def __init__(self, infile, moldb=None, atomdb=None, bonddb=None):
formats = {"pdb": PDBReader, "gro": GROReader}
try:
ext = os.path.splitext(infile)[1][1:]
coords = formats[ext](infile)
except KeyError as e:
e.args = ("File extension '{0}' not recognised".format(ext), )
raise
self.coords = coords
self.moldb = MolDatabase() if moldb is None else moldb
self.atomdb = AtomDatabase() if atomdb is None else atomdb
self.bonddb = BondDatabase() if bonddb is None else bonddb
self.moltypes = []
self.atomtypes = []
self.lentypes = []
self.angtypes = []
self.dihtypes = []
self.imptypes = []
self.lenstyles = []
self.angstyles = []
self.dihstyles = []
self.impstyles = []
self.natoms = Counter()
self.nlengths = Counter()
self.nangles = Counter()
self.ndihedrals = Counter()
self.nimpropers = Counter()
def __init__(self, infile):
self._suppress_atom_names = False
formats = {"pdb": PDBReader,
"gro": GROReader}
try:
ext = os.path.splitext(infile)[1][1:]
coords = formats[ext](infile)
except KeyError as e:
e.args = ("File extension '{0}' not recognised".format(ext),)
raise
self.coords = coords
self.moldb = MolDatabase()
self.atomdb = AtomDatabase()
self.bonddb = BondDatabase()
self.moltypes = []
self.atomtypes = []
self.lentypes = []
self.angtypes = []
self.dihtypes = []
self.imptypes = []
self.lenstyles = []
self.angstyles = []
self.dihstyles = []
self.impstyles = []
self.natoms = Counter()
self.nlengths = Counter()
self.nangles = Counter()
self.ndihedrals = Counter()
self.nimpropers = Counter()
def test_read_database_atoms(self):
db = AtomDatabase()
self.assertTrue("MEOH" in db.atoms)
self.assertTrue("ETOH" in db.atoms)
self.assertEqual(db.atoms["MEOH"].type, "MEOH")
self.assertEqual(db.atoms["MEOH"].mass, 30.026)
self.assertEqual(db.atoms["MEOH"].charge, 0)
self.assertEqual(db.atoms["MEOH"].dipole, 0.354)
self.assertEqual(db.atoms["MEOH"].diameter, 12.7)
self.assertEqual(db.atoms["MEOH"].rotmass, 30.026)
self.assertEqual(db.atoms["ETOH"].mass, 44.053)
class PDB2LMP:
def __init__(self, infile):
self._suppress_atom_names = False
formats = {"pdb": PDBReader,
"gro": GROReader}
try:
ext = os.path.splitext(infile)[1][1:]
coords = formats[ext](infile)
except KeyError as e:
e.args = ("File extension '{0}' not recognised".format(ext),)
raise
self.coords = coords
self.moldb = MolDatabase()
self.atomdb = AtomDatabase()
self.bonddb = BondDatabase()
self.moltypes = []
self.atomtypes = []
self.lentypes = []
self.angtypes = []
self.dihtypes = []
self.imptypes = []
self.lenstyles = []
self.angstyles = []
self.dihstyles = []
self.impstyles = []
self.natoms = Counter()
self.nlengths = Counter()
self.nangles = Counter()
self.ndihedrals = Counter()
self.nimpropers = Counter()
def collect_types(self):
def collect_type(values, counter, db_vals, typelist, stylelist):
for val in values:
counter.total += 1
if val.type not in typelist:
typelist.append(val.type)
counter.types += 1
if db_vals[val.type].style not in stylelist:
stylelist.append(db_vals[val.type].style)
atnum = 0
for mol in self.coords.molecules:
dbmol = self.moldb.molecules[mol.name]
if mol.name not in self.moltypes:
self.moltypes.append(mol.name)
collect_type(dbmol.lengths, self.nlengths, self.bonddb.length,
self.lentypes, self.lenstyles)
collect_type(dbmol.angles, self.nangles, self.bonddb.angle,
self.angtypes, self.angstyles)
collect_type(dbmol.dihedrals, self.ndihedrals, self.bonddb.dihedral,
self.dihtypes, self.dihstyles)
collect_type(dbmol.impropers, self.nimpropers, self.bonddb.improper,
self.imptypes, self.impstyles)
coordfile_atoms = [self.coords.atoms[x] for x in mol.atoms]
if len(coordfile_atoms) != len(dbmol.atoms):
raise ValueError("Number of atoms does not match between coordinate file and force field for molecule {0}.".format(mol.name))
for coordfile_atom, dbmol_atom in zip(coordfile_atoms, dbmol.atoms.values()):
if dbmol_atom.type not in self.atomtypes:
self.atomtypes.append(dbmol_atom.type)
self.natoms.types += 1
if coordfile_atom.name != dbmol_atom.name:
if self._suppress_atom_names:
coordfile_atom.name = dbmol_atom.name
else:
raise NonMatchingAtomException(atnum, coordfile_atom.name, dbmol_atom.name)
self.natoms.total += 1
atnum += 1
def populate_pdb_data(self):
for mol in self.moldb.molecules.values():
for atom in mol.atoms.values():
atom.populate(self.atomdb.atoms[atom.type])
for atom in self.coords.atoms:
atom.populate(self.moldb.molecules[atom.resname].atoms[atom.name])
def write_data(self, filename):
with open(filename, "w") as data:
print("LAMMPS 'data.' input file created by PDB2LMP", file=data)
print(file=data)
print("{0:8d} atoms".format(self.natoms.total), file=data)
print("{0:8d} bonds".format(self.nlengths.total), file=data)
print("{0:8d} angles".format(self.nangles.total), file=data)
print("{0:8d} dihedrals".format(self.ndihedrals.total), file=data)
print("{0:8d} impropers".format(self.nimpropers.total), file=data)
print(file=data)
print("{0:8d} atom types".format(self.natoms.types), file=data)
print("{0:8d} bond types".format(self.nlengths.types), file=data)
print("{0:8d} angle types".format(self.nangles.types), file=data)
print("{0:8d} dihedral types".format(self.ndihedrals.types), file=data)
print("{0:8d} improper types".format(self.nimpropers.types), file=data)
print(file=data)
cell = [val / 2 for val in self.coords.cell]
print("{0:8.3f} {1:8.3f} xlo xhi".format(-cell[0], cell[0]), file=data)
print("{0:8.3f} {1:8.3f} ylo yhi".format(-cell[1], cell[1]), file=data)
print("{0:8.3f} {1:8.3f} zlo zhi".format(-cell[2], cell[2]), file=data)
print(file=data)
print("Atoms", file=data)
print(file=data)
atomline = "{0:6d} {1:4d} {2:8.3f} {3:8.3f} {4:8.3f} {5:4d} {6:5.2f} {7:8.3f} {8:8.3f} {9:8.3f} {10:5.2f} {11:5.2f}"
for i, atom in enumerate(self.coords.atoms, start=1):
# Write atom line
# Dipoles are all oriented up - this should equilibrate out quickly
print(atomline.format(i, self.atomtypes.index(atom.type)+1,
atom.x, atom.y, atom.z, atom.resid, atom.charge,
atom.dipole, 0, 0, atom.diameter, atom.rotmass), file=data)
def write_bonds(n, types, header):
if n <= 0:
return
print("\n" + header + "\n", file=data)
i = 1
for ii, mol in enumerate(self.coords.molecules):
mol_db = self.moldb.molecules[mol.name]
atom_list = list(mol_db.atoms.keys())
for bond in getattr(mol_db, header.lower()):
print("{0:6d} {1:4d}".format(i, types.index(bond.type) + 1), file=data, end="")
for atom in bond.atoms:
try:
atom_num = mol.atoms[atom_list.index(atom)]
except ValueError:
if atom.startswith("+"):
other_mol = self.coords.molecules[ii + 1]
elif atom.startswith("-"):
other_mol = self.coords.molecules[ii - 1]
else:
raise
other_mol_db = self.moldb.molecules[other_mol.name]
try:
if not mol_db.polymer_type.intersection(other_mol_db.polymer_type):
raise PolymerError(mol.name, other_mol.name) from None
except AttributeError:
raise PolymerError(mol.name, other_mol.name) from None
other_atom_list = list(other_mol_db.atoms.keys())
atom_num = other_mol.atoms[other_atom_list.index(atom[1:])]
print(" {0:6d}".format(atom_num + 1), file=data, end="")
print(file=data)
i += 1
write_bonds(self.nlengths.total, self.lentypes, "Bonds")
write_bonds(self.nangles.total, self.angtypes, "Angles")
write_bonds(self.ndihedrals.total, self.dihtypes, "Dihedrals")
write_bonds(self.nimpropers.total, self.imptypes, "Impropers")
def write_forcefield(self, filename):
with open(filename, "w") as ff:
print("# Forcefield prepared by PDB2LMP", file=ff)
print(file=ff)
# TODO change these to "0.0 1.0 1.0 12.0" - ELBA standard
print("pair_style lj/sf/dipole/sf 12.0", file=ff)
print("special_bonds lj/coul 0.0 0.0 0.0", file=ff)
print(file=ff)
def write_styles(styles, header):
if styles:
print(header, file=ff, end="")
for style in styles:
print(" " + style, file=ff, end="")
