def read_sdf_to_fb_mol(filename):
""" read sdf file and return ForceBalance.molecule.Molecule object """
from forcebalance.molecule import Molecule, Elements
import numpy as np
mol_list = read_split_mols(filename)
assert len(mol_list) == 1, 'file contains multiple molecules'
oe_mol = mol_list[0]
# create a new molecule
fb_mol = Molecule()
# load elems
fb_mol.elem = [Elements[a.GetAtomicNum()] for a in oe_mol.GetAtoms()]
noa = len(fb_mol.elem)
# load coordinates
coords_dict = oe_mol.GetCoords()
fb_mol.xyzs = [np.array([coords_dict[i] for i in range(noa)])]
# load bonds
bonds, bond_orders = [], []
for oe_bond in oe_mol.GetBonds():
idx_a = oe_bond.GetBgnIdx()
idx_b = oe_bond.GetEndIdx()
bond = (idx_a, idx_b) if idx_a <= idx_b else (idx_b, idx_a)
bonds.append(bond)
bond_orders.append(oe_bond.GetOrder())
fb_mol.bonds = bonds
fb_mol.bond_orders = bond_orders
# load atomic formal charges
atomic_formal_charges = [a.GetFormalCharge() for a in oe_mol.GetAtoms()]
molecular_charge = sum(atomic_formal_charges)
fb_mol.Data['molecular_charge'] = molecular_charge
fb_mol.Data['atomic_formal_charges'] = atomic_formal_charges
# set the oe_mol as one attribute
fb_mol.oe_mol = oe_mol
# set the cmiles id
mapped_smiles = cmiles.utils.mol_to_smiles(oe_mol)
fb_mol.Data['cmiles_id'] = cmiles.generator.get_molecule_ids(mapped_smiles)
return fb_mol
def GenerateBox(pdbin, pdbout, box, nmol, tries):
"""
Call genbox. (Confirmed working with Gromacs version 4.6.7 and 5.1.4).
Mainly checks whether genbox ran correctly.
Parameters
----------
pdbin : str
Name of input PDB file containing a single molecule.
pdbout : str
Name of output PDB file containing solvent box.
box : float
Solvent box size, should be determined previously.
nmol : int
Number of molecules to go into the solvent box
tries : int
Parameter for genbox to try inserting each molecule (tries) times
Returns
-------
None
If successful, produces "pdbout" containing solvent box.
"""
if which('gmx'):
gmxcmd = 'gmx insert-molecules'
elif which('genbox'):
gmxcmd = 'genbox'
else:
raise RuntimeError(
'gmx and/or genbox not in PATH. Please source Gromacs environment variables.'
)
fout = open('genbox.out', 'w')
ferr = open('genbox.err', 'w')
subprocess.Popen(
'%s -ci %s -o genbox.pdb -box %.3f %.3f %.3f -nmol %i -try %i' %
(gmxcmd, pdbin, box, box, box, nmol, tries),
shell=True,
stdout=fout,
stderr=ferr)
fout.close()
ferr.close()
t0 = time.time()
print("Running %s to create a solvent box..." % gmxcmd)
print("Time elapsed: % .3f seconds" % (time.time() - t0))
nmol_out = 0
for line in open('genbox.err').readlines():
if 'Output configuration contains' in line:
nmol_out = int(line.split()[-2])
if nmol_out == 0:
raise RuntimeError('genbox failed to produce an output configuration')
elif nmol_out != nmol:
raise RuntimeError(
'genbox failed to create a box with %i molecules (actual %i); '
'please retry with increased box size or number of tries' %
(nmol, nmol_out))
else:
# genbox throws away the CONECT records in the PDB, this operation adds them back.
M1 = Molecule(pdbin, build_topology=False)
M = Molecule('genbox.pdb', build_topology=False)
solventbox_bonds = []
# Loop over the number of molecules in the solvent box
for i in range(nmol):
for j in M1.bonds:
# Add the bonds for molecule number "i" in the solvent box
solventbox_bonds.append((j[0] + i * M1.na, j[1] + i * M1.na))
M.bonds = solventbox_bonds
M.write(pdbout)
print(
"-=# Output #=- Created %s containing solvent box with %i molecules and length %.3f"
% (pdbout, nmol, box))
