usage()
sys.exit()
m = Read(filename)[0]
if verbose: print('read ', filename)
#validate specified ligand file
assert hasattr(m, 'torTree'), "specified ligand does not have a torsion tree"
ndihe = m.parser.keys.count('BRANCH')
if verbose: print(m.name, ' has ', ndihe, ' torsions')
#1. prepare molecule
m.buildBondsByDistance()
orig_coords = m.allAtoms.coords[:]
m.allAtoms.addConformation(m.allAtoms.coords)
coord_index = 1
origin = m.getCenter()
m.stoc = StateToCoords(m, origin, 1)
#build reference dictionary of original bonds
orig = len(m.allAtoms.bonds[0])
orig_d = {}
for a in m.allAtoms: orig_d[a]=set(a.bonds.getAtoms())
#try a new random state up to ntries times
# convert trans to space centered on m
for new_try in range(ntries):
#reset coords in working slot to original coords for new try
m.allAtoms.updateCoords(orig_coords, ind=coord_index)
TRANS = []
for ind in range(3):
#do not subtract origin here, i don't understand why not
#TRANS.append((random.uniform(-1,1)*tscale)-origin[i])
class PDBINFO:
def __init__(self, pdb):
# if not is valid
self.exception = None
try:
self.mol = Read(pdb)[0]
except Exception as inst:
self.exception = inst # the exception instance
self.het = []
self.zn_atoms = []
self.size = None
self.center = None
self.selection_center = None
self.prot = []
if not self.exception:
self.get_info()
self.center = self.mol.getCenter()
def __call__(self, *args, **kwargs):
pass
def check_select(self, selection):
res_list = selection.split(';')
for res in res_list:
res = res.strip()
if not res:
return
res = res.split(':')
if not res in [[x[0].name, x[1].name[:3], x[2]]
for x in self.prot]:
return
return True
def get_info(self):
for chain in self.mol.chains:
for res in chain.residues:
# exclude water residues
if res.name[:3] in ['WAT', 'HOH', 'SOL']:
continue
if res.name[:3] == ' ZN':
self.zn_atoms.append([chain, res])
elif res.hetatm():
self.het.append([chain, res])
elif res.name[:3] in aa:
self.prot.append([chain, res, res.name[3:]])
def get_het(self):
if self.exception:
return
het = []
for lst in self.het:
het.append([lst[0].name, lst[1].name])
return het
def get_zn(self):
if self.exception:
return
zn = []
for lst in self.zn_atoms:
zn.append([lst[0].name, lst[1].name])
return zn
def get_ha(self):
if self.exception:
return
return len([x for x in self.mol.allAtoms if x.element != "H"])
def get_box(self):
if self.exception:
return
prot = []
for res in self.mol.chains.residues:
if res.name[:3] in aa:
prot.append(res)
minimx = min([at.coords[0] for res in prot for at in res.atoms]) - 5
minimy = min([at.coords[1] for res in prot for at in res.atoms]) - 5
minimz = min([at.coords[2] for res in prot for at in res.atoms]) - 5
maximx = max([at.coords[0] for res in prot for at in res.atoms]) + 5
maximy = max([at.coords[1] for res in prot for at in res.atoms]) + 5
maximz = max([at.coords[2] for res in prot for at in res.atoms]) + 5
self.size = [
int(maximx - minimx),
int(maximy - minimy),
int(maximz - minimz)
]
self.center = [(minimx + maximx) / 2, (minimy + maximy) / 2,
(minimz + maximz) / 2]
def get_ligand(self, sel, filename):
selection = sel.split(':')
new_mol = None
for chain in self.mol.chains:
for res in chain.residues:
# exclude water residues
if res.name[:3] in ['WAT', 'HOH', 'SOL', ' ZN']:
continue
if selection == [chain.name, res.name[:3], res.name[3:]]:
new_mol = makeMoleculeFromAtoms('ligand', res.atoms)
writer = PdbWriter()
writer.write(filename,
new_mol.allAtoms,
records=['ATOM', 'HETATM'])
return new_mol
def get_center_selection(self, selection):
# check if exist duplicate and deleted it
res_list = []
for x in selection.split(';'):
x = str(x).strip()
if x and not x in res_list:
res_list.append(x)
coords = []
for res in res_list:
res = res.split(':')
for c in self.mol.chains:
for mkres in self.mol.chains.residues:
