class DockingParameter42FileMaker:
"""Accept a <ligand>.pdbqt and <receptor>.pdbqt and create
<ligand>_<receptor>42.dpf
"""
def __init__(self, verbose=None):
self.verbose = verbose
self.dpo = DockingParameters()
def getTypes(self, molecule):
if not len(molecule.allAtoms.bonds[0]):
molecule.buildBondsByDistance()
ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
ad4_typer.setAutoDockElements(molecule)
dict = {}
for a in molecule.allAtoms:
dict[a.autodock_element] = 1
d_types = dict.keys()
d_types.sort()
mol_types = d_types[0]
for t in d_types[1:]:
mol_types = mol_types + " " + t
if self.verbose:
print "end of getTypes: types=", mol_types, ' class=', mol_types.__class__
return mol_types
def set_write_all(self, value):
verbose = self.verbose
self.dpo['write_all_flag']['value'] = True
if verbose:
print "set write_all_flag to", self.dpo['write_all_flag']['value']
def set_ligand(self, ligand_filename):
verbose = self.verbose
self.ligand_filename = os.path.basename(ligand_filename)
if verbose: print "set ligand_filename to", self.ligand_filename
self.dpo.set_ligand(ligand_filename)
#expect a filename like ind.out.pdbq: get 'ind' from it
self.ligand_stem = string.split(self.ligand_filename, '.')[0]
if verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
if self.ligand == None:
print 'ERROR reading: ', ligand_filename
return
if verbose: print "read ", self.ligand.name
#set dpo:
#move
self.dpo['move']['value'] = self.ligand_filename
if verbose: print "set move to ", self.dpo['move']['value']
#ndihe
#assumes ligand has torTree
self.dpo['ndihe']['value'] = self.ligand.parser.keys.count("BRANCH")
#self.dpo['ndihe']['value'] = len(self.ligand.torTree.torsionMap)
if verbose: print "set ndihe to ", self.dpo['ndihe']['value']
#torsdof
#caution dpo['torsdof4']['value'] is a list [ndihe, 0.274]
try:
self.dpo['torsdof4']['value'][0] = self.ligand.TORSDOF
except:
print 'setting torsdof to ligand.ndihe=', self.ligand.ndihe
self.dpo['torsdof4']['value'][0] = self.ligand.ndihe
if verbose: print "set torsdof4 to ", self.dpo['torsdof4']['value']
#types
self.ligand.types = self.getTypes(self.ligand)
self.dpo['ligand_types']['value'] = self.ligand.types
if verbose: print "set types to ", self.dpo['ligand_types']['value']
#about
self.ligand.getCenter()
cen = self.ligand.center
self.dpo['about']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
if verbose: print "set about to ", self.dpo['about']['value']
def set_receptor(self, receptor_filename):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.dpo.set_receptor(receptor_filename)
def set_flexres(self, flexres_filename):
flexmol = Read(flexres_filename)[0]
flexres_filename = os.path.basename(flexres_filename)
self.dpo['flexres_flag']['value'] = True
self.dpo['flexres']['value'] = flexres_filename
#make sure each atom type in flexres molecule is in ligand_types
d = {}
current_types = self.dpo['ligand_types']['value'].split()
for t in current_types:
d[t] = 1
for a in flexmol.allAtoms:
d[a.autodock_element] = 1
self.dpo['ligand_types']['value'] = string.join(d.keys())
def set_docking_parameters(self, **kw):
"""Any docking parameters should be set here
"""
# like this:
# newdict = {'ga_num_evals':1750000, 'ga_pop_size':150,
# 'ga_run':20, 'rmstol':2.0}
# self.mv.dpo['<parameter>']['value'] = <new value>
for parm, newvalue in kw.items():
self.dpo[parm]['value'] = newvalue
if parm == 'set_sw1':
self.dpo['set_psw1']['value'] = not newvalue
if parm == 'set_psw1':
self.dpo['set_sw1']['value'] = not newvalue
if parm == 'flexres':
self.set_flexres(newvalue)
if parm == 'write_all':
self.set_write_all(newvalue)
def write_dpf(self,
dpf_filename,
parm_list=genetic_algorithm_local_search_list4_2,
pop_seed=False):
if not dpf_filename:
dpf_filename = "%s%s%s%s" % \
(self.ligand_stem, "_",
self.receptor_stem, ".dpf")
# now that we have a filename...
# set initial conformation
if pop_seed:
self.dpo['tran0']['value'] = self.dpo['about']['value']
self.dpo['axisangle0']['value'] = '0 0 0 0'
#self.dpo['quat0']['value'] = '1.0 0. 0. 0.'
