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)
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)
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)
if res == "ERROR": raise Exception('unreadable file' + ligand_filename)
if verbose:
print("ligand_types=", DPO4['ligand_types']['value'])
print('set ligand to ', ligand_filename)
DPO4.set_receptor(receptor_filename)
if verbose: print('set receptor to ', receptor_filename)
if outputfilename is None:
outputfilename = dpf3_stem + '_4.dpf'
DPO4.write4(outputfilename, parms[parameter_list])
if verbose:
print("wrote ", outputfilename, ' using:')
for p in parameter_list:
print(p)
# To execute this command type:
# dpf3_to_dpf4.py -s dpf3_stem -r receptor_filename -l ligand_filename -v
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)
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)
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)
if res=="ERROR": raise 'unreadable file', ligand_filename
if verbose:
print "ligand_types=", DPO4['ligand_types']['value']
print 'set ligand to ', ligand_filename
DPO4.set_receptor(receptor_filename)
if verbose: print 'set receptor to ', receptor_filename
if outputfilename is None:
outputfilename = dpf3_stem + '_4.dpf'
DPO4.write4(outputfilename, parms[parameter_list])
if verbose:
print "wrote ", outputfilename, ' using:'
for p in parameter_list:
print p
# To execute this command type:
# dpf3_to_dpf4.py -s dpf3_stem -r receptor_filename -l ligand_filename -v