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 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
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 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