dihe0 = '0. ' * self.dpo['ndihe']['value']
dihe0.rstrip()
self.dpo['dihe0']['value'] = dihe0
if self.verbose:
print "writing ", dpf_filename
self.dpo.write42(dpf_filename, parm_list)
def __init__(self, verbose=None):
self.verbose = verbose
self.dpo = DockingParameters()
class DockingParameterFileMaker:
"""Accept a <ligand>.pdbq and <receptor>.pdbqs and create
<ligand>_<receptor>.dpf
"""
def __init__(self, verbose = None):
self.verbose = verbose
self.dpo = DockingParameters()
def set_ligand(self, ligand_filename):
self.ligand_filename = os.path.basename(ligand_filename)
if verbose:
print "set ligand_filename to", self.ligand_filename
self.dpo.set_ligand(ligand_filename)
#expect a filename like ind.out.pdbq: get 'ind' from it
self.ligand_stem = string.split(self.ligand_filename,'.')[0]
if verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
if self.ligand==None:
print 'ERROR reading: ', ligand_filename
return
if verbose:
print "read ", self.ligand.name
#set dpo:
#move
self.dpo['move']['value'] = self.ligand_filename
if verbose: print "set move to ", self.dpo['move']['value']
#ndihe
#assumes ligand has torTree
self.dpo['ndihe']['value'] = self.ligand.parser.keys.count("BRANCH")
#self.dpo['ndihe']['value'] = len(self.ligand.torTree.torsionMap)
if verbose: print "set ndihe to ", self.dpo['ndihe']['value']
#torsdof
#caution dpo['torsdof']['value'] is a list [ndihe, 0.3113]
self.dpo['torsdof']['value'][0] = self.ligand.TORSDOF
if verbose: print "set torsdof to ", self.dpo['torsdof']['value']
#types
d = {}
for a in self.ligand.allAtoms:
d[a.autodock_element] = 1
sortKeyList = ['C','A','N','O','S','H','P','n','f','F','c','b','I','M']
lig_types = ""
for t in sortKeyList:
if t in d.keys():
lig_types = lig_types + t
self.ligand.types = lig_types
self.dpo['types']['value'] = self.ligand.types
if verbose: print "set types to ", self.dpo['types']['value']
#about
self.ligand.getCenter()
cen = self.ligand.center
self.dpo['about']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
if verbose: print "set about to ", self.dpo['about']['value']
def set_receptor(self, receptor_filename):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.dpo.set_receptor(receptor_filename)
#def set_docking_parameters(self, newdict={}):
def set_docking_parameters(self, **kw):
"""Any docking paramters should be set here
"""
# like this:
# newdict = {'ga_num_evals':1750000, 'ga_pop_size':150,
# 'ga_run':20, 'rmstol':2.0}
# self.dpo['<parameter>']['value'] = <new value>
# eg self.dpo['rmstol']['value'] = 2.0
for parm, newvalue in kw.items():
#print "parm=", parm, ' newvalue=', newvalue
self.dpo[parm]['value'] = newvalue
if parm=='set_sw1':
self.dpo['set_psw1']['value'] = not newvalue
if parm=='set_psw1':
self.dpo['set_sw1']['value'] = not newvalue
def write_dpf(self, dpf_filename,
parm_list = genetic_algorithm_local_search_list):
if not dpf_filename:
dpf_filename = "%s%s%s%s" % \
(self.ligand_stem, "_",
self.receptor_stem, ".dpf")
# now that we have a filename...
if self.verbose:
print "writing ", dpf_filename
self.dpo.write(dpf_filename, parm_list)
def __init__(self, verbose = None):
self.verbose = verbose
self.dpo = DockingParameters()
def _buildDpo(self, lines):
dpo = DockingParameters()
dpo._parse(lines)
return dpo
print("dpf3_to_dpf4: using default receptor_filename:",
receptor_filename)
if not dpf3_filename:
print(
'dpf3_to_dpf4: no dpf3_filename specified using GridParameter defaults'
)
parms = {}
parms['simulated_annealing_list4'] = simulated_annealing_list4
parms['genetic_algorithm_list4'] = genetic_algorithm_list4
parms[
'genetic_algorithm_local_search_list4'] = genetic_algorithm_local_search_list4
parms['local_search_list4'] = local_search_list4
#what about nucleic acids???
