def _generate_aa_wat(residue, molidx, sysdata, include):
n = len(sysdata.atoms)
charges = [-0.834, 0.417, 0.417]
mass = [9.9514, 3.024, 3.024]
nt = len(include.masses)
types = [nt - 1, nt, nt]
for i, ratom in enumerate(residue.atoms):
atom = lammps.Atom()
atom.idx = n + i + 1
atom.set_xyz(ratom.xyz)
atom.molecule = molidx
atom.q = charges[i]
atom.atype = types[i]
atom.comment = "# water"
atom.diameter = 0.0
atom.density = mass[i]
atom.set_mu([0.0, 0.0, 0.0])
sysdata.atoms.append(atom)
nb = len(include.bondparams)
b = lammps.Connectivity(record="%d %d %d %d" %
(len(sysdata.bonds) + 1, nb, n + 1, n + 2))
b.comment = "# O-H bond"
sysdata.bonds.append(b)
b = lammps.Connectivity(record="%d %d %d %d" %
(len(sysdata.bonds) + 1, nb, n + 1, n + 3))
b.comment = "# O-H bond"
sysdata.bonds.append(b)
na = len(include.angleparams)
a = lammps.Connectivity(record="%d %d %d %d %d" %
(len(sysdata.angles) + 1, na, n + 2, n + 1, n + 3))
a.comment = "# H-O-H angle"
sysdata.angles.append(a)
def _generate_aa_residue(residue, molidx, resdata, sysdata):
"""
Generates an aa residue by copying most of the structure
from a datafile template, but the coordinates from a PDB residue
"""
n = len(sysdata.atoms)
for i, (ratom, datom) in enumerate(zip(residue.atoms, resdata.atoms)):
atom = copy.deepcopy(datom)
atom.idx = atom.idx + n
atom.set_xyz(ratom.xyz)
atom.molecule = molidx
sysdata.atoms.append(atom)
for bond in resdata.bonds:
b = lammps.Connectivity(
record="%d %d %d %d" %
(len(sysdata.bonds) + 1, bond[0], bond[1] + n, bond[2] + n))
sysdata.bonds.append(b)
for angle in resdata.angles:
a = lammps.Connectivity(record="%d %d %d %d %d" %
(len(sysdata.angles) + 1, angle[0],
angle[1] + n, angle[2] + n, angle[3] + n))
sysdata.angles.append(a)
for dihedral in resdata.dihedrals:
a = lammps.Connectivity(
record="%d %d %d %d %d %d" %
(len(sysdata.dihedrals) + 1, dihedral[0], dihedral[1] + n,
dihedral[2] + n, dihedral[3] + n, dihedral[4] + n))
sysdata.dihedrals.append(a)
def _make_cyclohexanedata(atoms, box, ligands, infilename):
"""
Make a datafile for a CG box with cyclohexane molecules
"""
outdata = lammps.Datafile()
c1_atoms = atoms[::18] # Map to first carbon
c2_atoms = atoms[1::18] # Map to second carbon
c3_atoms = atoms[3::18] # Map to fourth carbon
for i, (c1atom, c2atom,
c3atom) in enumerate(zip(c1_atoms, c2_atoms, c3_atoms)):
aatoms = [c1atom, c2atom, c3atom]
for j in range(3):
cgatom = lammps.Atom()
cgatom.idx = i * 3 + j + 1
cgatom.atype = 6
cgatom.set_xyz(aatoms[j].xyz)
cgatom.charge = 0
cgatom.set_mu([0, 0, 0])
cgatom.diameter = 4.5
cgatom.density = 0.9
cgatom.kind = "cg"
cgatom.molecule = i + 1
outdata.atoms.append(cgatom)
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 1, i * 3 + 2)))
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 1, i * 3 + 3)))
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 3, i * 3 + 2)))
outdata.atomtypes = [None] * 6
outdata.bondtypes = [None] * 5
outdata.angletypes = [None] * 5
outdata.box = np.array(box, copy=True)
outdata.title = "Converted to CG with convert_aa.py from %s" % os.path.basename(
infilename)
outdata.write("data.%s-chexanebox" % ligand)