
finally:
os.remove(mobile_filename)
os.remove(target_filename)
# TMalign >= 2012/04/17
if os.path.exists(matrix_filename):
lines += open(matrix_filename).readlines()
os.remove(matrix_filename)
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(lines)
alignment = []
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = list(map(float, line.split()))
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = []
for i in range(3):
alignment.append(line_it.next().rstrip())
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print(line.rstrip())
if not quiet:
for i in range(0, len(alignment[0]) - 1, 78):
for line in alignment:
print(line[i:i + 78])
print('')
assert len(matrix) == 3 * 4
matrix.extend([0, 0, 0, 1])
if int(transform):
cmd.transform_selection('byobject (%s)' % mobile, matrix, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
cmd.iterate(mobile_ca_sele,
'mobile_idx.append("%s`%d" % (model, index))',
space=space)
cmd.iterate(target_ca_sele,
'target_idx.append("%s`%d" % (model, index))',
space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if len(mobile_idx) == len(target_idx) == len(alignment[2]):
cmd.rms_cur(' '.join(idx
for (idx, m) in zip(mobile_idx, alignment[1])
if m in ':.'),
' '.join(idx
for (idx, m) in zip(target_idx, alignment[1])
if m in ':.'),
matchmaker=4,
object=object)
else:
print('Could not load alignment object')
if not quiet and r is not None:
print('Found in output TM-score = %.4f' % r)
return r
}
autoload = {}
plugins = {}
HAVE_QT = False
# exception types
class QtNotAvailableError(Exception):
pass
# plugins from PYMOL_DATA
startup.__path__.append(cmd.exp_path('$PYMOL_DATA/startup'))
N_NON_USER_PATHS = len(startup.__path__)
# API functions
def is_verbose(debug=0):
verbose = pref_get('verbose')
if debug and verbose < 0:
return True
return verbose and pymol.invocation.options.show_splash
def get_startup_path(useronly=False):
if useronly:
# assume last item is always from installation directory
return startup.__path__[:-N_NON_USER_PATHS]
return startup.__path__
def poseview(ligand='organic inorganic', protein='polymer', width=0, height=0,
filename='', exe='poseview', state=-1, quiet=1):
'''
DESCRIPTION
PoseView wrapper
http://www.biosolveit.de/poseview/
USAGE
poseview [ ligand [, protein [, width [, height [, exe [, state ]]]]]]
ARGUMENTS
ligand = string: atom selection {default: organic inorganic}
protein = string: atom selection {default: polymer}
width = int: image width {default: viewport width}
height = int: image height {default: viewport height}
filename = string: output PNG file name {default: temporary}
exe = string: path to executable {default: poseview}
SETUP
1) Put poseview executable to PATH (e.g. /usr/bin/poseview)
2) Set environment variable BIOSOLVE_LICENSE_FILE="/path/to/poseview.lic"
'''
import tempfile
import subprocess
import os
import shutil
width, height = int(width), int(height)
state, quiet = int(state), int(quiet)
if width == 0 or height == 0:
viewport = cmd.get_viewport()
if width != 0:
height = int(viewport[0] / float(width) * viewport[1])
elif height != 0:
width = int(viewport[1] / float(height) * viewport[0])
else:
width, height = viewport
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
ligand_filename = os.path.join(tempdir, 'ligand.sdf')
protein_filename = os.path.join(tempdir, 'protein.pdb')
if not filename:
filename = os.path.join(tempdir, 'image.png')
cmd.save(ligand_filename, ligand, state)
cmd.save(protein_filename, protein, state)
args = [exe, '-l', ligand_filename, '-p', protein_filename, '-t', '',
'-o', filename, '-s', str(width), str(height)]
if not quiet:
print(' poseview: running...')
process = subprocess.Popen(args,
universal_newlines=True,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
stdout, _ = process.communicate()
if not quiet:
print(stdout)
print(' poseview: done')
if filename.endswith('.png'):
cmd.load(filename)
elif not quiet:
print(' Warning: cannot load "%s" into PyMOL, unsupported file type' % (filename))
except OSError:
print(' Error: Cannot execute "%s", please provide full path to poseview executable' % (exe))
raise CmdException
finally:
shutil.rmtree(tempdir)
def load_aln_multi(filename, object=None, mapping='', alignioformat='', guide='',
quiet=1, _self=cmd):
'''
DESCRIPTION
Load a multiple sequence alignment from file and apply it to already
loaded structures.
Requires Biopython (conda install biopython)
USAGE
load_aln_multi filename [, object [, mapping [, alignioformat [, guide ]]]]
ARGUMENTS
filename = str: alignment file
object = str: name of the new alignment object {default: filename prefix}
mapping = str: space separated list of sequence-id to object-name
mappings {default: assume sequence-id = object-name}
alignioformat = str: file format, see http://biopython.org/wiki/AlignIO
{default: guess from first line in file}
guide = str: object name of "guide" object (PyMOL only knows many-to-one
alignment, not true multiple alignments) {default: random object}
SEE ALSO
psico.importing.load_aln
'''
import os
quiet = int(quiet)
if object is None:
object = os.path.basename(filename).rsplit('.', 1)[0]
# load alignment file
alignment = aln_magic_read(cmd.exp_path(filename), alignioformat)
# object name mapping
if isinstance(mapping, str):
mapping = mapping.split()
mapping = dict(zip(mapping[0::2], mapping[1::2]))
i2index = [None] * len(alignment)
onames = [None] * len(alignment)
indices = [-1] * len(alignment)
# get structure models and sequences
for r, record in enumerate(alignment):
oname = mapping.get(record.id, record.id)
if not oname:
continue
atoms = []
n = _self.iterate('?{} & guide'.format(oname), 'atoms.append((oneletter or "?", index))',
space=locals())
if n == 0:
print(" Warning: no atoms for object '{}'".format(oname))
continue
# align sequences from file to structures
aln = needle_alignment(str(record.seq), ''.join(a[0] for a in atoms))
# get index mappings
i2index[r] = dict((i, atoms[j][1])
for (i, j) in alignment_mapping(*aln))
onames[r] = oname
if len(onames) < 2:
raise CmdException('Failed to map alignment to objects')
# build alignment list
raw = []
for c in range(len(alignment[0])):
rawcol = []
for r, aa in enumerate(alignment[:, c]):
if onames[r] is None:
continue
if aa != '-':
indices[r] += 1
index = i2index[r].get(indices[r], -1)
if index >= 0:
rawcol.append((onames[r], index))
if len(rawcol) > 1:
raw.append(rawcol)
_self.set_raw_alignment(object, raw, guide=guide)
return raw
def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object=None, quiet=0):
'''
DESCRIPTION
TMalign wrapper
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
USAGE
tmalign mobile, target [, args [, exe ]]
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign executable {default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
SEE ALSO
tmscore, mmalign
'''
import subprocess, tempfile, os, re
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
if ter:
save = cmd.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele)
save(target_filename, target_ca_sele)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
except OSError:
print 'Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe)
raise CmdException
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(process.stdout)
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = map(float, line.split())
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = [line_it.next().rstrip() for i in range(3)]
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print line.rstrip()
if not quiet:
for i in range(0, len(alignment[0])-1, 78):
for line in alignment:
print line[i:i+78]
print ''
assert len(matrix) == 3*4
matrix.extend([0,0,0,1])
if int(transform):
cmd.transform_selection('byobject (%s)' % (mobile), matrix, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
cmd.iterate(mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
cmd.iterate(target_ca_sele, 'target_idx.append("%s`%d" % (model, index))', space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
cmd.rms_cur(
' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
cycles=0, matchmaker=4, object=object)
else:
print 'Could not load alignment object'
if not quiet and r is not None:
print 'Found in output TM-score = %.4f' % (r)
os.remove(mobile_filename)
os.remove(target_filename)
return r
def _normalmodes(selection,
cutoff,
force,
mass,
first,
last,
choose,
substruct,
blocksize,
exe,
diag_exe,
prefix,
states,
factor,
clean,
quiet,
wiz=None):
import tempfile, subprocess, os, shutil, sys
from chempy import cpv
cutoff, force = float(cutoff), float(force)
first, last, blocksize = int(first), int(last), int(blocksize)
clean, quiet = int(clean), int(quiet)
exe = cmd.exp_path(exe)
diag_exe = cmd.exp_path(diag_exe)
tempdir = tempfile.mkdtemp()
if not quiet:
print(' normalmodes: Temporary directory is', tempdir)
try:
sele_name = cmd.get_unused_name('__pdbmat')
except AttributeError:
sele_name = '__pdbmat'
try:
filename = os.path.join(tempdir, 'mobile.pdb')
commandfile = os.path.join(tempdir, 'pdbmat.dat')
cmd.select(sele_name, '(%s) and not hetatm' % (selection))
cmd.save(filename, sele_name)
f = open(commandfile, 'w')
f.write('''! pdbmat file
Coordinate FILENAME = %s
MATRIx FILENAME = matrix.sdijb
INTERACtion DISTance CUTOF = %.3f
INTERACtion FORCE CONStant = %.3f
Origin of MASS values = %s
Output PRINTing level = 0
MATRix FORMat = BINA
''' % (filename, cutoff, force, mass.upper()))
f.close()
if not quiet:
print(' normalmodes: running', exe, '...')
