def parse(self, **kwargs):
pbmol = next(pybel.readfile('cif', self.filename))
unpack_symmetry(pbmol)
natoms = len(pbmol.atoms)
names = np.zeros(natoms, dtype=object)
charges = np.zeros(natoms, dtype=np.float32)
masses = np.zeros(natoms, dtype=np.float64)
for i, atom in enumerate(pbmol.atoms):
names[i] = atom.type
masses[i] = atom.exactmass
charges[i] = atom.partialcharge
attrs = [
Atomnames(names),
Charges(charges),
Masses(masses),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(['SYSTEM'], dtype=object)),
]
return Topology(natoms, 1, 1, attrs=attrs)
def parse(self):
"""
Access ESPResSo data and return the topology object
Returns
-------
top : :class:`MDAnalysis.core.topology.Topology`
a topology object
"""
espresso = self.kwargs['espresso']
names = []
atomtypes = []
masses = []
charges = []
for p in espresso.part:
names.append("A" + repr(p.type))
atomtypes.append("T" + repr(p.type))
masses.append(p.mass)
charges.append(p.q)
natoms = len(espresso.part)
attrs = [
Atomnames(np.array(names, dtype=object)),
Atomids(np.arange(natoms) + 1),
Atomtypes(np.array(atomtypes, dtype=object)),
Masses(masses),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(['System'], dtype=object)),
AltLocs(np.array([' '] * natoms, dtype=object)),
Resnames(np.array(['R'], dtype=object)),
Occupancies(np.zeros(natoms)),
Tempfactors(np.zeros(natoms)),
ICodes(np.array([' '], dtype=object)),
Charges(np.array(charges)),
]
top = Topology(natoms, 1, 1, attrs=attrs)
return top
atoms = mol.getAtoms()
for atom in atoms:
charge = atom._sire_object.property("charge").value()
if mol.getResidues()[0].name() == 'LIG':
charge = (1 - L) * charge
charges.append(charge)
#sys.exit(-1)
#creating the universe
u = MDAnalysis.Universe(PRM7, DCD)
# select solute atoms
#selection = u.select_atoms('resname LIG')
#to include ions we should use
selection = u.select_atoms('not resname WAT')
# construct restricted ligand or complex Universe
system_u = MDAnalysis.core.universe.Merge(selection)
system_u.add_TopologyAttr(Radii(rads))
system_u.add_TopologyAttr(Charges(charges))
# write pqr file
system_u.atoms.write('../../pqr_snapshots/rad_bss/LIG_opt_free_L_' +
str(L) + '.pqr')
os.chdir("../")
radO, radC, radO, radC, radC, radC, radC, radC, radC, radO3, radC, radO4,
radC, radH, radH, radH, radH, radH, radH, radH
]
ligand_u.add_TopologyAttr(Radii(rad))
# how to customize the charges
topo = MDAnalysis.topology.TOPParser.TOPParser("input/SYSTEM.top")
topology_parsed = topo.parse()
tab_charges = topology_parsed.charges.values
first_charges = []
for i in range(len(selection)):
first_charges.append(tab_charges[i])
lambda_charges = []
for charge in first_charges:
lambda_charges.append(charge * (1 - L))
ligand_u.add_TopologyAttr(Charges(lambda_charges))
# write pqr file
ligand_u.atoms.write('pqr_snapshots/LIG_free_1st_L_' + str(L) + '.pqr',
frames=[0])
def parse(self):
"""
Access ESPResSo data and return the topology object.
Returns
-------
top : :class:`MDAnalysis.core.topology.Topology`
a topology object
"""
espresso = self.kwargs['espresso']
names = []
atomtypes = []
masses = []
charges = []
bonds = []
angles = []
dihedrals = []
for p in espresso.part:
names.append("A" + repr(p.type))
atomtypes.append("T" + repr(p.type))
masses.append(p.mass)
charges.append(p.q)
for bond in p.bonds:
partner_ids = bond[1:]
n_partner = len(partner_ids)
if n_partner == 1:
bonds.append((p.id, partner_ids[0]))
elif n_partner == 2:
angles.append((partner_ids[0], p.id, partner_ids[1]))
elif n_partner == 3:
dihedrals.append(
(partner_ids[0], p.id, partner_ids[1], partner_ids[2]))
else:
continue
natoms = len(espresso.part)
attrs = [
Atomnames(np.array(names, dtype=object)),
Atomids(np.arange(natoms) + 1),
Atomtypes(np.array(atomtypes, dtype=object)),
Masses(masses),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(['System'], dtype=object)),
AltLocs(np.array([' '] * natoms, dtype=object)),
Resnames(np.array(['R'], dtype=object)),
Occupancies(np.zeros(natoms)),
Tempfactors(np.zeros(natoms)),
ICodes(np.array([' '], dtype=object)),
Charges(np.array(charges)),
Bonds(bonds),
Angles(angles),
Dihedrals(dihedrals)
]
top = Topology(natoms, 1, 1, attrs=attrs)
return top