本文整理汇总了Python中mdtraj.core.topology.Topology类的典型用法代码示例。如果您正苦于以下问题：Python Topology类的具体用法？Python Topology怎么用？Python Topology使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Topology类的13个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
def __init__(self, topology):
self._ref_topology = topology.copy()
self._N_coeff = np.array([0.48318, 0.70328, -0.18643]) # CA_i-1, CA_i, O_i-1
self._C_coeff = np.array([0.44365, 0.23520, 0.32115]) # CA_i, CA_i+1, O_i
self._H_coeff = np.array([0.84100, 0.89296, -0.73389]) # CA_i-1, CA_i, O_i-1
newTopology = Topology()
CACBO_idxs = []; N_idxs = []; C_idxs = []; H_idxs = []
res_idx = 1
atm_idx = 0
prev_ca = None
prev_o = None
for chain in topology._chains:
newChain = newTopology.add_chain()
for residue in chain._residues:
newTopology, atm_idx, res_idx = self._add_residue(newTopology,
newChain, residue, chain, res_idx, atm_idx,
N_idxs, C_idxs, H_idxs, CACBO_idxs, prev_ca, prev_o)
self._CACBO_idxs = np.array(CACBO_idxs)
self._N_idxs = np.array(N_idxs)
self._C_idxs = np.array(C_idxs)
self._H_idxs = np.array(H_idxs)
self.topology = newTopology示例2: _initialize
def _initialize(self, simulation):
"""Deferred initialization of the reporter, which happens before
processing the first report.
At the time that the first report is processed, we now have access
to the simulation object, which we don't have at the point when the
reporter is instantiated
Parameters
----------
simulation : simtk.openmm.app.Simulation
The Simulation to generate a report for
"""
if self._atomSubset is not None:
if not min(self._atomSubset) >= 0:
raise ValueError('atomSubset must be zero indexed. '
'the smallest allowable value is zero')
if not max(self._atomSubset) < simulation.system.getNumParticles():
raise ValueError('atomSubset must be zero indexed. '
'the largest value must be less than the number '
'of particles in the system')
if not all(a==int(a) for a in self._atomSubset):
raise ValueError('all of the indices in atomSubset must be integers')
self._atomSlice = self._atomSubset
if hasattr(self._traj_file, 'topology'):
self._traj_file.topology = _topology_from_subset(
Topology.from_openmm(simulation.topology), self._atomSubset)
else:
self._atomSlice = slice(None)
if hasattr(self._traj_file, 'topology'):
self._traj_file.topology = Topology.from_openmm(simulation.topology)
system = simulation.system
if self._temperature:
# Compute the number of degrees of freedom.
dof = 0
for i in range(system.getNumParticles()):
if system.getParticleMass(i) > 0*units.dalton:
dof += 3
dof -= system.getNumConstraints()
if any(type(system.getForce(i)) == mm.CMMotionRemover for i in range(system.getNumForces())):
dof -= 3
self._dof = dof
if simulation.topology.getUnitCellDimensions() is None:
self._cell = False示例3: load_mol2
def load_mol2(filename):
"""Load a TRIPOS mol2 file from disk.
Parameters
----------
filename : str
Path to the prmtop file on disk.
Returns
-------
traj : md.Trajectory
The resulting topology, as an md.Topology object.
Notes
-----
This function should work on GAFF and sybyl style MOL2 files, but has
been primarily tested on GAFF mol2 files.
This function does NOT accept multi-structure MOL2 files!!!
The elements are guessed using GAFF atom types or via the atype string.