DPO4 = DockingParameters()
print("default: ligand_types=", DPO4['ligand_types']['value'])
orig_compute_unbound_extended_flag = DPO4['compute_unbound_extended_flag'][
'value']
if dpf3_filename:
DPO4.read(dpf3_filename)
if verbose: print('read ', dpf3_filename)
DPO4['compute_unbound_extended_flag'][
'value'] = orig_compute_unbound_extended_flag
else:
if verbose: print('using dpo defaults')
DPO4.set_ligand(ligand_filename)
DPO4.set_version("4.1")
DPO4['set_sw1']['value'] = 0
DPO4['set_sw1_flag']['value'] = 0
DPO4['set_psw1']['value'] = 1
class DockingParameterFileMaker:
"""Accept a <ligand>.pdbq and <receptor>.pdbqs and create
<ligand>_<receptor>.dpf
"""
def __init__(self, verbose=None):
self.verbose = verbose
self.dpo = DockingParameters()
def set_ligand(self, ligand_filename):
self.ligand_filename = os.path.basename(ligand_filename)
if verbose:
print "set ligand_filename to", self.ligand_filename
self.dpo.set_ligand(ligand_filename)
#expect a filename like ind.out.pdbq: get 'ind' from it
self.ligand_stem = string.split(self.ligand_filename, '.')[0]
if verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
if self.ligand == None:
print 'ERROR reading: ', ligand_filename
return
if verbose:
print "read ", self.ligand.name
#set dpo:
#move
self.dpo['move']['value'] = self.ligand_filename
if verbose: print "set move to ", self.dpo['move']['value']
#ndihe
#assumes ligand has torTree
self.dpo['ndihe']['value'] = self.ligand.parser.keys.count("BRANCH")
#self.dpo['ndihe']['value'] = len(self.ligand.torTree.torsionMap)
if verbose: print "set ndihe to ", self.dpo['ndihe']['value']
#torsdof
#caution dpo['torsdof']['value'] is a list [ndihe, 0.3113]
self.dpo['torsdof']['value'][0] = self.ligand.TORSDOF
if verbose: print "set torsdof to ", self.dpo['torsdof']['value']
#types
d = {}
for a in self.ligand.allAtoms:
d[a.autodock_element] = 1
sortKeyList = [
'C', 'A', 'N', 'O', 'S', 'H', 'P', 'n', 'f', 'F', 'c', 'b', 'I',
'M'
]
lig_types = ""
for t in sortKeyList:
if t in d.keys():
lig_types = lig_types + t
self.ligand.types = lig_types
self.dpo['types']['value'] = self.ligand.types
if verbose: print "set types to ", self.dpo['types']['value']
#about
self.ligand.getCenter()
cen = self.ligand.center
self.dpo['about']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
if verbose: print "set about to ", self.dpo['about']['value']
def set_receptor(self, receptor_filename):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.dpo.set_receptor(receptor_filename)
#def set_docking_parameters(self, newdict={}):
def set_docking_parameters(self, **kw):
"""Any docking paramters should be set here
"""
# like this:
# newdict = {'ga_num_evals':1750000, 'ga_pop_size':150,
# 'ga_run':20, 'rmstol':2.0}
# self.dpo['<parameter>']['value'] = <new value>
# eg self.dpo['rmstol']['value'] = 2.0
for parm, newvalue in kw.items():
#print "parm=", parm, ' newvalue=', newvalue
self.dpo[parm]['value'] = newvalue
if parm == 'set_sw1':
self.dpo['set_psw1']['value'] = not newvalue
if parm == 'set_psw1':
self.dpo['set_sw1']['value'] = not newvalue
def write_dpf(self,
dpf_filename,
parm_list=genetic_algorithm_local_search_list):
if not dpf_filename:
dpf_filename = "%s%s%s%s" % \
(self.ligand_stem, "_",
self.receptor_stem, ".dpf")