print(file=ff)
write_styles(self.lenstyles, "bond_style hybrid")
write_styles(self.angstyles, "angle_style hybrid")
write_styles(self.dihstyles, "dihedral_style hybrid")
write_styles(self.impstyles, "improper_style hybrid")
print(file=ff)
line = "mass {0:4d} {1:8.3f} # {2}"
for i, atomtype in enumerate(self.atomtypes, start=1):
print(line.format(i, self.atomdb.atoms[atomtype].mass, atomtype), file=ff)
print(file=ff)
line = "set type{0:4d} diameter {1:8.3f} # {2}"
for i, atomtype in enumerate(self.atomtypes, start=1):
print(line.format(i, self.atomdb.atoms[atomtype].diameter, atomtype), file=ff)
print(file=ff)
line = "pair_coeff {0:4d} {1:4d} {2:6.3f} {3:6.3f} # {4}-{5}"
for i, atomtype in enumerate(self.atomtypes, start=1):
for j, atomtype2 in enumerate(self.atomtypes, start=1):
if i > j:
continue
sig, eps = self.atomdb.lj(atomtype, atomtype2)
print(line.format(i, j, eps, sig, atomtype, atomtype2), file=ff)
def write_types(types, db_vals, line_prefix):
if types:
print(file=ff)
line = line_prefix + " {0:4d} {1} {2} # {3}"
for i, tipe in enumerate(types, start=1):
db_type = db_vals[tipe]
print(line.format(i, db_type.style, db_type.params, tipe), file=ff)
write_types(self.lentypes, self.bonddb.length, "bond_coeff")
write_types(self.angtypes, self.bonddb.angle, "angle_coeff")
write_types(self.dihtypes, self.bonddb.dihedral, "dihedral_coeff")
write_types(self.imptypes, self.bonddb.improper, "improper_coeff")
class PDB2LMP:
def __init__(self, infile, moldb=None, atomdb=None, bonddb=None):
formats = {"pdb": PDBReader, "gro": GROReader}
try:
ext = os.path.splitext(infile)[1][1:]
coords = formats[ext](infile)
except KeyError as e:
e.args = ("File extension '{0}' not recognised".format(ext), )
raise
self.coords = coords
self.moldb = MolDatabase() if moldb is None else moldb
self.atomdb = AtomDatabase() if atomdb is None else atomdb
self.bonddb = BondDatabase() if bonddb is None else bonddb
self.moltypes = []
self.atomtypes = []
self.lentypes = []
self.angtypes = []
self.dihtypes = []
self.imptypes = []
self.lenstyles = []
self.angstyles = []
self.dihstyles = []
self.impstyles = []
self.natoms = Counter()
self.nlengths = Counter()
self.nangles = Counter()
self.ndihedrals = Counter()
self.nimpropers = Counter()
def collect_types(self, add_water=True, allow_atom_subset=False):
"""
Collect all bead and bond types used in simulation.
Args:
add_water: Add water bead type even if not present in input coordinates?
allow_atom_subset: Allow converting only a subset of the atoms in coordinate file
"""
def collect_type(values, counter, db_vals, typelist, stylelist,
nextmol_name):
for val in values:
try:
if re.fullmatch(val.ifnext, nextmol_name) is None:
continue
except AttributeError:
pass
except TypeError:
continue
counter.total += 1
if val.type not in typelist:
typelist.append(val.type)
counter.types += 1
if db_vals[val.type].style not in stylelist:
stylelist.append(db_vals[val.type].style)
atnum = 0
for i, mol in enumerate(self.coords.molecules):
dbmol = self.moldb.molecules[mol.name]
try:
nextmol_name = self.coords.molecules[i + 1].name
except IndexError:
nextmol_name = None
if mol.name not in self.moltypes:
self.moltypes.append(mol.name)
collect_type(dbmol.lengths, self.nlengths, self.bonddb.length,
self.lentypes, self.lenstyles, nextmol_name)
collect_type(dbmol.angles, self.nangles, self.bonddb.angle,
self.angtypes, self.angstyles, nextmol_name)
collect_type(dbmol.dihedrals, self.ndihedrals,
self.bonddb.dihedral, self.dihtypes, self.dihstyles,
nextmol_name)
collect_type(dbmol.impropers, self.nimpropers,
self.bonddb.improper, self.imptypes, self.impstyles,
nextmol_name)
coordfile_atoms = [self.coords.atoms[x] for x in mol.atoms]
if allow_atom_subset:
if len(coordfile_atoms) < len(dbmol.atoms):
raise ValueError(
"Number of atoms is greater in coordinate file ({0}) than force field ({1}) for molecule {2}."
