def GetBondFromPrm(row):
"""Parses bond row into a Bond object.
Args:
row (str*): Array of strings from line of prm file.
Returns:
bond (mmlib.molecule.Bond): Bond object with attributes from row.
Raises:
IndexError: If insufficient number of fields.
ValueError: If incorrect data type of any field.
"""
if len(row) < 5:
raise IndexError('Insufficient columns to parse prm file row into Bond '
'object: %s' % ' '.join(row))
at1, at2, k_b, r_eq = row[1:5]
if not _IsType(int, at1) or not int(at1) > 0:
raise ValueError('Bond atom1 index must be positive integer: %s' % at1)
if not _IsType(int, at2) or not int(at2) > 0:
raise ValueError('Bond atom2 index must be positive integer: %s' % at2)
if not _IsType(float, k_b) or not float(k_b) > 0.0:
raise ValueError(
'Bond spring constant must be positive numeric value: %s' % k_b)
if not _IsType(float, r_eq) or not float(r_eq) > 0.0:
raise ValueError(
'Equilibrium bond length must be positive numeric value: %s' % r_eq)
return molecule.Bond(int(at1)-1, int(at2)-1, float(k_b), float(r_eq))
def GetBonds(atoms, bond_graph):
"""Determine covalently bonded atoms from bond graph and get parameters.
Search bond graph for bonded atom pairs, and parameter tables for mm
parameters. Use to create a new Bond object and append to Molecule.
Args:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
bond_graph (int:(int: float)): Dictionary of bond connectivity.
Returns:
bonds (mmlib.molecule.Bond*): Array of molecule's Bond objects.
"""
bonds = []
for i, at1 in enumerate(atoms):
for j in bond_graph[i]:
if i > j:
continue
at2 = atoms[j]
r_ij = bond_graph[i][j]
k_b, r_eq = param.GetBondParam(at1.type_, at2.type_)
if k_b:
bonds.append(molecule.Bond(i, j, k_b, r_eq, r_ij))
bonds.sort(key=lambda b: (b.at1, b.at2))
return bonds
def GetBondFromPrm(record, atoms):
"""Parses bond record into a Bond object.
Args:
record (str*): Array of strings from line of prm file.
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
bond (mmlib.molecule.Bond): Bond object with attributes from record.
"""
at1, at2 = (x - 1 for x in map(int, record[1:3]))
k_b, r_eq = tuple(map(float, record[3:5]))
c1, c2 = (atoms[i].coords for i in (at1, at2))
r_ij = geomcalc.GetRij(c1, c2)
return molecule.Bond(at1, at2, r_ij, r_eq, k_b)
def get_bond(mol, record):
"""Parse bond record into a bond object and append to molecule.
Appends mmlib.molecule.Bond object to mmlib.molecule.Molecule
object. Contents of bond object include (int) 2 atomic indices,
(float) spring constant [kcal/(mol*A^2)], (float) equilibrium bond
length [Angstrom], (float) bond length [Angstrom].
Args:
mol (mmlib.molecule.Molecule): Molecule to append bond.
record (str*): Array of strings from line of prm file.
"""
at1, at2 = int(record[1])-1, int(record[2])-1
k_b, r_eq = float(record[3]), float(record[4])
c1, c2 = mol.atoms[at1].coords, mol.atoms[at2].coords
r_ij = geomcalc.get_r_ij(c1, c2)
bond = molecule.Bond(at1, at2, r_ij, r_eq, k_b)
mol.bonds.append(bond)
mol.bond_graph[at1][at2] = r_ij
mol.bond_graph[at2][at1] = r_ij
def _GetBond(mol, record):
"""Parse bond record into a bond object and append to molecule.
Appends mmlib.molecule.Bond object to mmlib.molecule.Molecule object. Contents
of bond object include (int) 2 atomic indices, (float) spring constant
[kcal/(mol*A^2)], (float) equilibrium bond length [Angstrom], (float) bond
length [Angstrom].
Args:
mol (mmlib.molecule.Molecule): Molecule to append bond.
record (str*): Array of strings from line of prm file.
"""
at1, at2 = [x-1 for x in list(map(int, record[1:3]))]
k_b, r_eq = list(map(float, record[3:5]))
c1, c2 = [mol.atoms[i].coords for i in [at1, at2]]
r_ij = geomcalc.GetRij(c1, c2)
bond = molecule.Bond(at1, at2, r_ij, r_eq, k_b)
mol.bonds.append(bond)
mol.bond_graph[at1][at2] = r_ij
mol.bond_graph[at2][at1] = r_ij
def GetBonds(records, atoms):
"""Parses bond records into an array of Bond objects.
Args:
records (str**): 2d array of strings from lines of prm file.
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
Returns:
bonds (mmlib.molecule.Bond*): Array of Bond objects with parameters from
records.
"""
bonds = []
for record in records:
if not record[0].upper() == 'BOND':
continue
at1, at2 = [x - 1 for x in list(map(int, record[1:3]))]
k_b, r_eq = list(map(float, record[3:5]))
c1, c2 = [atoms[i].coords for i in [at1, at2]]
r_ij = geomcalc.GetRij(c1, c2)
bonds.append(molecule.Bond(at1, at2, r_ij, r_eq, k_b))
return bonds
def GetBonds(mol):
"""Determine covalently bonded atoms from bond graph and get parameters.
Search bond graph for bonded atom pairs, and parameter tables for mm
parameters. Use to create a new Bond object and append to Molecule.
Args:
mol (mmlib.molecule.Molecule): Molecule object with bond graph of atom pairs
within covalent radius cutoff threshold.
"""
for i in range(mol.n_atoms):
at1 = mol.atoms[i]
for j in mol.bond_graph[i].keys():
at2 = mol.atoms[j]
if i >= j:
r_ij = mol.bond_graph[i][j]
k_b, r_eq = param.GetBondParam(at1.type_, at2.type_)
if k_b > 0.0:
mol.bonds.append(molecule.Bond(i, j, r_ij, r_eq, k_b))
mol.bonds = sorted(mol.bonds, key=lambda b: b.at2)
mol.bonds = sorted(mol.bonds, key=lambda b: b.at1)
mol.n_bonds = len(mol.bonds)
def testArbitrary(self):
"""Asserts correct Bond object for arbitrary input parameters."""
param = ['BOND', '455', '27', '8.484', '6.63']
test.assertObjectEqual(self, fileio.GetBondFromPrm(param),
molecule.Bond(454, 26, 8.484, 6.63))
def testSmallestValues(self):
"""Asserts correct Bond object for smallest allowed values."""
param = ['BOND', '1', '2', '0.000001', '0.000001']
test.assertObjectEqual(self, fileio.GetBondFromPrm(param),
molecule.Bond(0, 1, 0.000001, 0.000001))