if wiz is not None:
wiz.message[1] = 'running pdbmat'
cmd.refresh_wizard()
process = subprocess.Popen([exe],
cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
try:
natoms = len(
open(os.path.join(tempdir, 'pdbmat.xyzm')).readlines())
except Exception as e:
print(e)
natoms = cmd.count_atoms(sele_name)
if natoms != cmd.count_atoms(sele_name):
print('Error: pdbmat did not recognize all atoms')
raise CmdException
commandfile = os.path.join(tempdir, 'diagrtb.dat')
f = open(commandfile, 'w')
f.write('''! diagrtb file
MATRIx FILENAME = matrix.sdijb
COORdinates filename = %s
Eigenvector OUTPut filename= diagrtb.eigenfacs
Nb of VECTors required = %d
EigeNVALues chosen = %s
Type of SUBStructuring = %s
Nb of residues per BLOck = %d
Origin of MASS values = %s
Temporary files cleaning = ALL
MATRix FORMat = BINA
Output PRINting level = 0
''' % (filename, last, choose.upper(), substruct.upper(), blocksize,
mass.upper()))
f.close()
exe = diag_exe
if not quiet:
print(' normalmodes: running', exe, '...')
if wiz is not None:
wiz.message[1] = 'running diagrtb'
cmd.refresh_wizard()
process = subprocess.Popen([exe],
cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
eigenfacs, frequencies = parse_eigenfacs(
os.path.join(tempdir, 'diagrtb.eigenfacs'), last)
if wiz is not None:
wiz.message[1] = 'generating objects'
cmd.refresh_wizard()
states = int(states)
factor = float(factor)
if factor < 0:
factor = natoms**0.5
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1]))
for state in range(1, states + 1):
cmd.create(name, sele_name, 1, state, zoom=0)
cmd.alter_state(
state,
name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(next(myit), myfac))',
space={
'cpv': cpv,
'myit': iter(eigenfacs[mode - 1]),
'next': next,
'myfac': factor * (state - (states + 1) / 2.0)
})
# if CA only selection, show ribbon trace
if natoms == cmd.count_atoms('(%s) and name CA' % sele_name):
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
# store results
if not hasattr(stored, 'nma_results'):
stored.nma_results = []
stored.nma_results.append({
'facs': eigenfacs,
'freq': frequencies,
'sele': sele_name,
})
except OSError:
print('Cannot execute "%s", please provide full path to executable' %
(exe))
except CmdException as e:
print(' normalmodes: failed!', e)
finally:
if clean:
shutil.rmtree(tempdir)
elif not quiet:
print(' normalmodes: Working directory "%s" not removed!' %
(tempdir))
# cmd.delete(sele_name)
if wiz is not None:
cmd.set_wizard_stack(
[w for w in cmd.get_wizard_stack() if w != wiz])
def pdb2pqr_cli(name,
selection,
options,
state=-1,
preserve=0,
exe='pdb2pqr',
quiet=1,
fixrna=0,
_proclist=None):
import os, tempfile, subprocess, shutil
state, preserve, quiet = int(state), int(preserve), int(quiet)
if cmd.is_string(options):
import shlex
options = shlex.split(options)
args = [cmd.exp_path(exe)] + list(options)
tmpdir = tempfile.mkdtemp()
infile = os.path.join(tmpdir, 'in.pdb')
outfile = os.path.join(tmpdir, 'out.pqr')
args.extend([infile, outfile])
# For some reason, catching stdout/stderr with PIPE and communicate()
# blocks terminate() calls from terminating early. Using a file
# redirect doesn't show this problem.
f_stdout = open(os.path.join(tmpdir, 'stdout.txt'), 'w+')
# RNA resdiue names must be RA, RC, RG, and RU
tmpmodel = ''
if int(fixrna) and cmd.count_atoms('(%s) & resn A+C+G+U' % (selection)):
tmpmodel = cmd.get_unused_name('_tmp')
cmd.create(tmpmodel, selection, zoom=0)
cmd.alter(tmpmodel + ' & polymer.nucleic & resn A+C+G+U',
'resn = "R" + resn')
selection = tmpmodel
try:
cmd.save(infile, selection, state)
p = subprocess.Popen(
args,
cwd=tmpdir,
stdin=subprocess.PIPE, # Windows pythonw fix
stdout=f_stdout,
stderr=f_stdout)
p.stdin.close() # Windows pythonw fix
if _proclist is not None:
_proclist.append(p)
p.wait()
# This allows PyMOL to capture it and display the output in the GUI.
f_stdout.seek(0)
print(f_stdout.read().rstrip())
if p.returncode == -15: # SIGTERM
raise CmdException('pdb2pqr terminated')
if p.returncode != 0:
raise CmdException('%s failed with exit status %d' %
(args[0], p.returncode))
warnings = [
L[10:] for L in open(outfile) if L.startswith('REMARK 5')
]
warnings = ''.join(warnings).strip()
cmd.load(outfile, name)
return warnings
except OSError as e:
print(e)
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if tmpmodel:
cmd.delete(tmpmodel)
f_stdout.close()
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
def _normalmodes(selection, cutoff, force, mass,
first, last, choose, substruct, blocksize,
exe, diag_exe, prefix, states, factor, clean, quiet, wiz=None):
import tempfile, subprocess, os, shutil, sys
from chempy import cpv
cutoff, force = float(cutoff), float(force)
first, last, blocksize = int(first), int(last), int(blocksize)
clean, quiet = int(clean), int(quiet)
exe = cmd.exp_path(exe)
diag_exe = cmd.exp_path(diag_exe)
tempdir = tempfile.mkdtemp()
if not quiet:
print ' normalmodes: Temporary directory is', tempdir
try:
sele_name = cmd.get_unused_name('__pdbmat')
except AttributeError:
sele_name = '__pdbmat'
try:
filename = os.path.join(tempdir, 'mobile.pdb')
commandfile = os.path.join(tempdir, 'pdbmat.dat')
cmd.select(sele_name, '(%s) and not hetatm' % (selection))
cmd.save(filename, sele_name)
f = open(commandfile, 'w')
f.write('''! pdbmat file
Coordinate FILENAME = %s
MATRIx FILENAME = matrix.sdijb
INTERACtion DISTance CUTOF = %.3f
INTERACtion FORCE CONStant = %.3f
Origin of MASS values = %s
Output PRINTing level = 0
MATRix FORMat = BINA
''' % (filename, cutoff, force, mass.upper()))
f.close()
if not quiet:
print ' normalmodes: running', exe, '...'