# now that we have a filename...
if self.verbose:
print "writing ", dpf_filename
self.dpo.write(dpf_filename, parm_list)
class DockingParameter4FileMaker:
"""Accept a <ligand>.pdbqt and <receptor>.pdbqt and create
<ligand>_<receptor>4.dpf
"""
def __init__(self, verbose = None):
self.verbose = verbose
self.dpo = DockingParameters()
def getTypes(self, molecule):
if not len(molecule.allAtoms.bonds[0]):
molecule.buildBondsByDistance()
ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
ad4_typer.setAutoDockElements(molecule)
dict = {}
for a in molecule.allAtoms:
dict[a.autodock_element] = 1
d_types = dict.keys()
d_types.sort()
mol_types = d_types[0]
for t in d_types[1:]:
mol_types = mol_types + " " + t
if self.verbose: print "end of getTypes: types=", mol_types, ' class=', mol_types.__class__
return mol_types
def set_write_all(self, value):
verbose = self.verbose
self.dpo['write_all_flag']['value'] = True
if verbose: print "set write_all_flag to", self.dpo['write_all_flag']['value']
def set_ligand(self, ligand_filename):
verbose = self.verbose
self.ligand_filename = os.path.basename(ligand_filename)
if verbose: print "set ligand_filename to", self.ligand_filename
self.dpo.set_ligand(ligand_filename)
#expect a filename like ind.out.pdbq: get 'ind' from it
self.ligand_stem = string.split(self.ligand_filename,'.')[0]
if verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
if self.ligand==None:
print 'ERROR reading: ', ligand_filename
return
if verbose: print "read ", self.ligand.name
#set dpo:
#move
self.dpo['move']['value'] = self.ligand_filename
if verbose: print "set move to ", self.dpo['move']['value']
#ndihe
#assumes ligand has torTree
self.dpo['ndihe']['value'] = self.ligand.parser.keys.count("BRANCH")
#self.dpo['ndihe']['value'] = len(self.ligand.torTree.torsionMap)
if verbose: print "set ndihe to ", self.dpo['ndihe']['value']
#torsdof
#caution dpo['torsdof4']['value'] is a list [ndihe, 0.274]
try:
self.dpo['torsdof4']['value'][0] = self.ligand.TORSDOF
except:
print 'setting torsdof to ligand.ndihe=', self.ligand.ndihe
self.dpo['torsdof4']['value'][0] = self.ligand.ndihe
if verbose: print "set torsdof4 to ", self.dpo['torsdof4']['value']
#types
self.ligand.types = self.getTypes(self.ligand)
self.dpo['ligand_types']['value'] = self.ligand.types
if verbose: print "set types to ", self.dpo['ligand_types']['value']
#about
self.ligand.getCenter()
cen = self.ligand.center
self.dpo['about']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
if verbose: print "set about to ", self.dpo['about']['value']
def set_receptor(self, receptor_filename):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.dpo.set_receptor(receptor_filename)
def set_flexres(self, flexres_filename):
flexmol = Read(flexres_filename)[0]
flexres_filename = os.path.basename(flexres_filename)
self.dpo['flexres_flag']['value'] = True
self.dpo['flexres']['value'] = flexres_filename
#make sure each atom type in flexres molecule is in ligand_types
d = {}
current_types = self.dpo['ligand_types']['value'].split()
for t in current_types:
d[t] = 1
for a in flexmol.allAtoms:
d[a.autodock_element] = 1
self.dpo['ligand_types']['value'] = string.join(d.keys())
def set_docking_parameters(self, **kw):
"""Any docking parameters should be set here
"""
# like this:
# newdict = {'ga_num_evals':1750000, 'ga_pop_size':150,
# 'ga_run':20, 'rmstol':2.0}
# self.mv.dpo['<parameter>']['value'] = <new value>
for parm, newvalue in kw.items():
self.dpo[parm]['value'] = newvalue
if parm=='set_sw1':
self.dpo['set_psw1']['value'] = not newvalue
if parm=='set_psw1':
self.dpo['set_sw1']['value'] = not newvalue
if parm=='flexres':
self.set_flexres(newvalue)
if parm=='write_all':
self.set_write_all(newvalue)
def write_dpf(self, dpf_filename,
parm_list = genetic_algorithm_local_search_list4,
pop_seed = False):
if not dpf_filename:
dpf_filename = "%s%s%s%s" % \
(self.ligand_stem, "_",
self.receptor_stem, ".dpf")
# now that we have a filename...
# set initial conformation
if pop_seed:
self.dpo['tran0']['value'] = self.dpo['about']['value']
self.dpo['axisangle0']['value'] = '0 0 0 0'
#self.dpo['quat0']['value'] = '1.0 0. 0. 0.'