if res == [c.name, mkres.name[:3], mkres.name[3:]]:
for at in mkres.atoms:
coords.append(at.coords)
x = sum([c[0] for c in coords]) / (len(coords) * 1.0)
y = sum([c[1] for c in coords]) / (len(coords) * 1.0)
z = sum([c[2] for c in coords]) / (len(coords) * 1.0)
self.selection_center = [x, y, z]
for i in range(3):
self.selection_center[i] = str(round(self.selection_center[i], 4))
def get_gyrate(self):
x = [at.coords[0] for at in self.mol.allAtoms if at.element != "H"]
y = [at.coords[1] for at in self.mol.allAtoms if at.element != "H"]
z = [at.coords[2] for at in self.mol.allAtoms if at.element != "H"]
ref = [sum(x) / len(x), sum(y) / len(y), sum(z) / len(z)]
xm = [((float(i) - ref[0]), (float(j) - ref[1]), (float(k) - ref[2]))
for (i, j, k) in zip(x, y, z)]
numerator = sum(i**2 + j**2 + k**2 for (i, j, k) in xm)
rg = sqrt(numerator / len(x))
'''Aspect ratio = 0.23 [Feinstein and Brylinski. Calculating an optimal box size for ligand docking and virtual
screening against experimental and predicted binding pockets. Journal of Cheminformatics (2015)]
If we use the automatic way of detemination of the binding site of the ligand, then the aspect ratio
changes 0.21 (this difference results in an additional small margin)
'''
return rg / 0.21
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 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 GridParameter4FileMaker:
"""Accept a <ligand>.pdbqt, <receptor>.pdbqt, reference4.gpf and create
<receptor>4.gpf
sets gridcenter to center of bounding box
sets npts according to bounding box
"""
def __init__(self, verbose=None, size_box_to_include_ligand=True):
self.verbose = verbose
self.gpo = GridParameters()
self.size_box_to_include_ligand = size_box_to_include_ligand
def read_reference(self, reference_filename):
if self.verbose: print "reading ", reference_filename
self.gpo.read4(reference_filename)
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 set_ligand(self, ligand_filename, center_on_ligand=False):
self.ligand = Read(ligand_filename)[0]
if self.ligand == None:
print 'ERROR reading: ', ligand_filename
return
if self.verbose:
print "read ", self.ligand.name
ligand_types = self.getTypes(self.ligand)
self.gpo.set_ligand4(ligand_filename, types=ligand_types)
#this sets ligand_types, gpo.ligand_stem and gpo.ligand_filename
if self.verbose:
print "set gpo.ligand_stem to", self.gpo.ligand_stem
print "set gpo.ligand_filename to", self.gpo.ligand_filename
print "set gpo.ligand_types to", self.gpo['ligand_types'][
'value'].__class__
#need to get npts
if self.size_box_to_include_ligand:
self.getSideLengths(self.ligand) #sets ligand.center
#gridcenter IS NOT SET BY THIS!!!
if center_on_ligand:
cen = self.ligand.getCenter()
self.gpo['gridcenter']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
self.gpo['gridcenterAuto']['value'] = 0
if self.verbose:
print "set gridcenter to ", self.gpo['gridcenter']['value']
#only make the box bigger, do NOT make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
#npts
if hasattr(self.ligand, 'npts'):
npts = self.ligand.npts
if npts[ix] > val:
self.gpo['npts']['value'][ix] = npts[ix]
if self.verbose: print "set npts to ", self.gpo['npts']['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 getSideLengths(self, mol):
c = mol.allAtoms.coords
maxo = Numeric.maximum.reduce(c)
mino = Numeric.minimum.reduce(c)
sideLengths = maxo - mino
mol.npts = map(int,
map(ceil, sideLengths / (self.gpo['spacing']['value'])))
for ix, npts in enumerate(mol.npts):
if npts > 126:
mol.npts[ix] = 126
#FIX THIS:
#use this center instead of mol.getCenter which returns averaged
#coords:
#this should make sure the ligand fits inside the box
#mino+(maxo-mino)/2.0
mol.center = mino + (maxo - mino) / 2.0
def set_receptor(self, receptor_filename, gpf_filename=None):