if wiz is not None:
wiz.message[1] = 'running pdbmat'
cmd.refresh_wizard()
process = subprocess.Popen([exe], cwd=tempdir,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
natoms = len(open(os.path.join(tempdir, 'pdbmat.xyzm')).readlines())
if natoms != cmd.count_atoms(sele_name):
print 'Error: pdbmat did not recognize all atoms'
raise CmdException
commandfile = os.path.join(tempdir, 'diagrtb.dat')
f = open(commandfile, 'w')
f.write('''! diagrtb file
MATRIx FILENAME = matrix.sdijb
COORdinates filename = pdbmat.xyzm
Eigenvector OUTPut filename= diagrtb.eigenfacs
Nb of VECTors required = %d
EigeNVALues chosen = %s
Type of SUBStructuring = %s
Nb of residues per BLOck = %d
Origin of MASS values = %s
Temporary files cleaning = ALL
MATRix FORMat = BINA
Output PRINting level = 0
''' % (last, choose.upper(), substruct.upper(), blocksize, mass.upper()))
f.close()
exe = diag_exe
if not quiet:
print ' normalmodes: running', exe, '...'
if wiz is not None:
wiz.message[1] = 'running diagrtb'
cmd.refresh_wizard()
process = subprocess.Popen([exe], cwd=tempdir,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
eigenfacs, frequencies = parse_eigenfacs(
os.path.join(tempdir, 'diagrtb.eigenfacs'), last)
if wiz is not None:
wiz.message[1] = 'generating objects'
cmd.refresh_wizard()
states = int(states)
factor = float(factor)
if factor < 0:
factor = natoms**0.5
for mode in range(first, last+1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print ' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1])
for state in range(1, states+1):
cmd.create(name, sele_name, 1, state, zoom=0)
cmd.alter_state(state, name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(myit.next(), myfac))',
space={'cpv': cpv, 'myit': iter(eigenfacs[mode-1]),
'myfac': factor * (state - (states+1)/2.0)})
# if CA only selection, show ribbon trace
if natoms == cmd.count_atoms('(%s) and name CA' % sele_name):
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
# store results
if not hasattr(stored, 'nma_results'):
stored.nma_results = []
stored.nma_results.append({
'facs': eigenfacs,
'freq': frequencies,
'sele': sele_name,
})
except OSError:
print 'Cannot execute "%s", please provide full path to executable' % (exe)
except CmdException, e:
print ' normalmodes: failed!', e
def save_pdb(filename,
selection='(all)',
state=-1,
symm=1,
ss=1,
aniso=0,
seqres=0,
quiet=1):
'''
DESCRIPTION
Save the coordinates of a selection as pdb including the
secondary structure information and, if possible, the unit
cell. The latter requires the selction of a single object
USAGE
save_pdb filename, selection [, state [, symm [, ss [, aniso ]]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
Note: to include the unit cell information you
need to select a single object
state = integer: state to save {default: -1 (current state)}
symm = 0 or 1: save symmetry info if possible {default: 1}
ss = 0 or 1: save secondary structure info {default: 1}
aniso = 0 or 1: save ANISO records {default: 0}
SEE ALSO
save
'''
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
symm, ss = int(symm), int(ss)
filename = cmd.exp_path(filename)
f = open(filename, 'w')
print('REMARK 200 Generated with PyMOL and psico'.ljust(80), file=f)
# Write sequence
if int(seqres):
f.write(get_pdb_seqres(selection))
# Write the CRYST1 line if possible
if symm:
try:
obj1 = cmd.get_object_list(selection)[0]
sym = cmd.get_symmetry(obj1)
if len(sym) != 7:
raise
f.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-10s%4d\n" %
tuple(sym + [1]))
if not quiet:
print(' Info: Wrote unit cell and space group info')
except:
if not quiet:
print(' Info: No crystal information')
# Write secondary structure
if ss:
try:
sss = get_pdb_sss(selection, state, quiet)
if not sss:
raise
f.write(sss)
if not quiet:
print(' Info: Wrote secondary structure info')
except:
if not quiet:
print(' Info: No secondary structure information')
# Write coordinates of selection
pdbstr = cmd.get_pdbstr(selection, state)
# fix END records
if state == 0 and cmd.get_version()[1] < 1.6:
pdbstr = '\n'.join(
line for line in pdbstr.splitlines() if line != 'END') + '\nEND\n'
# anisotropic b-factors
from . import pymol_version
if int(aniso) and pymol_version < 1.6 and \
cmd.get_model('first (%s)' % selection).atom[0].u_aniso[0] != 0.0:
def mergeaniso():
atom_it = iter(cmd.get_model(selection, state).atom)
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ['ATOM ', 'HETATM']:
yield 'ANISOU' + line[6:28] + \
''.join('%7.0f' % (u*1e4) for u in atom_it.next().u_aniso) + \
line[70:]
pdbstr = ''.join(mergeaniso())
f.write(pdbstr)
f.close()
if not quiet:
print('Wrote PDB to \'' + filename + '\'')
def fiber(seq, num=4, name='', rna=0, single=0, repeats=0,
preserve=0, exe='$X3DNA/bin/fiber', quiet=1, *, _self=cmd):
'''
DESCRIPTION
Run X3DNA's "fiber" tool.
For the list of structure identification numbers, see for example:
http://xiang-jun.blogspot.com/2009/10/fiber-models-in-3dna.html
USAGE
fiber seq [, num [, name [, rna [, single ]]]]
ARGUMENTS
seq = str: single letter code sequence or number of repeats for
repeat models.
num = int: structure identification number {default: 4}
name = str: name of object to create {default: random unused name}
rna = 0/1: 0=DNA, 1=RNA {default: 0}
single = 0/1: 0=double stranded, 1=single stranded {default: 0}
EXAMPLES
# environment (this could go into ~/.pymolrc or ~/.bashrc)
os.environ["X3DNA"] = "/opt/x3dna-v2.3"
# B or A DNA from sequence
fiber CTAGCG
fiber CTAGCG, 1, ADNA
# double or single stranded RNA from sequence
fiber AAAGGU, name=dsRNA, rna=1
fiber AAAGGU, name=ssRNA, rna=1, single=1
# poly-GC Z-DNA repeat model with 10 repeats
fiber 10, 15
'''
import os, tempfile, subprocess, shutil
rna, single = int(rna), int(single)
preserve, quiet = int(preserve), int(quiet)
if 'X3DNA' not in os.environ:
raise CmdException('please set X3DNA environment variable')
args = [cmd.exp_path(exe), '-seq=' + seq, '-' + str(num)]
if rna:
args.append('-rna')
if single:
args.append('-single')
if not name:
name = _self.get_unused_name('fiber-' + str(num) + '_')
tmpdir = tempfile.mkdtemp()
outfile = os.path.join(tmpdir, 'out.pdb')
args.append(outfile)
if seq.endswith('help'):
# call fiber with no arguments to get help page
args[1:] = []
try:
p = subprocess.Popen(args, cwd=tmpdir,
universal_newlines=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
stdout, _ = p.communicate(str(int(repeats) or seq))
if not quiet:
print(stdout)
if len(args) != 1:
if p.returncode != 0:
raise CmdException('Returned non-zero status: ' + str(args))
_self.load(outfile, name, quiet=quiet)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
def prepwizard(name, selection='all', options='', state=-1,
preserve=0, exe='$SCHRODINGER/utilities/prepwizard', quiet=1,
*, _self=cmd):
'''
DESCRIPTION
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side
chains and converts MSE to MET. Other non-default options need to be
passed with the "options=" argument.
