def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd):
pymol=_self._pymol
cmd=_self
if ((string.split(selection)!=[selection]) or
selection not in cmd.get_names('objects')):
print " Error: must provide an object name"
raise cmd.QuietException
obj_name = selection + "_e_chg"
map_name = selection + "_e_map"
pot_name = selection + "_e_pot"
cmd.disable(selection)
cmd.delete(obj_name)
cmd.delete(map_name)
cmd.delete(pot_name)
cmd.create(obj_name,"((polymer and ("+selection+
") and (not resn A+C+T+G+U)) or ((bymol (polymer and ("+
selection+"))) and resn NME+NHE+ACE)) and (not hydro)")
# try to just get protein...
protein_assign_charges_and_radii(obj_name,_self=_self)
ext = cmd.get_extent(obj_name)
max_length = max(abs(ext[0][0] - ext[1][0]),abs(ext[0][1] - ext[1][1]),abs(ext[0][2]-ext[1][2])) + 2*border
# compute an grid with a maximum dimension of 50, with 10 A borders around molecule, and a 1.0 A minimum grid
sep = max_length/50.0
if sep<1.0: sep = 1.0
print " Util: Calculating electrostatic potential..."
if mode==0: # absolute, no cutoff
cmd.map_new(map_name,"coulomb",sep,obj_name,border)
elif mode==1: # neutral, no cutoff
cmd.map_new(map_name,"coulomb_neutral",sep,obj_name,border)
else: # local, with cutoff
cmd.map_new(map_name,"coulomb_local",sep,obj_name,border)
cmd.ramp_new(pot_name, map_name, selection=obj_name,zero=1)
cmd.hide("everything",obj_name)
cmd.show("surface",selection)
cmd.set("surface_color",pot_name,selection)
cmd.set("surface_ramp_above_mode",1,selection)
def map_new_apbs(name, selection='all', grid=0.5, buffer=10.0, state=1,
preserve=0, exe='', assign=-1, focus='', quiet=1, _template=''):
'''
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)
# path to apbs executable
exe = validate_apbs_exe(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(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)
extentfocus = cmd.get_extent(focus) if focus else extent
fglen = [(emax-emin + 2*buffer) for (emin, emax) in zip(*extentfocus)]
cglen = [(emax-emin + 4*buffer) for (emin, emax) in zip(*extent)]
if not preserve:
cmd.delete(tmpname)
apbs_in = {
'pqrfile': pqrfile,
'fgcent': 'mol 1',
'fglen': '%f %f %f' % tuple(fglen),
'cglen': '%f %f %f' % tuple(cglen),
'srad': cmd.get('solvent_radius'),
'mapfile': stem,
}
if focus:
apbs_in['fgcent'] = '%f %f %f' % tuple((emax + emin) / 2.0
for (emin, emax) in zip(*extentfocus))
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)
# apbs input file
with open(infile, 'w') as f:
f.write((_template or template_apbs_in).format(**apbs_in))
# run apbs
r = subprocess.call([exe, infile], cwd=tempdir)
if r == 0:
break
if r in (-6, -9):
grid *= 2.0
if not quiet:
print(' Warning: retry with grid =', grid)
continue
raise CmdException('apbs failed with code ' + str(r))
dx_list = glob.glob(stem + '*.dx')
if len(dx_list) != 1:
raise CmdException('dx file missing')
# load map
cmd.load(dx_list[0], name, quiet=quiet)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tempdir)
elif not quiet:
print(' Notice: not deleting %s' % (tempdir))
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 map_new_apbs(name,
selection='all',
grid=0.5,
buffer=10.0,
state=1,
preserve=0,
exe='',
assign=-1,
focus='',
quiet=1,
_template=''):
'''
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)
# path to apbs executable
exe = validate_apbs_exe(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(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)
extentfocus = cmd.get_extent(focus) if focus else extent
fglen = [(emax - emin + 2 * buffer) for (emin, emax) in zip(*extentfocus)]
cglen = [(emax - emin + 4 * buffer) for (emin, emax) in zip(*extent)]
if not preserve:
cmd.delete(tmpname)
apbs_in = {
'pqrfile': pqrfile,
'fgcent': 'mol 1',
'fglen': '%f %f %f' % tuple(fglen),
'cglen': '%f %f %f' % tuple(cglen),
'srad': cmd.get('solvent_radius'),
'mapfile': stem,
}
if focus:
apbs_in['fgcent'] = '%f %f %f' % tuple(
(emax + emin) / 2.0 for (emin, emax) in zip(*extentfocus))
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)
# apbs input file
with open(infile, 'w') as f:
f.write((_template or template_apbs_in).format(**apbs_in))
# run apbs
r = subprocess.call([exe, infile], cwd=tempdir)
if r == 0:
break
if r in (-6, -9):
grid *= 2.0
if not quiet:
print(' Warning: retry with grid =', grid)
continue
raise CmdException('apbs failed with code ' + str(r))
dx_list = glob.glob(stem + '*.dx')
if len(dx_list) != 1:
raise CmdException('dx file missing')
# load map
cmd.load(dx_list[0], name, quiet=quiet)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tempdir)
elif not quiet:
print(' Notice: not deleting %s' % (tempdir))
def map_new_apbs(name, selection='all', grid=0.5, buffer=10.0, state=1,
preserve=0, exe='', assign=-1, focus='', 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)
if exe:
exe = cmd.exp_path(exe)
else:
try:
import freemol.apbs
exe = freemol.apbs.get_exe_path()
except:
pass
if not 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)
# 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)
extentfocus = cmd.get_extent(focus) if focus else extent
fglen = [(emax-emin + 2*buffer) for (emin, emax) in zip(*extentfocus)]
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)
if focus:
apbs_in['fgcent'] = '%f %f %f' % tuple((emax + emin) / 2.0
for (emin, emax) in zip(*extentfocus))
# apbs input file
def write_input_file():
f = open(infile, 'w')
print('''
read
mol pqr "%s"
end
elec
mg-auto
''' % (pqrfile), file=f)
for (k,v) in apbs_in.items():
if v is None:
print(k, file=f)
elif isinstance(v, list):
for vi in v:
print(k, vi, file=f)
else:
print(k, v, file=f)
print('''
end
quit
''', file=f)
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 in (-6, -9):
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))