def mol_graph_to_schrodinger_struct(mol_graph: MoleculeGraph):
"""
Convert a pymatgen MoleculeGraph object to a Schrodinger Structure object
Args:
mol_graph (pymatgen.analysis.graphs.MoleculeGraph): MoleculeGraph to be
converted
Returns:
struct: schrodinger.structure.Structure object
"""
struct = create_new_structure(num_atoms=0)
for site in mol_graph.molecule:
symbol = site.specie.name
pos = site.coords
struct.addAtom(symbol, pos[0], pos[1], pos[2])
for atom in struct.atom:
atom.formal_charge = 0
struct.atom[1].formal_charge = mol_graph.molecule.charge
# Credit to Xiaowei Xie
for edge in mol_graph.graph.edges.data():
struct.addBond(edge[0] + 1, edge[1] + 1, 1)
return struct
def __init__(self, pv_file = None):
self.distances = red_black_tree()
self.min_res = None
self.max_res = None
self.pv_file = pv_file
if self.pv_file is not None:
self.get_receptor_structure()
else:
self.receptor = structure.create_new_structure()
self.fingerprints = sift_gen(self.receptor)
def split_protein_protein_complex(st_path):
st = structure.StructureReader(st_path).next()
chains = [c for c in st.chain]
print chains
antibody = structure.create_new_structure()
antibody.title = '%s_antibody' %(st.title)
antigen = structure.create_new_structure()
antigen.title = '%s_antigen' %(st.title)
for chain in chains:
# considering this chain
for a in st.chain[chain.name].atom:
#if a.bond_total == 0:continue
if chain.name in 'HLAB':# it is antibody
antibody.addAtom(a.element,a.x,a.y,a.z,a.color,a.atom_type)
else:
antigen.addAtom(a.element,a.x,a.y,a.z,a.color,a.atom_type)
antibody.write('%s.pdb' %antibody.title)
antigen.write('%s.pdb' %antigen.title)
return antigen, antibody
def ase_atoms_to_structure(atoms):
"""
Convert an ase atoms instance into a structure instance
"""
#print("atoms[0]: ", atoms[0])
# for i in range(0, atoms.get_number_of_atoms()):
# print("atoms[%d]: %s"%(i, atoms[i]))
st = create_new_structure()
elements = list(map(mm.mmat_get_element_by_atomic_number, atoms.get_atomic_numbers()))
carts = atoms.get_positions()
natoms = len(atoms)
for iat in range(natoms):
st.addAtom(elements[iat], carts[iat, 0], carts[iat, 1], carts[iat, 2])
if all(atoms.get_pbc()):
unit_cell = atoms.get_cell()
abc_keys = [
xtal.Crystal.CHORUS_BOX_A_KEYS,
xtal.Crystal.CHORUS_BOX_B_KEYS,
xtal.Crystal.CHORUS_BOX_C_KEYS,
]
# lattice vecs are rows of ASE unit cell
for ivec, abc_key in enumerate(abc_keys):
for jvec, key in enumerate(abc_key):
st.property[key] = unit_cell[ivec, jvec]
# tell xtal this is P1
xtal.make_p1(st, in_place=True)
maximally_bonded, bonds, pbc_bonds = xtal.connect_atoms(st)
st.property[xtal.PBC_POSITION_KEY] = xtal.ANCHOR_PBC_POSITION % ('0', '0', '0')
st_out = xtal.get_cell(
st,
xtal_kwargs={'bonding': 'on', 'bond_orders': 'off', 'translate': 'off'}
)
#print("maximally_bonded", maximally_bonded)
#print("bonds", bonds)
#print("pbc_bonds", pbc_bonds)
#print(st_out.getXYZ())
return st_out
def read_structure(conn):
"""
Read a structure from the particle and bond tables of a database
connection. Returns a schrodinger.structure.Structure object.
The atoms get properties added with their database id and their
sigma and epsilon parameters.
"""
st = structure.create_new_structure()
c = conn.cursor()
atoms = {}
for id, anum, x, y, z, sigma, epsilon, formal_charge in c.execute(
"select particle.id, anum, x, y, z, sigma, epsilon, formal_charge "
"from particle, nonbonded_param "
"where particle.nbtype==nonbonded_param.id"):
el = mm.mmat_get_element_by_atomic_number(anum)
atom = atoms[id] = st.addAtom(el, x, y, z)
atom.property[FORMAL_CHARGE_PROP] = formal_charge
atom.property[ID_PROP] = id
atom.property[SIGMA_PROP] = sigma
atom.property[EPSILON_PROP] = epsilon
for p0, p1, order in c.execute('select p0, p1, "order" from bond'):
st.addBond(atoms[p0], atoms[p1], int(order))
return st
def read_structure(conn):
"""
Read a structure from the particle and bond tables of a database
connection. Returns a schrodinger.structure.Structure object.
The atoms get properties added with their database id and their
sigma and epsilon parameters.
"""
st = structure.create_new_structure()
c = conn.cursor()
atoms = {}
for id, anum, x, y, z, charge in c.execute(
"select particle.id, anum, x, y, z,charge "
"from particle, nonbonded_param "
"where particle.nbtype==nonbonded_param.id"):
el = mm.mmat_get_element_by_atomic_number(anum)
atom = atoms[id] = st.addAtom(el, x, y, z)
atom.property[CHARGE] = charge
atom.property[ID_PROP] = id
for p0, p1, order in c.execute('select p0, p1, "order" from bond'):
st.addBond(atoms[p0], atoms[p1], int(order))
return st
def get_receptor_structure(self):
if os.path.exists(self.pv_file):
self.receptor = structure.StructureReader(self.pv_file).next()
else:
self.receptor = structure.create_new_structure()