USAGE
prepwizard name [, selection [, options [, state ]]]
ARGUMENTS
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
'''
import os, tempfile, subprocess, shutil, shlex
state, preserve, quiet = int(state), int(preserve), int(quiet)
exe = cmd.exp_path(exe)
if not os.path.exists(exe):
if 'SCHRODINGER' not in os.environ:
print(' Warning: SCHRODINGER environment variable not set')
raise CmdException('no such script: ' + exe)
args = [exe, '-mse', '-fillsidechains', '-WAIT']
if options:
if isinstance(options, (str, bytes)):
options = shlex.split(options)
args.extend(options)
tmpdir = tempfile.mkdtemp()
infile = 'in.pdb'
outfile = 'out.mae'
args.extend([infile, outfile])
try:
_self.save(os.path.join(tmpdir, infile), selection, state)
p = subprocess.Popen(args, cwd=tmpdir,
universal_newlines=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
print(p.communicate()[0].rstrip())
if p.returncode != 0:
logfile = os.path.join(tmpdir, 'in.log')
if os.path.exists(logfile):
with open(logfile) as handle:
print(handle.read())
raise CmdException('%s failed with exit status %d' % (args[0], p.returncode))
_self.load(os.path.join(tmpdir, outfile), name)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' prepwizard: done')
def pdb2pqr(name, selection='all', ff='AMBER', debump=1, opt=1, assignonly=0,
ffout='', ph=None, neutraln=0, neutralc=0, state=-1, preserve=0,
exe='pdb2pqr30', quiet=1, *, keep_chain=1, _self=cmd):
'''
DESCRIPTION
Creates a new molecule object from a selection and adds missing atoms,
assignes charges and radii using PDB2PQR.
http://www.poissonboltzmann.org/pdb2pqr/
USAGE
pdb2pqr name [, selection [, ff [, debump [, opt [, assignonly [, ffout [,
ph [, neutraln [, neutralc [, state [, preserve ]]]]]]]]]]]
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object {default: all}
ff = string: forcefield {default: AMBER}
'''
import os, tempfile, subprocess, shutil
debump, opt, assignonly = int(debump), int(opt), int(assignonly)
neutraln, neutralc = int(neutraln), int(neutralc)
state, preserve, quiet = int(state), int(preserve), int(quiet)
args = [cmd.exp_path(exe), '--ff=' + ff]
if int(keep_chain):
args.append('--keep-chain')
if not debump:
args.append('--nodebump')
if not opt:
args.append('--noopt')
if assignonly:
args.append('--assign-only')
if ffout:
args.append('--ffout=' + ffout)
if ph is not None:
args.append('--with-ph=%f' % float(ph))
if neutraln:
args.append('--neutraln')
if neutralc:
args.append('--neutralc')
tmpdir = tempfile.mkdtemp()
infile = os.path.join(tmpdir, 'in.pdb')
outfile = os.path.join(tmpdir, 'out.pqr')
args.extend([infile, outfile])
try:
_self.save(infile, selection, state)
p = subprocess.Popen(args, cwd=tmpdir,
universal_newlines=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
print(p.communicate()[0].rstrip())
if p.returncode != 0:
raise CmdException('%s failed with exit status %d' % (args[0], p.returncode))
remark5 = [L for L in open(outfile) if L.startswith('REMARK 5')]
if remark5:
print(''.join(remark5))
_self.load(outfile, name)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' pdb2pqr: done')
def tmalign(mobile, target, mobile_state=1, target_state=1, args='',
exe='TMalign', ter=0, transform=1, object=None, quiet=0):
'''
DESCRIPTION
TMalign wrapper. You may also use this as a TMscore or MMalign wrapper
if you privide the corresponding executable with the "exe" argument.
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
ARGUMENTS
mobile, target = string: atom selections
mobile_state, target_state = int: object states {default: 1}
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign (or TMscore, MMalign) executable
{default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
'''
import subprocess, tempfile, os, re
from .exporting import save_pdb_without_ter
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
matrix_filename = tempfile.mktemp('.txt', 'matrix')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
if ter:
save = cmd.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele, state=mobile_state)
save(target_filename, target_ca_sele, state=target_state)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename, '-m', matrix_filename] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE,
universal_newlines=True)
lines = process.stdout.readlines()
except OSError:
print('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe))
raise CmdException
finally:
os.remove(mobile_filename)
os.remove(target_filename)
# TMalign >= 2012/04/17
if os.path.exists(matrix_filename):
lines += open(matrix_filename).readlines()
os.remove(matrix_filename)
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(lines)
headercheck = False
alignment = []
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = list(map(float, line.split()))
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif not headercheck and line.startswith(' * '):
a = line.split(None, 2)
if len(a) == 3:
headercheck = a[1]
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = [next(line_it).rstrip() for i in range(3)]
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print(line.rstrip())
if not quiet:
for i in range(0, len(alignment[0])-1, 78):
for line in alignment:
print(line[i:i+78])
print('')
assert len(matrix) == 3*4
matrix.extend([0,0,0,1])
if int(transform):
for model in cmd.get_object_list('(' + mobile + ')'):
cmd.transform_object(model, matrix, state=0, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
cmd.iterate_state(mobile_state, mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
cmd.iterate_state(target_state, target_ca_sele, 'target_idx.append("%s`%d" % (model, index))', space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
cmd.rms_cur(
' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
cycles=0, matchmaker=4, object=object)
else:
print('Could not load alignment object')
if not quiet:
if headercheck:
print('Finished Program:', headercheck)
if r is not None:
print('Found in output TM-score = %.4f' % (r))
return r
def tmalign(mobile, target, mobile_state=1, target_state=1, args='',
exe='TMalign', ter=0, transform=1, object=None, quiet=0, *, _self=cmd):
'''
DESCRIPTION
TMalign wrapper. You may also use this as a TMscore or MMalign wrapper
if you privide the corresponding executable with the "exe" argument.
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
ARGUMENTS
mobile, target = string: atom selections
mobile_state, target_state = int: object states {default: 1}
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign (or TMscore, MMalign) executable
{default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
'''
import pymol.exporting
import subprocess, tempfile, os, re
from .exporting import save_pdb_without_ter
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
matrix_filename = tempfile.mktemp('.txt', 'matrix')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
if ter:
save = pymol.exporting.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele, state=mobile_state, _self=_self)
save(target_filename, target_ca_sele, state=target_state, _self=_self)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename, '-m', matrix_filename] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE,
universal_newlines=True)
lines = process.stdout.readlines()
except OSError:
raise CmdException('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe))
finally:
os.remove(mobile_filename)
os.remove(target_filename)
# TMalign >= 2012/04/17
if os.path.exists(matrix_filename):
lines += open(matrix_filename).readlines()
os.remove(matrix_filename)
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(lines)
headercheck = False
alignment = []
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = list(map(float, line.split()))
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif not headercheck and line.startswith(' * '):
a = line.split(None, 2)
if len(a) == 3:
headercheck = a[1]
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = [next(line_it).rstrip() for i in range(3)]
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print(line.rstrip())
if not quiet:
for i in range(0, len(alignment[0])-1, 78):
for line in alignment:
print(line[i:i+78])
print('')
assert len(matrix) == 3*4
matrix.extend([0,0,0,1])
if int(transform):
for model in _self.get_object_list(mobile):
_self.transform_object(model, matrix, state=0, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
_self.iterate_state(mobile_state, mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
_self.iterate_state(target_state, target_ca_sele, 'target_idx.append("%s`%d" % (model, index))', space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
_self.rms_cur(
' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
cycles=0, matchmaker=4, object=object)
else:
print('Could not load alignment object')
if not quiet:
if headercheck:
print('Finished Program:', headercheck)
if r is not None:
print('Found in output TM-score = %.4f' % (r))
return r
def pdb2pqr(name,
selection='all',
ff='amber',
debump=1,
opt=1,
assignonly=0,
ffout='',
ph=None,
neutraln=0,
neutralc=0,
state=-1,
preserve=0,
exe='pdb2pqr',
quiet=1):
'''
DESCRIPTION
Creates a new molecule object from a selection and adds missing atoms,
assignes charges and radii using PDB2PQR.