Examples
--------
>>> traj = md.load_mol2('mysystem.mol2')
"""
from mdtraj.core.trajectory import Trajectory
from mdtraj.core.topology import Topology
atoms, bonds = mol2_to_dataframes(filename)
atoms_mdtraj = atoms[["name", "resName"]].copy()
atoms_mdtraj["serial"] = atoms.index
#Figure out 1 letter element names
# IF this is a GAFF mol2, this line should work without issues
atoms_mdtraj["element"] = atoms.atype.map(gaff_elements)
# If this is a sybyl mol2, there should be NAN (null) values
if atoms_mdtraj.element.isnull().any():
# If this is a sybyl mol2, I think this works generally.
atoms_mdtraj["element"] = atoms.atype.apply(lambda x: x.strip(".")[0])
atoms_mdtraj["resSeq"] = np.ones(len(atoms), 'int')
atoms_mdtraj["chainID"] = np.ones(len(atoms), 'int')
if bonds is not None:
bonds_mdtraj = bonds[["id0", "id1"]].values
offset = bonds_mdtraj.min() # Should this just be 1???
bonds_mdtraj -= offset
else:
bonds_mdtraj = None
top = Topology.from_dataframe(atoms_mdtraj, bonds_mdtraj)
xyzlist = np.array([atoms[["x", "y", "z"]].values])
xyzlist /= 10.0 # Convert from angstrom to nanometer
traj = Trajectory(xyzlist, top)
return traj示例4: create_water_topology_on_disc
def create_water_topology_on_disc(n):
topfile = tempfile.mktemp('.pdb')
top = Topology()
chain = top.add_chain()
for i in xrange(n):
res = top.add_residue('r%i' % i, chain)
h1 = top.add_atom('H', hydrogen, res)
o = top.add_atom('O', oxygen, res)
h2 = top.add_atom('H', hydrogen, res)
top.add_bond(h1, o)
top.add_bond(h2, o)
xyz = np.zeros((n * 3, 3))
Trajectory(xyz, top).save_pdb(topfile)
return topfile示例5: mutate
def mutate(self, mut_res_idx, mut_new_resname):
"""Mutate residue
Parameters
----------
mut_res_idx : int
Index of residue to mutate.
mut_new_resname : str
Three-letter code of residue to mutate to.
"""
assert (self.topology.residue(mut_res_idx).name != mut_new_resname), "mutating the residue to itself!"
# Build new topology
newTopology = Topology()
for chain in self.topology.chains:
newChain = newTopology.add_chain()
for residue in chain._residues:
res_idx = residue.index
if res_idx == mut_res_idx:
# create mutated residue
self._add_mutated_residue(mut_new_resname, newTopology, newChain, res_idx, residue)
else:
# copy old residue atoms directly
newResidue = newTopology.add_residue(residue.name, newChain, res_idx)
for atom in residue.atoms:
newTopology.add_atom(atom.name,
md.core.element.get_by_symbol(atom.element.symbol),
newResidue, serial=atom.index)
# The bond connectivity should stay identical
for atm1, atm2 in self.topology._bonds:
new_atm1 = newTopology.atom(atm1.index)
new_atm2 = newTopology.atom(atm2.index)
newTopology.add_bond(new_atm1, new_atm2)
self._prev_topology = self.topology.copy()
self.topology = newTopology示例6: topology
def topology(self):
"""Get the topology out from the file
Returns
-------
topology : mdtraj.Topology
A topology object
"""
try:
raw = self._get_node('/', name='topology')[0]
if not isinstance(raw, string_types):
raw = raw.decode()
topology_dict = json.loads(raw)
except self.tables.NoSuchNodeError:
return None
topology = Topology()
for chain_dict in sorted(topology_dict['chains'], key=operator.itemgetter('index')):
chain = topology.add_chain()
for residue_dict in sorted(chain_dict['residues'], key=operator.itemgetter('index')):
try:
resSeq = residue_dict["resSeq"]
except KeyError:
resSeq = None
warnings.warn('No resSeq information found in HDF file, defaulting to zero-based indices')
try:
segment_id = residue_dict["segmentID"]
except KeyError:
segment_id = ""
residue = topology.add_residue(residue_dict['name'], chain, resSeq=resSeq, segment_id=segment_id)
for atom_dict in sorted(residue_dict['atoms'], key=operator.itemgetter('index')):
try:
element = elem.get_by_symbol(atom_dict['element'])
except KeyError:
element = elem.virtual
topology.add_atom(atom_dict['name'], element, residue)
atoms = list(topology.atoms)
for index1, index2 in topology_dict['bonds']:
topology.add_bond(atoms[index1], atoms[index2])
return topology示例7: topology
def topology(self):
"""Get the topology out from the file
Returns
-------
topology : mdtraj.Topology
A topology object
"""
try:
raw = self._get_node("/", name="topology")[0]
if not isinstance(raw, string_types):
raw = raw.decode()
topology_dict = json.loads(raw)
except self.tables.NoSuchNodeError:
return None
topology = Topology()
for chain_dict in sorted(topology_dict["chains"], key=operator.itemgetter("index")):
chain = topology.add_chain()
for residue_dict in sorted(chain_dict["residues"], key=operator.itemgetter("index")):
try:
resSeq = residue_dict["resSeq"]
except KeyError:
resSeq = None
warnings.warn("No resSeq information found in HDF file, defaulting to zero-based indices")
residue = topology.add_residue(residue_dict["name"], chain, resSeq=resSeq)
for atom_dict in sorted(residue_dict["atoms"], key=operator.itemgetter("index")):
try:
element = elem.get_by_symbol(atom_dict["element"])
except KeyError:
element = None
topology.add_atom(atom_dict["name"], element, residue)
atoms = list(topology.atoms)
for index1, index2 in topology_dict["bonds"]:
topology.add_bond(atoms[index1], atoms[index2])
return topology示例8: _read_models
def _read_models(self):
if not self._mode == 'r':
raise ValueError('file not opened for reading')
self._topology = Topology()
pdb = PdbStructure(self._file, load_all_models=True)
atomByNumber = {}
for chain in pdb.iter_chains():
c = self._topology.add_chain()
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBTrajectoryFile._residueNameReplacements:
resName = PDBTrajectoryFile._residueNameReplacements[resName]
r = self._topology.add_residue(resName, c, residue.number)
if resName in PDBTrajectoryFile._atomNameReplacements:
atomReplacements = PDBTrajectoryFile._atomNameReplacements[resName]
else:
atomReplacements = {}
for atom in residue.atoms:
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element is None:
element = self._guess_element(atomName, residue)
newAtom = self._topology.add_atom(atomName, element, r, serial=atom.serial_number)
atomByNumber[atom.serial_number] = newAtom
# load all of the positions (from every model)
_positions = []
for model in pdb.iter_models(use_all_models=True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.atoms:
coords.append(atom.get_position())
_positions.append(coords)
if not all(len(f) == len(_positions[0]) for f in _positions):
raise ValueError('PDB Error: All MODELs must contain the same number of ATOMs')
self._positions = np.array(_positions)
## The atom positions read from the PDB file
self._unitcell_lengths = pdb.get_unit_cell_lengths()
self._unitcell_angles = pdb.get_unit_cell_angles()
self._topology.create_standard_bonds()
self._topology.create_disulfide_bonds(self.positions[0])
# Add bonds based on CONECT records.
connectBonds = []
for connect in pdb.models[0].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(self._topology.bonds)
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
self._topology.add_bond(bond[0], bond[1])
existingBonds.add(bond)示例9: PDBTrajectoryFile
class PDBTrajectoryFile(object):
"""Interface for reading and writing Protein Data Bank (PDB) files
Parameters
----------
filename : str
The filename to open. A path to a file on disk.
mode : {'r', 'w'}
The mode in which to open the file, either 'r' for read or 'w' for write.
force_overwrite : bool
If opened in write mode, and a file by the name of `filename` already
exists on disk, should we overwrite it?
