def _topology_from_arrays(AtomID, AtomNames, ChainID, ResidueID, ResidueNames):
"""Build topology object from the arrays stored in the lh5 file"""
# Delayed import due to wacky recursive imports in compatibilty
from mdtraj import Topology
topology = Topology()
# assert that the ChainID is just an array of empty strings, which appears
# to be the case in our test systems for this legacy format
if not np.all(chainid == '' for chainid in ChainID):
raise NotImplementedError('Im not prepared to parse multiple chains')
chain0 = topology.add_chain()
# register the residues
registered_residues = {}
for i in np.argsort(ResidueID):
residue_name = ResidueNames[i]
if not isinstance(residue_name, basestring):
residue_name = residue_name.decode()
if ResidueID[i] not in registered_residues:
res = topology.add_residue(residue_name, chain0)
registered_residues[ResidueID[i]] = res
# register the atoms
for i in np.argsort(AtomID):
atom_name = AtomNames[i]
if not isinstance(atom_name, basestring):
atom_name = atom_name.decode()
element_symbol = atom_name.lstrip('0123456789')[0]
element = mdtraj.pdb.element.get_by_symbol(element_symbol)
topology.add_atom(atom_name, element,
registered_residues[ResidueID[i]])
topology.create_standard_bonds()
return topology
def _topology_from_arrays(AtomID, AtomNames, ChainID, ResidueID, ResidueNames):
topology = Topology()
# assert that the ChainID is just an array of empty strings, which appears
# to be the case in our test systems for this legacy format
assert np.all(chainid == '' for chainid in ChainID), 'Im not prepaed to parse multiple chains'
chain0 = topology.add_chain()
# register the residues
registered_residues = {}
for i in np.argsort(ResidueID):
residue_name = ResidueNames[i]
if not isinstance(residue_name, str):
residue_name = residue_name.decode()
if ResidueID[i] not in registered_residues:
res = topology.add_residue(residue_name, chain0)
registered_residues[ResidueID[i]] = res
# register the atoms
for i in np.argsort(AtomID):
atom_name = AtomNames[i]
if not isinstance(atom_name, str):
atom_name = atom_name.decode()
element_symbol = atom_name.lstrip('0123456789')[0]
element = mdtraj.pdb.element.get_by_symbol(element_symbol)
topology.add_atom(atom_name, element,
registered_residues[ResidueID[i]])
topology.create_standard_bonds()
return topology
def _topology_from_arrays(AtomID, AtomNames, ChainID, ResidueID, ResidueNames):
"""Build topology object from the arrays stored in the lh5 file"""
# Delayed import due to wacky recursive imports in compatibilty
from mdtraj import Topology
topology = Topology()
# assert that the ChainID is just an array of empty strings, which appears
# to be the case in our test systems for this legacy format
if not np.all(chainid == '' for chainid in ChainID):
raise NotImplementedError('Im not prepared to parse multiple chains')
chain0 = topology.add_chain()
# register the residues
registered_residues = {}
for i in np.argsort(ResidueID):
residue_name = ResidueNames[i]
if not isinstance(residue_name, basestring):
residue_name = residue_name.decode()
if ResidueID[i] not in registered_residues:
res = topology.add_residue(residue_name, chain0)
registered_residues[ResidueID[i]] = res
# register the atoms
for i in np.argsort(AtomID):
atom_name = AtomNames[i]
if not isinstance(atom_name, basestring):
atom_name = atom_name.decode()
element_symbol = atom_name.lstrip('0123456789')[0]
try:
element = elem.get_by_symbol(element_symbol)
except KeyError:
element = None
topology.add_atom(atom_name, element,
registered_residues[ResidueID[i]])
topology.create_standard_bonds()
return topology