http://www.poissonboltzmann.org/pdb2pqr/
USAGE
pdb2pqr name [, selection [, ff [, debump [, opt [, assignonly [, ffout [,
ph [, neutraln [, neutralc [, state [, preserve ]]]]]]]]]]]
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object {default: all}
ff = string: forcefield {default: amber}
'''
import os, tempfile, subprocess, shutil
debump, opt, assignonly = int(debump), int(opt), int(assignonly)
neutraln, neutralc = int(neutraln), int(neutralc)
state, preserve, quiet = int(state), int(preserve), int(quiet)
args = [cmd.exp_path(exe), '--ff=' + ff, '--chain']
if not debump:
args.append('--nodebump')
if not opt:
args.append('--noopt')
if assignonly:
args.append('--assign-only')
if ffout:
args.append('--ffout=' + ffout)
if ph is not None:
args.append('--with-ph=%f' % float(ph))
if neutraln:
args.append('--neutraln')
if neutralc:
args.append('--neutralc')
if not quiet:
args.append('--verbose')
tmpdir = tempfile.mkdtemp()
infile = os.path.join(tmpdir, 'in.pdb')
outfile = os.path.join(tmpdir, 'out.pqr')
args.extend([infile, outfile])
try:
cmd.save(infile, selection, state)
subprocess.check_call(args, cwd=tmpdir)
cmd.load(outfile, name)
except OSError:
print(' Error: Cannot execute "%s"' % (exe))
raise CmdException
except subprocess.CalledProcessError as e:
print(' Error: %s failed with exit status %d' %
(args[0], e.returncode))
raise CmdException
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' pdb2pqr: done')
def dss_promotif(selection='all', exe='', raw='', state=-1, quiet=1):
'''
DESCRIPTION
Secondary structure assignment with PROMOTIF.
http://www.rubic.rdg.ac.uk/~gail/#Software
SEE ALSO
dss, dssp, stride
'''
from subprocess import Popen, PIPE
import tempfile, os, shutil
state, quiet = int(state), int(quiet)
ss_map = {
'B': 'S',
'E': 'S',
'H': 'H',
'G': 'H',
}
exe = cmd.exp_path(exe)
if not exe:
_assert_package_import()
from . import which
motifdir = os.environ.get('motifdir')
exe = which('p_sstruc3',
'p_sstruc2',
'promotif.scr',
path=[motifdir] if motifdir else None)
tmpdir = tempfile.mkdtemp()
tmpfilepdb = os.path.join(tmpdir, 'xxxx.pdb')
tmpfilesst = os.path.join(tmpdir, 'xxxx.sst')
ss_dict = dict()
try:
for model in cmd.get_object_list('(' + selection + ')'):
cmd.save(tmpfilepdb, 'model %s and (%s)' % (model, selection),
state)
process = Popen([exe, tmpfilepdb], cwd=tmpdir, stdin=PIPE)
process.communicate(tmpfilepdb + os.linesep)
with open(tmpfilesst) as handle:
for line in handle:
if line.startswith(' num seq.no'):
break
for line in handle:
if not line.strip():
break
chain = line[6].strip('-')
resi = line[7:12].strip()
ss = line[23]
ss_dict[model, chain, resi] = ss
os.remove(tmpfilesst)
except OSError:
print(' Error: Cannot execute exe=' + exe)
raise CmdException
finally:
shutil.rmtree(tmpdir)
_common_ss_alter(selection, ss_dict, ss_map, raw)
def prepwizard(name,
selection='all',
options='',
state=-1,
preserve=0,
exe='$SCHRODINGER/utilities/prepwizard',
quiet=1,
_proclist=None):
'''
DESCRIPTION
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side
chains and converts MSE to MET. Other non-default options need to be
passed with the "options=" argument.
USAGE
prepwizard name [, selection [, options [, state ]]]
ARGUMENTS
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
'''
import os, tempfile, subprocess, shutil, shlex
state, preserve, quiet = int(state), int(preserve), int(quiet)
exe = cmd.exp_path(exe)
if not _is_exe(exe):
if 'SCHRODINGER' not in os.environ:
print(' Warning: SCHRODINGER environment variable not set')
raise CmdException('no such script: ' + exe)
args = [exe, '-mse', '-fillsidechains', '-WAIT']
if options:
if cmd.is_string(options):
options = shlex.split(options)
args.extend(options)
tmpdir = tempfile.mkdtemp()
infile = 'in.pdb'
outfile = 'out.mae'
args.extend([infile, outfile])
try:
cmd.save(os.path.join(tmpdir, infile), selection, state)
env = dict(os.environ)
env.pop('PYTHONEXECUTABLE', '') # messes up Python on Mac
p = subprocess.Popen(
args,
cwd=tmpdir,
env=env,
stdin=subprocess.PIPE, # Windows pythonw fix
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
if _proclist is not None:
_proclist.append(p)
print(p.communicate()[0].rstrip())
if p.wait() == -15: # SIGTERM
raise CmdException('prepwizard terminated')
if p.returncode != 0:
logfile = os.path.join(tmpdir, 'in.log')
if os.path.exists(logfile):
with open(logfile) as handle:
print(handle.read())
raise CmdException('%s failed with exit status %d' %
(args[0], p.returncode))
cmd.load(os.path.join(tmpdir, outfile), name)
except OSError as e:
print(e)
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' prepwizard: done')
def map_new_apbs(name, selection='all', grid=0.5, buffer=10.0, state=1,
preserve=0, exe='apbs', assign=-1, quiet=1):
'''
DESCRIPTION
Create electrostatic potential map with APBS.
For more control over parameters and a graphical user interface I
recommend to use the APBS Tools Plugin instead.
In case of missing atoms or residues I recommend to remodel the input
structure with modeller before calculating the electrostatic potential.
If selection has no charges and radii, they will be automatically assigned
with PyMOL (not with pdb2pqr).