dihe0 = '0. '*self.dpo['ndihe']['value']
dihe0.rstrip()
self.dpo['dihe0']['value'] = dihe0
if self.verbose:
print "writing ", dpf_filename
self.dpo.write4(dpf_filename, parm_list)
# @@ ASSUMPTIONS: WCG conventions for dpf and gpf names @@
# @@ from docking directory name @@
dpf_pathname = os.path.join(docking_pathname, docking_name) + ".dpf"
dpf_filename = os.path.basename(dpf_pathname)
# remove "faahNNNN_ from docking name
gpf_pathname = os.path.join(docking_pathname, docking_name[9:]) + ".gpf"
gpf_filename = os.path.basename(gpf_pathname)
#
# get filenames from the dpf and gpf
#
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.GridParameters import GridParameters
dpo = DockingParameters()
log.info("reading dpf: %s" % dpf_pathname)
dpo.read(dpf_pathname)
ligand_filename = dpo["move"]["value"]
ligand_pathname = os.path.join(docking_pathname, ligand_filename)
log.info("ligand_filename: %s" % ligand_filename)
log.debug("ligand_pathname: %s" % ligand_pathname)
gpo = GridParameters()
log.info("reading gpf: %s" % gpf_pathname)
gpo.read(gpf_pathname)
receptor_filename = gpo["receptor"]["value"]
receptor_pathname = os.path.join(docking_pathname, receptor_filename)
log.info("receptor_filename: %s" % receptor_filename)
log.debug("receptor_pathname: %s" % receptor_pathname)
usage()
sys.exit()
if not receptor_filename:
receptor_filename = dpf3_stem + '.pdbqt'
print "dpf3_to_dpf4: using default receptor_filename:", receptor_filename
if not dpf3_filename:
print 'dpf3_to_dpf4: no dpf3_filename specified using GridParameter defaults'
parms= {}
parms['simulated_annealing_list4'] = simulated_annealing_list4
parms['genetic_algorithm_list4'] = genetic_algorithm_list4
parms['genetic_algorithm_local_search_list4'] = genetic_algorithm_local_search_list4
parms['local_search_list4'] = local_search_list4
#what about nucleic acids???
DPO4 = DockingParameters()
print "default: ligand_types=", DPO4['ligand_types']['value']
orig_compute_unbound_extended_flag = DPO4['compute_unbound_extended_flag']['value']
if dpf3_filename:
DPO4.read(dpf3_filename)
if verbose: print 'read ', dpf3_filename
DPO4['compute_unbound_extended_flag']['value'] = orig_compute_unbound_extended_flag
else:
if verbose: print 'using dpo defaults'
DPO4.set_ligand(ligand_filename)
DPO4.set_version("4.1")
DPO4['set_sw1']['value'] = 0
DPO4['set_sw1_flag']['value'] = 0
DPO4['set_psw1']['value'] = 1
DPO4['set_psw1_flag']['value'] = 1
res = DPO4.set_ligand_types_from_filename(ligand_filename)
class LibraryDpfWriter:
def __init__(self, dpffile, extension='pdbq', \
err_file="write_lib_dpf_errors",
prefix='', verbose=0):
self.verbose = verbose
if verbose: print("self.verbose = ", verbose)
self.prefix = prefix
self.setup(dpffile)
self.parm_list_dict = {}
self.parm_list_dict['GALS'] = genetic_algorithm_local_search_list
self.parm_list_dict['GA'] = genetic_algorithm_list
self.parm_list_dict['LS'] = local_search_list
self.parm_list_dict['SA'] = simulated_annealing_list
self.ligandfilenames = []
self.extension = extension
self.error_file = open(err_file, 'w')
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
def getligands(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
self.ligandfilenames = glob.glob(key)
return self.ligandfilenames
def write(self, dpo, style='GALS'):
#one file per ligand
dpffiles = []
receptor_stem = self.dpo.receptor_stem
parm_list = self.parm_list_dict[style]
if not len(self.ligandfilenames):
self.getligands(self.extension)
#print "len(self.ligandfilenames)=", len(self.ligandfilenames)
for ligand_file in self.ligandfilenames:
#get the types
typeDict = {}
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
type_list = list(typeDict.keys())
#check that there is a map for each type
ok = 1
for t in type_list:
mapfile = receptor_stem + '.' + t + '.map'
try:
assert os.path.exists(mapfile)
except:
ok = 0
ostr = ligand_file + " missing map " + t + "\n"
self.error_file.write(ostr)
break #try to continue 'for' statement with next filename
#update dpo with ligand specific values
if not ok:
if self.verbose:
print("problem with ", ligand_file)
continue
types = string.join(type_list,'')
self.dpo['move']['value'] = ligand_file
if self.verbose: print("set types to ", types)
self.dpo['types']['value'] = types
#CAUTION: dpo['torsdof']['value'] is [0,0.3113]
self.dpo['torsdof']['value'][0] = m.TORSDOF
if hasattr(m, 'ndihe'):
ndihe = m.ndihe
elif hasattr(m, 'torscount'):
ndihe = m.torscount
elif hasattr(m, 'torTree'):
ndihe = len(m.torTree.torsionMap)
else:
msg = ligand_file + " is not properly formatted: no torsions!"
