def main():
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument("--ftfile-line",
"-n",
type=int,
default=0,
help="0 indexed")
parser.add_argument("--limit",
"-l",
type=int,
default=None,
help="limit for number of ft lines read")
parser.add_argument("ligand", help="ligand used for docking")
parser.add_argument("ft_file",
help="ftresults file to draw transformations from.")
parser.add_argument(
"rot_file",
help="Rotation file used during PIPER run to make ft_file.")
parser.add_argument("--ft_limit",
help="Speficy how many ftfile lines to read")
args = parser.parse_args()
rotations = read_rotations(args.rot_file)
#read ft_files
ftresults = read_ftresults(args.ft_file, args.limit)
#get center information for original ligands
lig_orig = parsePDB(args.ligand)
lig_center = np.mean(lig_orig.getCoords(), axis=0)
lig_name = args.ligand
lig_base = lig_name.rsplit('/', 1)[-1][:-4]
#apply ft lines to the aligned ligands
coords_apply = apply_ftresults_atom_group(lig_orig,
ftresults,
rotations,
center=lig_center)
#create new atom group for translated ligand
lig_new = AtomGroup('%s.%s.pdb' % (lig_base, args.ftfile_line))
#only choose one coordinate set (0 indexed)
coords_apply.setACSIndex(args.ftfile_line)
lig_new.setCoords(coords_apply.getCoords())
lig_new.setNames(lig_orig.getNames())
lig_new.setResnames(lig_orig.getResnames())
lig_new.setResnums(lig_orig.getResnums())
#write new ligand file
writePDB("%s.%s.pdb" % (lig_base, args.ftfile_line), lig_new)
def AddAtoms(initial_residue,
atoms2add,
atomnames_of_2_letters,
residue_data,
zmatrix,
verbose=True):
"""
This function returns a mutated residue with the atoms added.
This function gets a residue and a list of atomnames to add to the mutation.
:rtype : object
:param initial_residue:
:param atoms2add:
:param atomnames_of_2_letters:
:param residue_data:
:param zmatrix:
:param verbose:
"""
if verbose:
print('Adding new atoms:')
new_atoms_elements = []
for atom in atoms2add:
if verbose:
print(" # {}".format(atom))
if atom[:2] in atomnames_of_2_letters:
new_atoms_elements.append(atom[:2])
else:
new_atoms_elements.append(atom[0])
new_atoms = AtomGroup('New atoms')
number_of_new_atoms = len(atoms2add)
new_atoms.setNames(list(atoms2add))
new_atoms.setElements(new_atoms_elements)
new_atoms.setResnames([residue_data['fin_resname']] * number_of_new_atoms)
new_atoms.setResnums([residue_data['resnum']] * number_of_new_atoms)
new_atoms.setChids([residue_data['chain']] * number_of_new_atoms)
new_atoms.setAltlocs([''] * number_of_new_atoms)
new_atoms.setBetas([0] * number_of_new_atoms)
new_atoms.setIcodes([''] * number_of_new_atoms)
new_atoms.setOccupancies([1] * number_of_new_atoms)
new_atoms.setSegnames([''] * number_of_new_atoms)
new_atoms.setSerials([0] * number_of_new_atoms)
temporary_coords = np.ones([len(atoms2add), 3])
new_atoms.setCoords(temporary_coords)
incomplete_residue = initial_residue + new_atoms
for atom in new_atoms.iterAtoms():
atom_new_coordinates = GenerateCoordinatesFromZmatrix(
incomplete_residue, [atom.getName()], zmatrix)
atom.setCoords(atom_new_coordinates)
incomplete_residue = initial_residue + new_atoms
if verbose:
print('Done')
return initial_residue + new_atoms
def AddHfromPRO(initial_residue, zmatrix, mutation):
new_atom = AtomGroup('Hydrogen')
new_atom.setNames(['H'])
new_atom.setElements(['H'])
new_atom.setResnames([zmatrix.Name])
new_atom.setResnums([mutation['resnum']])
new_atom.setChids([mutation['chain']])
new_atom.setAltlocs([''])
new_atom.setBetas([0])
new_atom.setIcodes([''])
new_atom.setOccupancies([1])
new_atom.setSegnames([''])
new_atom.setSerials([0])
new_atom.setCoords(ModifyCoordinatesPRO(initial_residue, zmatrix, 'H', 'CD'))
return initial_residue + new_atom
def DefineNewAtom(atom_name, element, coordinates, resname, resnum, chain_id):
"""
This function creates a new AtomGroup instance containing one atom.
"""
new_atom = AtomGroup()
new_atom.setNames([atom_name])
new_atom.setElements([element])
new_atom.setCoords([coordinates])
new_atom.setResnames(resname)
new_atom.setResnums(resnum)
new_atom.setChids(chain_id)
new_atom.setAltlocs([''])
new_atom.setBetas([0])
new_atom.setIcodes([''])
new_atom.setOccupancies([1])
new_atom.setSegnames([''])
new_atom.setSerials([0])
# new_atom.setAnisous([[0.0, 0.0, 0.0]])
return new_atom