SEE ALSO
apbs_surface, map_new (coulomb), APBS Tools Plugin
'''
import tempfile, os, shutil, glob, subprocess
from pymol.util import protein_assign_charges_and_radii
from .modelling import add_missing_atoms
selection = '(%s) and not solvent' % (selection)
grid, buffer, state = float(grid), float(buffer), int(state)
preserve, assign, quiet = int(preserve), int(assign), int(quiet)
exe = cmd.exp_path(exe)
# temporary directory
tempdir = tempfile.mkdtemp()
if not quiet:
print ' Tempdir:', tempdir
# filenames
pqrfile = os.path.join(tempdir, 'mol.pqr')
infile = os.path.join(tempdir, 'apbs.in')
stem = os.path.join(tempdir, 'map')
# temporary object
tmpname = cmd.get_unused_name('mol' if preserve else '_')
cmd.create(tmpname, selection, state, 1)
# partial charges
assign = [assign]
if assign[0] == -1:
# auto detect if selection has charges and radii
cmd.iterate('first ((%s) and elem O)' % (tmpname),
'assign[0] = (elec_radius * partial_charge) == 0.0',
space=locals())
if assign[0]:
cmd.remove('hydro and model ' + tmpname)
add_missing_atoms(tmpname, quiet=quiet)
protein_assign_charges_and_radii(tmpname)
elif not quiet:
print ' Notice: using exsiting charges and radii'
cmd.save(pqrfile, tmpname, 1, format='pqr', quiet=quiet)
# grid dimensions
extent = cmd.get_extent(tmpname)
fglen = [(emax-emin + 2*buffer) for (emin, emax) in zip(*extent)]
cglen = [(emax-emin + 4*buffer) for (emin, emax) in zip(*extent)]
if not preserve:
cmd.delete(tmpname)
apbs_in = defaults_apbs_in.copy()
apbs_in['fglen'] = '%f %f %f' % tuple(fglen)
apbs_in['cglen'] = '%f %f %f' % tuple(cglen)
apbs_in['srad'] = cmd.get('solvent_radius')
apbs_in['write'] = 'pot dx "%s"' % (stem)
# apbs input file
def write_input_file():
f = open(infile, 'w')
print >> f, '''
read
mol pqr "%s"
end
elec
mg-auto
''' % (pqrfile)
for (k,v) in apbs_in.items():
if v is None:
print >> f, k
elif isinstance(v, list):
for vi in v:
print >> f, k, vi
else:
print >> f, k, v
print >> f, '''
end
quit
'''
f.close()
try:
# apbs will fail if grid does not fit into memory
# -> on failure repeat with larger grid spacing
for _ in range(3):
dime = [1 + max(64, n / grid) for n in fglen]
apbs_in['dime'] = '%d %d %d' % tuple(dime)
write_input_file()
# run apbs
r = subprocess.call([exe, infile], cwd=tempdir)
if r == 0:
break
if r == -6:
grid *= 2.0
if not quiet:
print ' Warning: retry with grid =', grid
continue
print ' Error: apbs failed with code', r
raise CmdException
dx_list = glob.glob(stem + '*.dx')
if len(dx_list) != 1:
print ' Error: dx file missing'
raise CmdException
# load map
cmd.load(dx_list[0], name, quiet=quiet)
except OSError:
print ' Error: Cannot execute "%s"' % (exe)
raise CmdException
finally:
if not preserve:
shutil.rmtree(tempdir)
elif not quiet:
print ' Notice: not deleting %s' % (tempdir)
def save_pdb(filename, selection="(all)", state=-1, symm=1, ss=1, aniso=0, quiet=1):
"""
DESCRIPTION
Save the coordinates of a selection as pdb including the
secondary structure information and, if possible, the unit
cell. The latter requires the selction of a single object
USAGE
save_pdb filename, selection [, state [, symm [, ss [, aniso ]]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
Note: to include the unit cell information you
need to select a single object
state = integer: state to save {default: -1 (current state)}
symm = 0 or 1: save symmetry info if possible {default: 1}
ss = 0 or 1: save secondary structure info {default: 1}
aniso = 0 or 1: save ANISO records {default: 0}
SEE ALSO
save
"""
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
symm, ss = int(symm), int(ss)
filename = cmd.exp_path(filename)
f = open(filename, "w")
print >> f, "REMARK 200 Generated with PyMOL and psico".ljust(80)
# Write the CRYST1 line if possible
if symm:
try:
obj1 = cmd.get_object_list(selection)[0]
sym = cmd.get_symmetry(obj1)
if len(sym) != 7:
raise
f.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-10s%4d\n" % tuple(sym + [1]))
if not quiet:
print " Info: Wrote unit cell and space group info"
except:
if not quiet:
print " Info: No crystal information"
# Write secondary structure
if ss:
try:
sss = get_pdb_sss(selection, state, quiet)
if not sss:
raise
f.write(sss)
if not quiet:
print " Info: Wrote secondary structure info"
except:
if not quiet:
print " Info: No secondary structure information"
# Write coordinates of selection
pdbstr = cmd.get_pdbstr(selection, state)
# fix END records
if state == 0 and cmd.get_version()[1] < 1.6:
pdbstr = "\n".join(line for line in pdbstr.splitlines() if line != "END") + "\nEND\n"
# anisotropic b-factors
if int(aniso) and cmd.get_model("first (%s)" % selection).atom[0].u_aniso[0] != 0.0:
def mergeaniso():
atom_it = iter(cmd.get_model(selection, state).atom)
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ["ATOM ", "HETATM"]:
yield "ANISOU" + line[6:28] + "".join("%7.0f" % (u * 1e4) for u in atom_it.next().u_aniso) + line[
70:
]
pdbstr = "".join(mergeaniso())
f.write(pdbstr)
f.close()
if not quiet:
print "Wrote PDB to '" + filename + "'"
def pdb2pqr(name, selection='all', ff='amber', debump=1, opt=1, assignonly=0,
ffout='', ph=None, neutraln=0, neutralc=0, state=-1, preserve=0,
exe='pdb2pqr', quiet=1):
'''
DESCRIPTION
Creates a new molecule object from a selection and adds missing atoms,
assignes charges and radii using PDB2PQR.
http://www.poissonboltzmann.org/pdb2pqr/
USAGE
pdb2pqr name [, selection [, ff [, debump [, opt [, assignonly [, ffout [,
ph [, neutraln [, neutralc [, state [, preserve ]]]]]]]]]]]
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object {default: all}
ff = string: forcefield {default: amber}
'''
import os, tempfile, subprocess, shutil
debump, opt, assignonly = int(debump), int(opt), int(assignonly)
neutraln, neutralc = int(neutraln), int(neutralc)
state, preserve, quiet = int(state), int(preserve), int(quiet)
args = [cmd.exp_path(exe), '--ff=' + ff, '--chain']
if not debump:
args.append('--nodebump')
if not opt:
args.append('--noopt')
if assignonly:
args.append('--assign-only')
if ffout:
args.append('--ffout=' + ffout)
if ph is not None:
args.append('--with-ph=%f' % float(ph))
if neutraln:
args.append('--neutraln')
if neutralc:
args.append('--neutralc')
if not quiet:
args.append('--verbose')
tmpdir = tempfile.mkdtemp()
infile = os.path.join(tmpdir, 'in.pdb')
outfile = os.path.join(tmpdir, 'out.pqr')
args.extend([infile, outfile])
try:
cmd.save(infile, selection, state)
subprocess.check_call(args, cwd=tmpdir)
cmd.load(outfile, name)
except OSError:
print(' Error: Cannot execute "%s"' % (exe))
raise CmdException
except subprocess.CalledProcessError as e:
print(' Error: %s failed with exit status %d' % (args[0], e.returncode))
raise CmdException
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' pdb2pqr: done')
def diagnostics(filename='', compact=0, quiet=1):
'''
DESCRIPTION
Get system level diagnostics data
USAGE
diagnostics [ filename ]
ARGUMENTS
filename = str: If given, write output to text file
'''
import time
from pymol import invocation
from pymol import cmd, CmdException
compact, quiet = int(compact), int(quiet)
TZ = '%+05d' % (time.timezone / 36)
version = cmd.get_version()
body = u'PyMOL %s\n' % version[0]
if not compact:
if version[3]:
body += 'build date: %s %s\n' % (time.ctime(version[3]), TZ)
if version[4]:
body += 'git sha: %s\n' % version[4]
body += diagnostics_conda(version[0])
if not compact:
body += '\nLicense Information:\n'
body += 'Open-Source Build\n'
body += diagnostics_platform()
if not compact:
body += '\nOpenGL Driver:\n'
renderer = cmd.get_renderer()
body += str(renderer[0] or '(none)') + '\n'
body += str(renderer[1] or '(none)') + '\n'
body += str(renderer[2] or '(none)') + '\n'
body += diagnostics_qt()
if not compact:
body += diagnostics_python()
body += '\nStartup Scripts:\n'
pymolrc = invocation.get_user_config()
if pymolrc:
pymolrc = map(_unicode, pymolrc)
body += '\n'.join(pymolrc) + '\n'
else:
body += '(no pymolrc file found)\n'
body += diagnostics_env_vars()
body += '\nDiagnostics collected on %s %s\n' % (time.ctime(), TZ)
if filename:
filename = cmd.exp_path(filename)
if not filename.endswith('.txt'):
raise CmdException('filename must have .txt extension')
with open(filename, 'w') as handle:
handle.write(body)
print('Diagnostics written to "%s"' % filename)
elif not quiet:
print(body.rstrip())
return body
def dyndom(mobile, target, window=5, domain=20, ratio=1.0, exe='', transform=1,
quiet=1, mobile_state=1, target_state=1, match='align', preserve=0,
*, _self=cmd):
'''
DESCRIPTION
DynDom wrapper
DynDom is a program to determine domains, hinge axes and hinge bending
residues in proteins where two conformations are available.