self.receptor = Read(receptor_filename)[0]
receptor_filename = os.path.basename(receptor_filename)
if self.receptor == None:
print 'ERROR reading: ', receptor_filename
return
if self.verbose: print "set_receptor filename to ", receptor_filename
receptor_types = self.getTypes(self.receptor)
self.gpo.set_receptor4(receptor_filename, types=receptor_types)
self.receptor_filename = os.path.basename(receptor_filename)
if hasattr(self, 'receptor'):
self.receptor_stem = self.receptor.name
else:
self.receptor_stem = os.path.splitext(self.receptor_filename)[0]
#all of this is handled by set_receptor4
#self.gpo['gridfld']['value'] = self.receptor_stem + '.maps.fld'
#self.gpo['elecmap']['value'] = self.receptor_stem + '.e.map'
#self.gpo['dsolvmap']['value'] = self.receptor_stem + '.d.map'
#this sets gpo.receptor_types, gpo.receptor_stem and gpo.receptor_filename
def set_grid_parameters(self, **kw):
"""Any grid parameters should be set here
"""
# like this:
# should it be **kw
# kw = {'spacing':1.0, 'receptor_types':'C A NA OA N SA HD MG'}
# self.mv.gpo['parm']['value'] = <new value>
# EXCEPT for 'npts' for which value must be 60,60,60
for parm, newvalue in kw.items():
if self.verbose:
print "parm=", parm
print "newvalue=", newvalue
if parm == 'gridcenter':
self.gpo['gridcenterAuto']['value'] = newvalue == 'auto'
self.gpo[parm]['value'] = newvalue
if parm == 'npts':
self.gpo['npts']['value'] = map(int, newvalue.split(','))
if parm == 'ligand_types':
if newvalue.find(',') > -1:
newvalue = newvalue.replace(',', ' ')
print "setting ligand_types: newvalue=", newvalue
self.gpo[parm]['value'] = newvalue
def write_gpf(self, gpf_filename=None, parm_list=grid_parameter_list4):
if not gpf_filename:
gpf_filename = self.receptor_stem + ".gpf"
# now that we have a filename...
if self.verbose:
print "writing ", gpf_filename
for item in parm_list:
print item,
print
self.gpo.write4(gpf_filename, parm_list)
usage()
sys.exit()
m = Read(filename)[0]
if verbose: print 'read ', filename
#validate specified ligand file
assert hasattr(m, 'torTree'), "specified ligand does not have a torsion tree"
ndihe = m.parser.keys.count('BRANCH')
if verbose: print m.name, ' has ', ndihe, ' torsions'
#1. prepare molecule
m.buildBondsByDistance()
orig_coords = m.allAtoms.coords[:]
m.allAtoms.addConformation(m.allAtoms.coords)
coord_index = 1
origin = m.getCenter()
m.stoc = StateToCoords(m, origin, 1)
#build reference dictionary of original bonds
orig = len(m.allAtoms.bonds[0])
orig_d = {}
for a in m.allAtoms: orig_d[a]=set(a.bonds.getAtoms())
#try a new random state up to ntries times
# convert trans to space centered on m
for new_try in range(ntries):
#reset coords in working slot to original coords for new try
m.allAtoms.updateCoords(orig_coords, ind=coord_index)
TRANS = []
for ind in range(3):
#do not subtract origin here, i don't understand why not
#TRANS.append((random.uniform(-1,1)*tscale)-origin[i])
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 GridParameterFileMaker:
"""Accept a <ligand>.pdbq , <receptor>.pdbqs, reference.gpf and create
<receptor>.gpf
sets gridcenter to center of bounding box
sets npts according to bounding box
"""
def __init__(self, verbose=None, size_box_to_include_ligand=True):
self.verbose = verbose
self.gpo = GridParameters()
self.size_box_to_include_ligand = size_box_to_include_ligand
def read_reference(self, reference_filename):
if self.verbose: print "reading ", reference_filename
self.gpo.read(reference_filename)
def set_ligand(self, ligand_filename):
self.ligand_filename = os.path.basename(ligand_filename)
if self.verbose:
print "set ligand_filename to", self.ligand_filename
self.gpo.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 self.verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
#IS THIS USEFUL???
