def set_types_from_directory(self, directory):
if self.verbose:
print("reading directory ", directory)
filelist = glob.glob(directory + "/*.pdb*")
if self.verbose:
print("len(filelist)=", len(filelist))
ad4_typer = AutoDock4_AtomTyper()
type_dict = {}
all_types = ""
for f in filelist:
ftype = os.path.splitext(f)[-1]
if ftype != ".pdbqt":
print("skipping ", f, " not in PDBQT format!")
continue
m = Read(f)[0]
m_types = ""
m_types = " ".join(list(set(m.allAtoms.autodock_element)))
self.getSideLengths(m) # sets ligand.center
npts = m.npts
# only make the box bigger, do NOT make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
if npts[ix] > val:
self.gpo['npts']['value'][ix] = npts[ix]
if self.verbose:
print(m.name, " increased grid dimension ", ix, " to ", npts[ix])
all_types = all_types + m_types
if self.verbose:
print("added ", m_types, " atom types in directory ", directory)
print("end: all_types = ", all_types)
self.gpo['ligand_types']['value'] = all_types
if self.verbose:
print("all ligand_types for ", directory, "= ", self.gpo['ligand_types']['value'])
def set_types_from_directory(self, directory):
if self.verbose:
print "reading directory ", directory
filelist = glob.glob(directory + "/*.pdb*")
if self.verbose:
print "len(filelist)=", len(filelist)
ad4_typer = AutoDock4_AtomTyper()
type_dict = {}
for f in filelist:
m = Read(f)[0]
m.buildBondsByDistance()
ad4_typer.setAutoDockElements(m)
for a in m.allAtoms:
type_dict[a.autodock_element] = 1
self.getSideLengths(m) #sets ligand.center
npts = m.npts
#only make the box bigger, do NOT make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
if npts[ix] > val:
self.gpo['npts']['value'][ix] = npts[ix]
if self.verbose:
print m.name, " increased grid dimension ", ix, " to ", npts[
ix]
d_types = type_dict.keys()
if self.verbose:
print "found ", d_types, " atom types in directory ", directory
self.gpo['ligand_types']['value'] = string.join(d_types)
if self.verbose:
print "now ligand_types is ", self.gpo['ligand_types']['value']
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_ligand4(self, ligand_filename, types=None):
#this should set ligand_types
#print "in set_ligand4: types=", types
if types is None:
ligand = Read(ligand_filename)[0]
ligand.buildBondsByDistance()
ad4_typer = AutoDock4_AtomTyper()
ad4_typer.setAutoDockElements(ligand)
dict = {}
for a in ligand.allAtoms:
dict[a.autodock_element] = 1
d_types = dict.keys()
d_types.sort()
types = d_types[0]
for t in d_types[1:]:
types = types + " " + t
self['ligand_types']['value'] = types
#print "set_ligand4: self['ligand_types']['value']=", self['ligand_types']['value']
self.ligand_filename = os.path.basename(ligand_filename)
#print "GPO: set ligand_filename to ", self.ligand_filename
self.ligand_stem = os.path.splitext(self.ligand_filename)[0]
def set_receptor4(self, receptor_filename, types=None):
#this should set receptor_types
if types is None:
receptor = Read(receptor_filename)[0]
receptor.buildBondsByDistance()
ad4_typer = AutoDock4_AtomTyper()
ad4_typer.setAutoDockElements(receptor)
dict = {}
for a in receptor.allAtoms:
dict[a.autodock_element] = 1
d_types = dict.keys()
d_types.sort()
types = d_types[0]
for t in d_types[1:]:
types = types + " " + t
self['receptor_types']['value'] = types
basename = os.path.basename(receptor_filename)
self.receptor_filename = basename
self.receptor_stem = os.path.splitext(basename)[0]
if receptor_filename != '':
self['receptor']['value'] = basename
self['gridfld']['value'] = self.receptor_stem + '.maps.fld'
self['elecmap']['value'] = self.receptor_stem + '.e.map'
self['dsolvmap']['value'] = self.receptor_stem + '.d.map'
sys.exit()
if not pdbqs_filename:
print('pdbqs_to_pdbqt: pdbqs_filename_stem must be specified.')
usage()
sys.exit()
#what about nucleic acids???
mols = Read(pdbqs_filename)
if verbose: print('read ', pdbqs_filename)
mol = mols[0]
#fix number for problem files with alternative positions
mol.allAtoms.number = list(range(1, len(mol.allAtoms) + 1))
#possible clean-up???
#need to type atoms + assign babel_types
AD4_typer = AutoDock4_AtomTyper(set_aromatic_carbons=False)
AD4_typer.setAutoDockElements(mol)
if verbose:
print("set autodock4 autodock_element for ", mol.name)
if charges_to_add is not None:
preserved = {}
preserved_types = preserve_charge_types.split(',')
for t in preserved_types:
if not len(t): continue
ats = mol.allAtoms.get(lambda x: x.autodock_element == t)
for a in ats:
if a.chargeSet is not None:
preserved[a] = [a.chargeSet, a.charge]
if charges_to_add == 'gasteiger':
GasteigerChargeCalculator().addCharges(mol.allAtoms)
if not pdbq_filename:
print('pdbq_to_pdbqt: stem of pdbq_filename must be specified.')
usage()
sys.exit()
#what about nucleic acids???
mols = Read(pdbq_filename)
if verbose: print('read ', pdbq_filename)
mol = mols[0]
mol.buildBondsByDistance()
#possible clean-up???
#need to type atoms + assign babel_types
AD4_typer = AutoDock4_AtomTyper()
AD4_typer.setAutoDockElements(mol)
if verbose:
print("set autodock4 autodock_element for ", mol.name)
writer = PdbqtWriter()
fptr = open(pdbqt_filename, 'w')
ctr = 0
for line in mol.parser.allLines:
#for at in mol.allAtoms:
if find(line, 'ATOM') < 0 and find(line, "HETA") < 0:
fptr.write(line)
else:
name = strip(line[12:16])
#ats = mol.allAtoms.get(lambda x: x.name==name)
##there could be (?) two atoms with the same name