http://fizz.cmp.uea.ac.uk/dyndom/
USAGE
dyndom mobile, target [, window [, domain [, ratio ]]]
'''
import tempfile, subprocess, os, shutil, sys
from .exporting import save_pdb_without_ter
window, domain, ratio = int(window), int(domain), float(ratio)
transform, quiet = int(transform), int(quiet)
mobile_state, target_state = int(mobile_state), int(target_state)
mm = MatchMaker(
'(%s) & polymer & state %d' % (mobile, mobile_state),
'(%s) & polymer & state %d' % (target, target_state), match, _self=_self)
chains = _self.get_chains(mm.mobile)
if len(chains) != 1:
raise CmdException('mobile selection must be single chain')
chain1id = chains[0]
chains = _self.get_chains(mm.target)
if len(chains) != 1:
raise CmdException('target selection must be single chain')
chain2id = chains[0]
if not exe:
from . import which
exe = which('DynDom', 'dyndom')
if not exe:
raise CmdException('Cannot find DynDom executable')
else:
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
filename1 = os.path.join(tempdir, 'mobile.pdb')
filename2 = os.path.join(tempdir, 'target.pdb')
commandfile = os.path.join(tempdir, 'command.txt')
infofile = os.path.join(tempdir, 'out_info')
save_pdb_without_ter(filename1, mm.mobile, state=mobile_state, _self=_self)
save_pdb_without_ter(filename2, mm.target, state=target_state, _self=_self)
f = open(commandfile, 'w')
f.write('title=out\nfilename1=%s\nchain1id=%s\nfilename2=%s\nchain2id=%s\n' \
'window=%d\ndomain=%d\nratio=%.4f\n' % (filename1, chain1id,
filename2, chain2id, window, domain, ratio))
f.close()
process = subprocess.Popen([exe, commandfile], cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
if process.poll() != 0:
raise CmdException('"%s" failed with status %d' % (exe, process.returncode))
_self.color('gray', mobile)
fixed_name = dyndom_parse_info(infofile, mm.mobile, quiet)
except OSError:
raise CmdException('Cannot execute "%s", please provide full path to DynDom executable' % (exe))
finally:
if not int(preserve):
shutil.rmtree(tempdir)
elif not quiet:
print(' Not deleting temporary directory:', tempdir)
if transform and fixed_name is not None:
_self.align(fixed_name, target)
def fiber(seq, num=4, name="", rna=0, single=0, repeats=0, preserve=0, exe="$X3DNA/bin/fiber", quiet=1):
"""
DESCRIPTION
Run X3DNA's "fiber" tool.
For the list of structure identification numbers, see for example:
http://xiang-jun.blogspot.com/2009/10/fiber-models-in-3dna.html
USAGE
fiber seq [, num [, name [, rna [, single ]]]]
ARGUMENTS
seq = str: single letter code sequence or number of repeats for
repeat models.
num = int: structure identification number {default: 4}
name = str: name of object to create {default: random unused name}
rna = 0/1: 0=DNA, 1=RNA {default: 0}
single = 0/1: 0=double stranded, 1=single stranded {default: 0}
EXAMPLES
# environment (this could go into ~/.pymolrc or ~/.bashrc)
os.environ["X3DNA"] = "/opt/x3dna-v2.3"
# B or A DNA from sequence
fiber CTAGCG
fiber CTAGCG, 1, ADNA
# double or single stranded RNA from sequence
fiber AAAGGU, name=dsRNA, rna=1
fiber AAAGGU, name=ssRNA, rna=1, single=1
# poly-GC Z-DNA repeat model with 10 repeats
fiber 10, 15
"""
import os, tempfile, subprocess, shutil
rna, single = int(rna), int(single)
preserve, quiet = int(preserve), int(quiet)
if "X3DNA" not in os.environ:
raise CmdException("please set X3DNA environment variable")
args = [cmd.exp_path(exe), "-seq=" + seq, "-" + str(num)]
if rna:
args.append("-rna")
if single:
args.append("-single")
if not name:
name = cmd.get_unused_name("fiber-" + str(num) + "_")
tmpdir = tempfile.mkdtemp()
outfile = os.path.join(tmpdir, "out.pdb")
args.append(outfile)
if seq.endswith("help"):
# call fiber with no arguments to get help page
args[1:] = []
try:
p = subprocess.Popen(args, cwd=tmpdir, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
stdout, _ = p.communicate(str(int(repeats) or seq))
if not quiet:
print(stdout)
if len(args) != 1:
if p.returncode != 0:
raise CmdException("Returned non-zero status: " + str(args))
cmd.load(outfile, name, quiet=quiet)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(" Notice: not deleting", tmpdir)
def dss_promotif(selection='all', exe='', raw='', state=-1, quiet=1):
'''
DESCRIPTION
Secondary structure assignment with PROMOTIF.
http://www.rubic.rdg.ac.uk/~gail/#Software
SEE ALSO
dss, dssp, stride
'''
from subprocess import Popen, PIPE
import tempfile, os, shutil
state, quiet = int(state), int(quiet)
ss_map = {
'B': 'S',
'E': 'S',
'H': 'H',
'G': 'H',
}
exe = cmd.exp_path(exe)
if not exe:
from . import which
motifdir = os.environ.get('motifdir')
exe = which('p_sstruc3', 'p_sstruc2', 'promotif.scr',
path=[motifdir] if motifdir else None)
tmpdir = tempfile.mkdtemp()
tmpfilepdb = os.path.join(tmpdir, 'xxxx.pdb')
tmpfilesst = os.path.join(tmpdir, 'xxxx.sst')
ss_dict = dict()
try:
for model in cmd.get_object_list('(' + selection + ')'):
cmd.save(tmpfilepdb, 'model %s and (%s)' % (model, selection), state)
process = Popen([exe, tmpfilepdb], cwd=tmpdir, stdin=PIPE)
process.communicate(tmpfilepdb + os.linesep)
with open(tmpfilesst) as handle:
for line in handle:
if line.startswith(' num seq.no'):
break
for line in handle:
if not line.strip():
break
chain = line[6].strip('-')
resi = line[7:12].strip()
ss = line[23]
ss_dict[model,chain,resi] = ss
os.remove(tmpfilesst)
except OSError:
print(' Error: Cannot execute exe=' + exe)
raise CmdException
finally:
shutil.rmtree(tmpdir)
_common_ss_alter(selection, ss_dict, ss_map, raw)
def prepwizard(
name, selection="all", options="", state=-1, preserve=0, exe="$SCHRODINGER/utilities/prepwizard", quiet=1
):
"""
DESCRIPTION
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side
chains and converts MSE to MET. Other non-default options need to be
passed with the "options=" argument.
USAGE
prepwizard name [, selection [, options [, state ]]]
ARGUMENTS
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
"""
import os, tempfile, subprocess, shutil, shlex
state, preserve, quiet = int(state), int(preserve), int(quiet)
exe = cmd.exp_path(exe)
if not os.path.exists(exe):
if "SCHRODINGER" not in os.environ:
print(" Warning: SCHRODINGER environment variable not set")
raise CmdException("no such script: " + exe)
args = [exe, "-mse", "-fillsidechains", "-WAIT"]
if options:
if cmd.is_string(options):
options = shlex.split(options)
args.extend(options)
tmpdir = tempfile.mkdtemp()
infile = "in.pdb"
outfile = "out.mae"
args.extend([infile, outfile])
try:
cmd.save(os.path.join(tmpdir, infile), selection, state)
p = subprocess.Popen(args, cwd=tmpdir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
print(p.communicate()[0].rstrip())
if p.returncode != 0:
logfile = os.path.join(tmpdir, "in.log")
if os.path.exists(logfile):
with open(logfile) as handle:
print(handle.read())
raise CmdException("%s failed with exit status %d" % (args[0], p.returncode))
cmd.load(os.path.join(tmpdir, outfile), name)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(" Notice: not deleting", tmpdir)
if not quiet:
print(" prepwizard: done")
def dyndom(mobile, target, window=5, domain=20, ratio=1.0, exe='', transform=1,
quiet=1, mobile_state=1, target_state=1, match='align', preserve=0):
'''
DESCRIPTION
DynDom wrapper
DynDom is a program to determine domains, hinge axes and hinge bending
residues in proteins where two conformations are available.