raise AttributeError(msg)
self.dpo['ndihe']['value'] = ndihe
outputfilename = self.prefix + m.name + "_" + style + ".dpf"
if self.verbose: print("writing ", outputfilename)
self.dpo.write(outputfilename, parm_list)
dpffiles.append(outputfilename)
return dpffiles
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
# @@ ASSUMPTIONS: WCG conventions for dpf and gpf names @@
# @@ from docking directory name @@
dpf_pathname = os.path.join(docking_pathname, docking_name) + ".dpf"
dpf_filename = os.path.basename(dpf_pathname)
# remove "faahNNNN_ from docking name
gpf_pathname = os.path.join(docking_pathname, docking_name[9:]) + ".gpf"
gpf_filename = os.path.basename(gpf_pathname)
#
# get filenames from the dpf and gpf
#
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.GridParameters import GridParameters
dpo = DockingParameters()
log.info("reading dpf: %s" % dpf_pathname)
dpo.read(dpf_pathname)
ligand_filename = dpo["move"]["value"]
ligand_pathname = os.path.join(docking_pathname, ligand_filename)
log.info ("ligand_filename: %s" % ligand_filename)
log.debug("ligand_pathname: %s" % ligand_pathname)
gpo = GridParameters()
log.info("reading gpf: %s" % gpf_pathname)
gpo.read(gpf_pathname)
receptor_filename = gpo["receptor"]["value"]
receptor_pathname = os.path.join(docking_pathname, receptor_filename)
log.info ("receptor_filename: %s" % receptor_filename)
log.debug("receptor_pathname: %s" % receptor_pathname)
class LibraryDpfWriter:
def __init__(self, dpffile, extension='pdbq', \
err_file="write_lib_dpf_errors",
prefix='', verbose=0):
self.verbose = verbose
if verbose: print "self.verbose = ", verbose
self.prefix = prefix
self.setup(dpffile)
self.parm_list_dict = {}
self.parm_list_dict['GALS'] = genetic_algorithm_local_search_list
self.parm_list_dict['GA'] = genetic_algorithm_list
self.parm_list_dict['LS'] = local_search_list
self.parm_list_dict['SA'] = simulated_annealing_list
self.ligandfilenames = []
self.extension = extension
self.error_file = open(err_file, 'w')
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
def getligands(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
self.ligandfilenames = glob.glob(key)
return self.ligandfilenames
def write(self, dpo, style='GALS'):
#one file per ligand
dpffiles = []
receptor_stem = self.dpo.receptor_stem
parm_list = self.parm_list_dict[style]
if not len(self.ligandfilenames):
self.getligands(self.extension)
#print "len(self.ligandfilenames)=", len(self.ligandfilenames)
for ligand_file in self.ligandfilenames:
#get the types
typeDict = {}
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
type_list = typeDict.keys()
#check that there is a map for each type
ok = 1
for t in type_list:
mapfile = receptor_stem + '.' + t + '.map'
try:
assert os.path.exists(mapfile)
except:
ok = 0
ostr = ligand_file + " missing map " + t + "\n"
self.error_file.write(ostr)
break #try to continue 'for' statement with next filename
#update dpo with ligand specific values
if not ok:
if self.verbose:
print "problem with ", ligand_file
continue
types = string.join(type_list,'')
self.dpo['move']['value'] = ligand_file
if self.verbose: print "set types to ", types
self.dpo['types']['value'] = types
#CAUTION: dpo['torsdof']['value'] is [0,0.3113]
self.dpo['torsdof']['value'][0] = m.TORSDOF
if hasattr(m, 'ndihe'):
ndihe = m.ndihe
elif hasattr(m, 'torscount'):
ndihe = m.torscount
elif hasattr(m, 'torTree'):
ndihe = len(m.torTree.torsionMap)
else:
msg = ligand_file + " is not properly formatted: no torsions!"
raise AttributeError, msg
self.dpo['ndihe']['value'] = ndihe
outputfilename = self.prefix + m.name + "_" + style + ".dpf"
if self.verbose: print "writing ", outputfilename
self.dpo.write(outputfilename, parm_list)
dpffiles.append(outputfilename)
return dpffiles
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