.format(len(coordfile_atoms), len(dbmol.atoms),
mol.name))
else:
if len(coordfile_atoms) != len(dbmol.atoms):
raise ValueError(
"Number of atoms does not match between coordinate file ({0}) and force field ({1}) for molecule {2}."
.format(len(coordfile_atoms), len(dbmol.atoms),
mol.name))
# Convert atoms from coordinate file that are present in database
for coordfile_atom in coordfile_atoms:
try:
dbmol_atom = dbmol.atoms[coordfile_atom.name]
except KeyError:
if allow_atom_subset:
continue
raise
if dbmol_atom.type not in self.atomtypes:
self.atomtypes.append(dbmol_atom.type)
self.natoms.types += 1
self.natoms.total += 1
atnum += 1
if add_water and "WAT" not in self.atomtypes:
self.atomtypes.append("WAT")
self.natoms.types += 1
def populate_pdb_data(self):
for mol in self.moldb.molecules.values():
for atom in mol.atoms.values():
atom.populate(self.atomdb.atoms[atom.type])
for atom in self.coords.atoms:
atom.populate(self.moldb.molecules[atom.resname].atoms[atom.name])
def write_data(self, filename):
with open(filename, "w") as data:
print("LAMMPS 'data.' input file created by PDB2LMP", file=data)
print(file=data)
print("{0:8d} atoms".format(self.natoms.total), file=data)
print("{0:8d} bonds".format(self.nlengths.total), file=data)
print("{0:8d} angles".format(self.nangles.total), file=data)
print("{0:8d} dihedrals".format(self.ndihedrals.total), file=data)
print("{0:8d} impropers".format(self.nimpropers.total), file=data)
print(file=data)
print("{0:8d} atom types".format(self.natoms.types), file=data)
print("{0:8d} bond types".format(self.nlengths.types), file=data)
print("{0:8d} angle types".format(self.nangles.types), file=data)
print("{0:8d} dihedral types".format(self.ndihedrals.types),
file=data)
print("{0:8d} improper types".format(self.nimpropers.types),
file=data)
print(file=data)
cell = [val / 2 for val in self.coords.cell]
if cell == [0, 0, 0]:
print("WARNING: The simulation box/unit cell size is zero.")
print(
" If this is not intentional, please check your input files."
)
print("{0:8.3f} {1:8.3f} xlo xhi".format(-cell[0], cell[0]),
file=data)
print("{0:8.3f} {1:8.3f} ylo yhi".format(-cell[1], cell[1]),
file=data)
print("{0:8.3f} {1:8.3f} zlo zhi".format(-cell[2], cell[2]),
file=data)
print(file=data)
print("Atoms", file=data)
print(file=data)
atomline = "{0:6d} {1:4d} {2:8.3f} {3:8.3f} {4:8.3f} {5:4d} {6:5.2f} {7:8.3f} {8:8.3f} {9:8.3f} {10:5.2f} {11:5.2f}"
for i, atom in enumerate(self.coords.atoms, start=1):
# Write atom line
# Dipoles are all oriented up - this should equilibrate out quickly
print(atomline.format(i,
self.atomtypes.index(atom.type) + 1,
atom.x, atom.y, atom.z, atom.resid,
atom.charge, atom.dipole, 0, 0,
atom.diameter, atom.rotmass),
file=data)
def write_bonds(n, types, header):
if n <= 0:
return
print("\n" + header + "\n", file=data)
i = 1
for ii, mol in enumerate(self.coords.molecules):
mol_db = self.moldb.molecules[mol.name]
try:
nextmol_name = self.coords.molecules[ii + 1].name
except IndexError:
nextmol_name = None
atom_list = list(mol_db.atoms.keys())
for bond in getattr(mol_db, header.lower()):
try:
if re.fullmatch(bond.ifnext, nextmol_name) is None:
continue
except AttributeError:
pass
except TypeError:
continue
print("{0:6d} {1:4d}".format(
i,
types.index(bond.type) + 1),
file=data,
end="")
for atom in bond.atoms:
try:
atom_num = mol.atoms[atom_list.index(atom)]
