def a2md_from_mol(mol: Mol2):
"""
returns the density model associated to a Mol2
:param mol:
:type mol: Mol2
:return:
:rtype: Molecule
"""
an = mol.get_atomic_numbers()
coords = mol.get_coordinates(units="au")
charge = mol.get_absolute_charges()
topology = mol.get_bonds()
segments = mol.segment_idx
topo_array = []
for i in range(mol.get_number_atoms()):
topo_array.append([])
for i in range(mol.get_number_bonds()):
begin = int(topology[i, 0])
end = int(topology[i, 1])
topo_array[begin - 1].append(end - 1)
topo_array[end - 1].append(begin - 1)
return Molecule(coordinates=coords,
atomic_numbers=an,
charge=charge,
topology=topo_array,
segments=segments)
def convert(mol : Mol2):
G = nx.Graph()
for i in range(mol.get_number_atoms()):
G.add_node(i, **mol.get_atom(i))
bonds = mol.get_bonds()
bonds = bonds - 1
for i in range(mol.get_number_bonds()):
G.add_edge(bonds[i, 0], bonds[i, 1])
bonds, angles, dihedrals = decompose_molecule_graph(G)
dbonds = np.zeros(len(bonds), dtype='float64')
dangles = np.zeros(len(angles), dtype='float64')
ddihedrals = np.zeros(len(dihedrals), dtype='float64')
for i in range(len(bonds)):
atom1, atom2 = bonds[i].split("|")
atom1 = int(atom1)
atom2 = int(atom2)
x1 = G.nodes[atom1]['coordinates']
x2 = G.nodes[atom2]['coordinates']
dbonds[i] = distance(x1, x2)
for i in range(len(angles)):
ends, center = angles[i].split(",")
atom1, atom3 = ends.split("|")
atom1 = int(atom1)
atom3 = int(atom3)
atom2 = int(center)
x1 = G.nodes[atom1]['coordinates']
x2 = G.nodes[atom2]['coordinates']
x3 = G.nodes[atom3]['coordinates']
dangles[i] = angle(x1, x2, x3)
for i in range(len(dihedrals)):
ends, center = dihedrals[i].split(",")
atom1, atom4 = ends.split("|")
atom2, atom3 = center.split("|")
atom1 = int(atom1)
atom3 = int(atom3)
atom2 = int(atom2)
atom4 = int(atom4)
x1 = G.nodes[atom1]['coordinates']
x2 = G.nodes[atom2]['coordinates']
x3 = G.nodes[atom3]['coordinates']
x4 = G.nodes[atom4]['coordinates']
ddihedrals[i] = dihedral(x1, x2, x3, x4)
return dbonds, dangles, ddihedrals