def ligand_preparation(ligand, output):
ligand_filename = None
verbose = None
add_bonds = False
repairs = ""
charges_to_add = 'gasteiger'
preserve_charge_types=''
cleanup = "nphs_lps"
allowed_bonds = "backbone"
root = 'auto'
outputfilename = output
check_for_fragments = False
bonds_to_inactivate = ""
inactivate_all_torsions = False
attach_nonbonded_fragments = False
attach_singletons = False
mode = 'automatic'
dict = None
mols = Read(ligand)
mol = mols[0]
mol.buildBondsByDistance()
LPO = AD4LigandPreparation(mol, mode, repairs, charges_to_add,
cleanup, allowed_bonds, root,
outputfilename=output,
dict=dict, check_for_fragments=check_for_fragments,
bonds_to_inactivate=bonds_to_inactivate,
inactivate_all_torsions=inactivate_all_torsions,
attach_nonbonded_fragments=attach_nonbonded_fragments,
attach_singletons=attach_singletons)
def prepare_ligand(self, molecule):
path = '{}_ligand.pdb'.format(self.tmpfile)
pathqt = path + 'qt'
pdb = molecule.write(absolute=path, filetype='pdb')
self._paths.append(path)
mol = MolKit.Read(path)[0]
mol.buildBondsByDistance()
RPO = AD4LigandPreparation(mol, outputfilename=pathqt)
# inactivate_all_torsions=True)
self._paths.append(pathqt)
return pathqt
if o in ('-h', '--'):
usage()
sys.exit()
if not pdbqt_filename:
print 'repair_ligand4: pdbqt_filename must be specified.'
usage()
sys.exit()
mol = Read(pdbqt_filename)[0]
if verbose: print 'read ', pdbqt_filename
mol.buildBondsByDistance()
mol.LPO = AD4LigandPreparation(mol,
mode='interactive',
repairs='',
charges_to_add=None,
root=0,
outputfilename=outputfilename,
cleanup='')
#rebuild torTree
allAts = mol.allAtoms
for b in allAts.bonds[0]:
if b.activeTors: b.activeTors = 0
torscount = 0
tM = mol.torTree.torsionMap
for i in range(len(tM)):
bnum0, bnum1 = tM[i].bond
a0 = allAts.get(lambda x: x.number == bnum0 + 1)[0]
a0.tt_ind = bnum0
a1 = allAts.get(lambda x: x.number == bnum1 + 1)[0]
a1.tt_ind = bnum1
print "key=", key
print "val =", val
if verbose:
print "setting up LPO with mode=", mode,
print "and outputfilename= ", outputfilename
print "and check_for_fragments=", check_for_fragments
print "and bonds_to_inactivate=", bonds_to_inactivate
LPO = AD4LigandPreparation(
mol,
mode,
repairs,
charges_to_add,
cleanup,
allowed_bonds,
root,
outputfilename=outputfilename,
dict=dict,
check_for_fragments=check_for_fragments,
bonds_to_inactivate=bonds_to_inactivate,
inactivate_all_torsions=inactivate_all_torsions,
attach_nonbonded_fragments=attach_nonbonded_fragments,
attach_singletons=attach_singletons)
#do something about atoms with too many bonds (?)
#FIX THIS: could be peptide ligand (???)
# ??use isPeptide to decide chargeSet??
if charges_to_add is not None:
#restore any previous charges
for atom, chargeList in preserved.items():
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
def preprocess_ligand(ligand_filename, outputfilename):
verbose = None
repairs = "" #"hydrogens_bonds"
charges_to_add = 'gasteiger'
preserve_charge_types=''
cleanup = ""
allowed_bonds = "backbone"
root = 'auto'
check_for_fragments = True
bonds_to_inactivate = ""
inactivate_all_torsions = True
attach_nonbonded_fragments = True
attach_singletons = True
mode = "automatic"
dict = None
mols = Read(ligand_filename)
if verbose: print 'read ', ligand_filename
mol = mols[0]
if len(mols)>1:
ctr = 1
for m in mols[1:]:
ctr += 1
if len(m.allAtoms)>len(mol.allAtoms):
mol = m
coord_dict = {}
for a in mol.allAtoms: coord_dict[a] = a.coords
mol.buildBondsByDistance()
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]
LPO = AD4LigandPreparation(mol, mode, repairs, charges_to_add,
cleanup, allowed_bonds, root,
outputfilename=outputfilename,
dict=dict, check_for_fragments=check_for_fragments,
bonds_to_inactivate=bonds_to_inactivate,
inactivate_all_torsions=inactivate_all_torsions,
attach_nonbonded_fragments=attach_nonbonded_fragments,
attach_singletons=attach_singletons)
if charges_to_add is not None:
for atom, chargeList in preserved.items():
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
bad_list = []
for a in mol.allAtoms:
if a in coord_dict.keys() and a.coords!=coord_dict[a]:
bad_list.append(a)
if len(bad_list):
print len(bad_list), ' atom coordinates changed!'
for a in bad_list:
print a.name, ":", coord_dict[a], ' -> ', a.coords
else:
if verbose: print "No change in atomic coordinates"
if mol.returnCode!=0:
sys.stderr.write(mol.returnMsg+"\n")
#to write output
#(2) setup default output filename if necessary
#-g : rigid output filename
if rigid_filename == None:
rigid_filename = rM.name + '_rigid.pdbqt'
if verbose: print("rigid filename is %s" % rigid_filename)
#-x : flexible output filename
if flexres_filename == None:
flexres_filename = rM.name + '_flex.pdbqt'
if verbose: print("flexible residue filename is %s" % flexres_filename)
#(3) use this class in AutoDockTools for writing formatted outputfiles...
frp = AD4FlexibleReceptorPreparation(rM,
mode='interactive',
rigid_filename=rigid_filename,
residues=[resP],
flexres_filename=flexres_filename)
frp.write_flex([resP], flexres_filename)
frp.write_rigid(rM, rigid_filename)
if new_flexres_filename is None:
new_flexres_filename = "new_" + flexres_filename
flexresMol = Read(flexres_filename)[0]
LPO = AD4LigandPreparation(flexresMol,
root=0,
outputfilename=new_flexres_filename)
# To execute this command type:
# prepare_covalent_flexres.py -l filename -r receptor_filename -l ligand_to_superimpose_filename -b atom1_atom2 -R residue
#specific example:
#python -i prepare_covalent_flexres.py -r 1pwc-protein.pdbqt -l 1pwc-ligand.pdbqt -b OG_CB -R SER62 -g 1pwc_rigid.pdbqt -x 1pwc_flex.pdbqt