http://fizz.cmp.uea.ac.uk/dyndom/
USAGE
dyndom mobile, target [, window [, domain [, ratio ]]]
'''
import tempfile, subprocess, os, shutil, sys
from .exporting import save_pdb_without_ter
window, domain, ratio = int(window), int(domain), float(ratio)
transform, quiet = int(transform), int(quiet)
mobile_state, target_state = int(mobile_state), int(target_state)
mm = MatchMaker(
'(%s) & polymer & state %d' % (mobile, mobile_state),
'(%s) & polymer & state %d' % (target, target_state), match)
chains = cmd.get_chains(mm.mobile)
if len(chains) != 1:
print('mobile selection must be single chain')
raise CmdException
chain1id = chains[0]
chains = cmd.get_chains(mm.target)
if len(chains) != 1:
print('target selection must be single chain')
raise CmdException
chain2id = chains[0]
if not exe:
from . import which
exe = which('DynDom', 'dyndom')
if not exe:
print(' Error: Cannot find DynDom executable')
raise CmdException
else:
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
filename1 = os.path.join(tempdir, 'mobile.pdb')
filename2 = os.path.join(tempdir, 'target.pdb')
commandfile = os.path.join(tempdir, 'command.txt')
infofile = os.path.join(tempdir, 'out_info')
save_pdb_without_ter(filename1, mm.mobile, state=mobile_state)
save_pdb_without_ter(filename2, mm.target, state=target_state)
f = open(commandfile, 'w')
f.write('title=out\nfilename1=%s\nchain1id=%s\nfilename2=%s\nchain2id=%s\n' \
'window=%d\ndomain=%d\nratio=%.4f\n' % (filename1, chain1id,
filename2, chain2id, window, domain, ratio))
f.close()
process = subprocess.Popen([exe, commandfile], cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
if process.poll() != 0:
raise CmdException('"%s" failed with status %d' % (exe, process.returncode))
cmd.color('gray', mobile)
fixed_name = dyndom_parse_info(infofile, mm.mobile, quiet)
except OSError:
print('Cannot execute "%s", please provide full path to DynDom executable' % (exe))
raise CmdException
finally:
if not int(preserve):
shutil.rmtree(tempdir)
elif not quiet:
print(' Not deleting temporary directory:', tempdir)
if transform and fixed_name is not None:
cmd.align(fixed_name, target)
def compare_10gs_11gs():
# it is possible to download proteins from RCSB (Protein Data Bank) to fetch_path, which is current working
# directory by default
cmd.set('fetch_path', cmd.exp_path(PATH_data))
cmd.fetch('10gs')
cmd.fetch('11gs')
cmd.load('{0}10gs.cif'.format(PATH_data), '10gs')
cmd.load('{0}11gs.cif'.format(PATH_data), '11gs')
# proteins
# pymol has several options for proteins alignment, align is better for proteins with high homology
align_command = cmd.align # or super, or cealign
align_res = align_command('10gs', '11gs')
if align_command == cmd.align:
print('aligned with rmsd {0}'.format(align_res[0]))
# cmd.create creates a separate object (copies everything to it)
# het stands for heteroatoms (non-protein)
cmd.create('10gs_protein', '10gs and not het')
cmd.create('11gs_protein', '11gs and not het')
# print protein sequences for fun
fasta_10gs = cmd.get_fastastr(selection='10gs_protein')
fasta_11gs = cmd.get_fastastr(selection='11gs_protein')
print('10gs sequence:{0}'.format(fasta_10gs))
print('11gs sequence:{0}'.format(fasta_11gs))
cmd.delete('*_protein') # delete objects
# ligands
cmd.select('10gs_ligands', '10gs and not resname HOH and het')
cmd.select('11gs_ligands', '11gs and not resname HOH and het')
space_10gs = {'lig_names': []} # or simpy lig_names = []
space_11gs = {'lig_names': []}
# strange pymol interface to iterate over atoms
cmd.iterate('10gs_ligands', 'lig_names.append(resn)', space=space_10gs)
cmd.iterate('11gs_ligands', 'lig_names.append(resn)', space=space_11gs)
ligs_10gs = set(space_10gs['lig_names'])
ligs_11gs = set(space_11gs['lig_names'])
# by the way, in both 10gs and 11gs we have MSE, which is actually a modified residue and not a ligand
print('ligands found in 10gs: {0}'.format(ligs_10gs))
print('ligands found in 11gs: {0}'.format(ligs_11gs))
for ligand_unique in ligs_10gs.symmetric_difference(ligs_11gs):
cmd.save(
'{0}{1}_{2}_ligand.sdf'.format(
PATH_data, '10gs' if ligand_unique in ligs_10gs else '11gs',
ligand_unique), 'resname {0}'.format(ligand_unique))
# deleting selection, objects remain unchanged
cmd.delete('ligs*')
print('drawing a figure (this will take some time)')
cmd.set('transparency_mode', 1)
cmd.bg_color('white')
cmd.show('sticks', 'het and not resname HOH')
cmd.color('white', 'not het')
cmd.show('surface', 'not het')
cmd.hide('lines')
cmd.set('transparency', '0.7')
cmd.show('spheres', 'resname HOH')
cmd.color('palecyan', 'resname HOH')
cmd.hide('nonbonded', 'resname HOH')
cmd.set('sphere_transparency', '0.7')
cmd.ray()
cmd.png('{0}fig.png'.format(PATH_data))
def poseview(ligand='organic inorganic', protein='polymer', width=0, height=0,
filename='', exe='poseview', state=-1, quiet=1):
'''
DESCRIPTION
PoseView wrapper
http://www.biosolveit.de/poseview/
USAGE
poseview [ ligand [, protein [, width [, height [, exe [, state ]]]]]]
ARGUMENTS
ligand = string: atom selection {default: organic inorganic}
protein = string: atom selection {default: polymer}
width = int: image width {default: viewport width}
height = int: image height {default: viewport height}
filename = string: output PNG file name {default: temporary}
exe = string: path to executable {default: poseview}
SETUP
1) Put poseview executable to PATH (e.g. /usr/bin/poseview)
2) Set environment variable BIOSOLVE_LICENSE_FILE="/path/to/poseview.lic"
'''
import tempfile, subprocess, os, shutil
width, height = int(width), int(height)
state, quiet = int(state), int(quiet)
if width == 0 or height == 0:
viewport = cmd.get_viewport()
if width != 0:
height = int(viewport[0] / float(width) * viewport[1])
elif height != 0:
width = int(viewport[1] / float(height) * viewport[0])
else:
width, height = viewport
exe = cmd.exp_path(exe)
tempdir = tempfile.mkdtemp()
try:
ligand_filename = os.path.join(tempdir, 'ligand.sdf')
protein_filename = os.path.join(tempdir, 'protein.pdb')
if not filename:
filename = os.path.join(tempdir, 'image.png')
cmd.save(ligand_filename, ligand, state)
cmd.save(protein_filename, protein, state)
args = [exe, '-l', ligand_filename, '-p', protein_filename, '-t', '',
'-o', filename, '-s', str(width), str(height)]
if not quiet:
print ' poseview: running...'
process = subprocess.Popen(args,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
stdout, _ = process.communicate()
if not quiet:
print stdout
print ' poseview: done'
if filename.endswith('.png'):
cmd.load(filename)
elif not quiet:
print ' Warning: cannot load "%s" into PyMOL, unsupported file type' % (filename)
except OSError:
print ' Error: Cannot execute "%s", please provide full path to poseview executable' % (exe)
raise CmdException
finally:
shutil.rmtree(tempdir)