self.gpo.ligand = self.ligand
if self.verbose: print "read ", self.ligand.name
#set gpo:
#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.gpo['types']['value'] = self.ligand.types
if self.verbose: print "set types to ", self.gpo['types']['value']
#gridcenter
self.ligand.center = self.ligand.getCenter()
if self.size_box_to_include_ligand:
self.getSideLengths(self.ligand) #sets ligand.center
cen = self.ligand.center
self.gpo['gridcenter']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
self.gpo['gridcenterAuto']['value'] = 0
if self.verbose:
print "set gridcenter to ", self.gpo['gridcenter']['value']
#only make the box bigger from npts, do not make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
if hasattr(self.ligand, 'npts'):
npts = self.ligand.npts
if npts[ix] > val:
if self.verbose:
print "increasing ", ix, " grid dimension to ", val
self.gpo['npts']['value'][ix] = npts[ix]
#if self.verbose: print "set npts to ", self.gpo['npts']['value']
def getSideLengths(self, mol):
c = mol.allAtoms.coords
maxo = Numeric.maximum.reduce(c)
mino = Numeric.minimum.reduce(c)
sideLengths = maxo - mino
mol.npts = map(int,
map(ceil, sideLengths / (self.gpo['spacing']['value'])))
for ix, npts in enumerate(mol.npts):
if npts > 126:
mol.npts[ix] = 126
#FIX THIS:
#use this center instead of mol.getCenter which returns averaged
#coords:
#this should make sure the ligand fits inside the box
#mino+(maxo-mino)/2.0
mol.center = mino + (maxo - mino) / 2.0
def set_receptor(self, receptor_filename, gpf_filename=None):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.gpo.set_receptor(receptor_filename)
#FIX THIS
#self.gpo['mset']['value'] = self.receptor.types
self.gpo['types']['value'] = self.ligand.types
def set_grid_parameters(self, **kw):
"""Any grid parameters should be set here
"""
# like this:
# should it be **kw
# kw = {'spacing':1.0, 'mset':'CNOSHXM'}
# self.mv.gpo['parm']['value'] = <new value>
# EXCEPT for 'npts' for which value must be 60,60,60
for parm, newvalue in kw.items():
self.gpo[parm]['value'] = newvalue
if parm == 'npts':
self.gpo['npts']['value'] = map(int, newvalue.split(','))
def write_gpf(self, gpf_filename=None, parm_list=grid_parameter_list):
if not gpf_filename:
gpf_filename = self.receptor_stem + ".gpf"
# now that we have a filename...
if self.verbose:
print "writing ", gpf_filename
self.gpo.write(gpf_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)
lig = lig[0]
if not hasattr(lig, 'ndihe'):
print ligandfile + "molecule has no torsion tree"
sys.exit()
lig.buildBondsByDistance()
# add extra slot to ._coords for changing coordinates
lig.allAtoms.addConformation(lig.allAtoms.coords)
#?is this necessary
lig.allAtoms.setConformation(1)
ntors = lig.ndihe
length_of_state = 7 + lig.ndihe
# @@ handle to the input ligLines
ligLines = lig.parser.allLines
#setup StateToCoords object
origin = lig.getCenter()
if use_zero_origin or interim_state:
origin = [0., 0., 0.]
#note: index of _coords to use is always 1
lig.stoc = StateToCoords(lig, origin, 1)
outptr = sys.stdout
if outputfile:
outptr = open(outputfile, 'w')
#if SINGLESTATE:
# eg:
#"State: 29.303 14.415 23.603 0.5609 0.4518 0.2662 -0.6406 -20.89 -0.65 81.86 -17.36 28.83 -10.80 -23.98 114.21"
#states = state.split()
#['State:', '29.303', '14.415', '23.603', '0.5609', '0.4518', '0.2662', '-0.6406', '-20.89', '-0.65', '81.86', '-17.36', '28.83', '-10.80', '-23.98', '114.21']
if statefile:
class GridParameter4FileMaker:
"""Accept a <ligand>.pdbqt, <receptor>.pdbqt, reference4.gpf and create
<receptor>4.gpf
sets gridcenter to center of bounding box
sets npts according to bounding box
"""
def __init__(self, verbose = None, size_box_to_include_ligand=True):
self.verbose = verbose
self.gpo = GridParameters()
self.size_box_to_include_ligand = size_box_to_include_ligand
def read_reference(self, reference_filename):
if self.verbose: print "reading ", reference_filename
self.gpo.read4(reference_filename)
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 set_ligand(self, ligand_filename, center_on_ligand=False):
self.ligand = Read(ligand_filename)[0]
if self.ligand==None:
print 'ERROR reading: ', ligand_filename
return
if self.verbose:
print "read ", self.ligand.name
ligand_types = self.getTypes(self.ligand)
self.gpo.set_ligand4(ligand_filename, types=ligand_types)
#this sets ligand_types, gpo.ligand_stem and gpo.ligand_filename
if self.verbose:
print "set gpo.ligand_stem to", self.gpo.ligand_stem
print "set gpo.ligand_filename to", self.gpo.ligand_filename
print "set gpo.ligand_types to", self.gpo['ligand_types']['value'].__class__
#need to get npts
if self.size_box_to_include_ligand:
self.getSideLengths(self.ligand) #sets ligand.center
#gridcenter IS NOT SET BY THIS!!!