except ValueError:
if atom.startswith("+"):
other_mol = self.coords.molecules[ii + 1]
elif atom.startswith("-"):
other_mol = self.coords.molecules[ii - 1]
else:
raise
other_mol_db = self.moldb.molecules[
other_mol.name]
try:
if not mol_db.polymer_type.intersection(
other_mol_db.polymer_type):
raise PolymerError(
mol.name, other_mol.name) from None
except AttributeError:
raise PolymerError(
mol.name, other_mol.name) from None
other_atom_list = list(
other_mol_db.atoms.keys())
atom_num = other_mol.atoms[
other_atom_list.index(atom[1:])]
print(" {0:6d}".format(atom_num + 1),
file=data,
end="")
print(file=data)
i += 1
write_bonds(self.nlengths.total, self.lentypes, "Bonds")
write_bonds(self.nangles.total, self.angtypes, "Angles")
write_bonds(self.ndihedrals.total, self.dihtypes, "Dihedrals")
write_bonds(self.nimpropers.total, self.imptypes, "Impropers")
def write_forcefield(self, filename):
with open(filename, "w") as ff:
print("# Forcefield prepared by PDB2LMP", file=ff)
print(file=ff)
# TODO change these to "0.0 1.0 1.0 12.0" - ELBA standard
print("pair_style lj/sf/dipole/sf 12.0", file=ff)
print("special_bonds lj/coul 0.0 0.0 0.0", file=ff)
print(file=ff)
def write_styles(styles, header):
if styles:
print(header, file=ff, end="")
for style in styles:
print(" " + style, file=ff, end="")
print(file=ff)
write_styles(self.lenstyles, "bond_style hybrid")
write_styles(self.angstyles, "angle_style hybrid")
write_styles(self.dihstyles, "dihedral_style hybrid")
write_styles(self.impstyles, "improper_style hybrid")
print(file=ff)
line = "mass {0:4d} {1:8.3f} # {2}"
for i, atomtype in enumerate(self.atomtypes, start=1):
print(line.format(i, self.atomdb.atoms[atomtype].mass,
atomtype),
file=ff)
print(file=ff)
line = "set type{0:4d} diameter {1:8.3f} # {2}"
for i, atomtype in enumerate(self.atomtypes, start=1):
print(line.format(i, self.atomdb.atoms[atomtype].diameter,
atomtype),
file=ff)
print(file=ff)
line = "pair_coeff {0:4d} {1:4d} {2:6.3f} {3:6.3f} # {4}-{5}"
for i, atomtype in enumerate(self.atomtypes, start=1):
for j, atomtype2 in enumerate(self.atomtypes, start=1):
if i > j:
continue
sig, eps = self.atomdb.lj(atomtype, atomtype2)
print(line.format(i, j, eps, sig, atomtype, atomtype2),
file=ff)
def write_types(types, db_vals, line_prefix):
if types:
print(file=ff)
line = line_prefix + " {0:4d} {1} {2} # {3}"
for i, tipe in enumerate(types, start=1):
db_type = db_vals[tipe]
print(line.format(i, db_type.style, db_type.params,
tipe),
file=ff)
write_types(self.lentypes, self.bonddb.length, "bond_coeff")
write_types(self.angtypes, self.bonddb.angle, "angle_coeff")
write_types(self.dihtypes, self.bonddb.dihedral, "dihedral_coeff")
write_types(self.imptypes, self.bonddb.improper, "improper_coeff")
def test_lj(self):
db = AtomDatabase()
self.helper_tuple_compare(db.lj("MEOH", "ETOH"), (3.963, 0.704))
self.helper_tuple_compare(db.lj("WAT", "WAT"), (3.050, 0.550))
self.helper_tuple_compare(db.lj("MEOH", "WAT"), (3.388, 0.621))
self.helper_tuple_compare(db.lj("WAT", "MEOH"), (3.388, 0.621))
def test_open_database(self):
db = AtomDatabase()
def test_lj(self):
db = AtomDatabase()
self.helper_tuple_compare(db.lj("MEOH", "ETOH"), (3.963, 0.704))
self.helper_tuple_compare(db.lj("WAT", "WAT"), (3.050, 0.550))
self.helper_tuple_compare(db.lj("MEOH", "WAT"), (3.388, 0.621))
self.helper_tuple_compare(db.lj("WAT", "MEOH"), (3.388, 0.621))