if center_on_ligand:
cen = self.ligand.getCenter()
self.gpo['gridcenter']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
self.gpo['gridcenterAuto']['value'] = 0
if self.verbose: print "set gridcenter to ", self.gpo['gridcenter']['value']
#only make the box bigger, do NOT make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
#npts
if hasattr(self.ligand, 'npts'):
npts = self.ligand.npts
if npts[ix]>val:
self.gpo['npts']['value'][ix] = npts[ix]
if self.verbose: print "set npts to ", self.gpo['npts']['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 getSideLengths(self, mol):
c = mol.allAtoms.coords
maxo = Numeric.maximum.reduce(c)
mino = Numeric.minimum.reduce(c)
sideLengths = maxo-mino
mol.npts = map(int, map(ceil, sideLengths/(self.gpo['spacing']['value'])))
for ix, npts in enumerate(mol.npts):
if npts>126:
mol.npts[ix] = 126
#FIX THIS:
#use this center instead of mol.getCenter which returns averaged
#coords:
#this should make sure the ligand fits inside the box
#mino+(maxo-mino)/2.0
mol.center = mino + (maxo - mino)/2.0
def set_receptor(self, receptor_filename, gpf_filename=None):
self.receptor = Read(receptor_filename)[0]
receptor_filename = os.path.basename(receptor_filename)
if self.receptor==None:
print 'ERROR reading: ', receptor_filename
return
if self.verbose: print "set_receptor filename to ", receptor_filename
receptor_types = self.getTypes(self.receptor)
self.gpo.set_receptor4(receptor_filename, types=receptor_types)
self.receptor_filename = os.path.basename(receptor_filename)
if hasattr(self, 'receptor'):
self.receptor_stem = self.receptor.name
else:
self.receptor_stem = os.path.splitext(self.receptor_filename)[0]
#all of this is handled by set_receptor4
#self.gpo['gridfld']['value'] = self.receptor_stem + '.maps.fld'
#self.gpo['elecmap']['value'] = self.receptor_stem + '.e.map'
#self.gpo['dsolvmap']['value'] = self.receptor_stem + '.d.map'
#this sets gpo.receptor_types, gpo.receptor_stem and gpo.receptor_filename
def set_grid_parameters(self, **kw):
"""Any grid parameters should be set here
"""
# like this:
# should it be **kw
# kw = {'spacing':1.0, 'receptor_types':'C A NA OA N SA HD MG'}
# self.mv.gpo['parm']['value'] = <new value>
# EXCEPT for 'npts' for which value must be 60,60,60
for parm, newvalue in kw.items():
if self.verbose:
print "parm=", parm
print "newvalue=", newvalue
if parm=='gridcenter':
self.gpo['gridcenterAuto']['value'] = newvalue=='auto'
self.gpo[parm]['value'] = newvalue
if parm=='npts':
self.gpo['npts']['value']= map(int, newvalue.split(','))
if parm=='ligand_types':
if newvalue.find(',')>-1:
newvalue = newvalue.replace(',', ' ')
print "setting ligand_types: newvalue=", newvalue
self.gpo[parm]['value']= newvalue
def write_gpf(self, gpf_filename=None,
parm_list = grid_parameter_list4):
if not gpf_filename:
gpf_filename = self.receptor_stem + ".gpf"
# now that we have a filename...
if self.verbose:
print "writing ", gpf_filename
for item in parm_list:
print item,
print
self.gpo.write4(gpf_filename, parm_list)
class GridParameterFileMaker:
"""Accept a <ligand>.pdbq , <receptor>.pdbqs, reference.gpf and create
<receptor>.gpf
sets gridcenter to center of bounding box
sets npts according to bounding box
"""
def __init__(self, verbose = None, size_box_to_include_ligand=True):
self.verbose = verbose
self.gpo = GridParameters()
self.size_box_to_include_ligand = size_box_to_include_ligand
def read_reference(self, reference_filename):
if self.verbose: print "reading ", reference_filename
self.gpo.read(reference_filename)
def set_ligand(self, ligand_filename):
self.ligand_filename = os.path.basename(ligand_filename)
if self.verbose:
print "set ligand_filename to", self.ligand_filename
self.gpo.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 self.verbose: print "set ligand_stem to", self.ligand_stem
self.ligand = Read(ligand_filename)[0]
#IS THIS USEFUL???
self.gpo.ligand = self.ligand
if self.verbose: print "read ", self.ligand.name
#set gpo:
#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.gpo['types']['value'] = self.ligand.types
if self.verbose: print "set types to ", self.gpo['types']['value']
#gridcenter
self.ligand.center = self.ligand.getCenter()
if self.size_box_to_include_ligand:
self.getSideLengths(self.ligand) #sets ligand.center
cen = self.ligand.center
self.gpo['gridcenter']['value'] = [round(cen[0],4), round(cen[1],4),\
round(cen[2],4)]
self.gpo['gridcenterAuto']['value'] = 0
if self.verbose: print "set gridcenter to ", self.gpo['gridcenter']['value']
#only make the box bigger from npts, do not make it smaller
for ix, val in enumerate(self.gpo['npts']['value']):
if hasattr(self.ligand, 'npts'):
npts = self.ligand.npts
if npts[ix]>val:
if self.verbose: print "increasing ", ix, " grid dimension to ", val
self.gpo['npts']['value'][ix] = npts[ix]
#if self.verbose: print "set npts to ", self.gpo['npts']['value']
def getSideLengths(self, mol):
c = mol.allAtoms.coords
maxo = Numeric.maximum.reduce(c)
mino = Numeric.minimum.reduce(c)
sideLengths = maxo-mino
mol.npts = map(int, map(ceil, sideLengths/(self.gpo['spacing']['value'])))
for ix, npts in enumerate(mol.npts):
if npts>126:
mol.npts[ix] = 126
#FIX THIS:
#use this center instead of mol.getCenter which returns averaged
#coords:
#this should make sure the ligand fits inside the box
#mino+(maxo-mino)/2.0
mol.center = mino + (maxo - mino)/2.0
def set_receptor(self, receptor_filename, gpf_filename=None):
self.receptor_filename = os.path.basename(receptor_filename)
self.receptor_stem = string.split(self.receptor_filename, '.')[0]
self.gpo.set_receptor(receptor_filename)
#FIX THIS
#self.gpo['mset']['value'] = self.receptor.types
self.gpo['types']['value'] = self.ligand.types
def set_grid_parameters(self, **kw):
"""Any grid parameters should be set here
"""
# like this:
# should it be **kw
# kw = {'spacing':1.0, 'mset':'CNOSHXM'}
# self.mv.gpo['parm']['value'] = <new value>
# EXCEPT for 'npts' for which value must be 60,60,60
for parm, newvalue in kw.items():
self.gpo[parm]['value'] = newvalue
if parm=='npts':
self.gpo['npts']['value']= map(int, newvalue.split(','))
def write_gpf(self, gpf_filename=None,
parm_list = grid_parameter_list):
if not gpf_filename:
gpf_filename = self.receptor_stem + ".gpf"
# now that we have a filename...
if self.verbose:
print "writing ", gpf_filename
self.gpo.write(gpf_filename, parm_list)
lig = lig[0]
if not hasattr(lig, 'ndihe'):
print ligandfile + "molecule has no torsion tree"
sys.exit()
lig.buildBondsByDistance()
# add extra slot to ._coords for changing coordinates
lig.allAtoms.addConformation(lig.allAtoms.coords)
#?is this necessary
lig.allAtoms.setConformation(1)
ntors = lig.ndihe
length_of_state = 7+lig.ndihe
# @@ handle to the input ligLines
ligLines = lig.parser.allLines
#setup StateToCoords object
origin = lig.getCenter()
if use_zero_origin or interim_state:
origin = [0.,0.,0.]
#note: index of _coords to use is always 1
lig.stoc = StateToCoords(lig, origin, 1)
outptr = sys.stdout
if outputfile:
outptr = open(outputfile, 'w')
#if SINGLESTATE:
# eg:
#"State: 29.303 14.415 23.603 0.5609 0.4518 0.2662 -0.6406 -20.89 -0.65 81.86 -17.36 28.83 -10.80 -23.98 114.21"
#states = state.split()
#['State:', '29.303', '14.415', '23.603', '0.5609', '0.4518', '0.2662', '-0.6406', '-20.89', '-0.65', '81.86', '-17.36', '28.83', '-10.80', '-23.98', '114.21']