Attributes
----------
positions : np.ndarray, shape=(n_frames, n_atoms, 3)
topology : mdtraj.Topology
closed : bool
Notes
-----
When writing pdb files, mdtraj follows the PDB3.0 standard as closely as
possible. During *reading* however, we try to be more lenient. For instance,
we will parse common nonstandard atom names during reading, and convert them
into the standard names. The replacement table used by mdtraj is at
{mdtraj_source}/formats/pdb/data/pdbNames.xml.
See Also
--------
mdtraj.load_pdb : High-level wrapper that returns a ``md.Trajectory``
"""
distance_unit = 'angstroms'
_residueNameReplacements = {}
_atomNameReplacements = {}
_chain_names = [chr(ord('A') + i) for i in range(26)]
def __init__(self, filename, mode='r', force_overwrite=True):
self._open = False
self._file = None
self._topology = None
self._positions = None
self._mode = mode
self._last_topology = None
if mode == 'r':
PDBTrajectoryFile._loadNameReplacementTables()
if _is_url(filename):
self._file = urlopen(filename)
if filename.lower().endswith('.gz'):
if six.PY3:
self._file = gzip.GzipFile(fileobj=self._file)
else:
self._file = gzip.GzipFile(fileobj=six.StringIO(
self._file.read()))
if six.PY3:
self._file = six.StringIO(self._file.read().decode('utf-8'))
else:
if filename.lower().endswith('.gz'):
self._file = gzip.open(filename, 'r')
self._file = six.StringIO(self._file.read().decode('utf-8'))
else:
self._file = open(filename, 'r')
self._read_models()
elif mode == 'w':
self._header_written = False
self._footer_written = False
if os.path.exists(filename) and not force_overwrite:
raise IOError('"%s" already exists' % filename)
self._file = open(filename, 'w')
else:
raise ValueError("invalid mode: %s" % mode)
self._open = True
def write(self, positions, topology, modelIndex=None, unitcell_lengths=None,
unitcell_angles=None, bfactors=None):
"""Write a PDB file to disk
Parameters
----------
positions : array_like
The list of atomic positions to write.
topology : mdtraj.Topology
The Topology defining the model to write.
modelIndex : {int, None}
If not None, the model will be surrounded by MODEL/ENDMDL records
with this index
unitcell_lengths : {tuple, None}
Lengths of the three unit cell vectors, or None for a non-periodic system
unitcell_angles : {tuple, None}
Angles between the three unit cell vectors, or None for a non-periodic system
bfactors : array_like, default=None, shape=(n_atoms,)
Save bfactors with pdb file. Should contain a single number for
each atom in the topology
"""
if not self._mode == 'w':
raise ValueError('file not opened for writing')
if not self._header_written:
#.........这里部分代码省略.........
示例10: _to_topology
def _to_topology(self, atom_list, chain_types=None, residue_types=None):
"""Create a mdtraj.Topology from a Compound.
Parameters
----------
atom_list :
chain_types :
residue_types :
Returns
-------
top : mtraj.Topology
"""
if isinstance(chain_types, Compound):
chain_types = [Compound]
if isinstance(chain_types, (list, set)):
chain_types = tuple(chain_types)
if isinstance(residue_types, Compound):
residue_types = [Compound]
if isinstance(residue_types, (list, set)):
residue_types = tuple(residue_types)
top = Topology()
atom_mapping = {}
default_chain = top.add_chain()
default_residue = top.add_residue('RES', default_chain)
last_residue_compound = None
last_chain_compound = None
last_residue = None
last_chain = None
for atom in atom_list:
# Chains
for parent in atom.ancestors():
if chain_types and isinstance(parent, chain_types):
if parent != last_chain_compound:
last_chain_compound = parent
last_chain = top.add_chain()
last_chain_default_residue = top.add_residue('RES', last_chain)
last_chain.compound = last_chain_compound
break
else:
last_chain = default_chain
last_chain.compound = last_chain_compound
# Residues
for parent in atom.ancestors():
if residue_types and isinstance(parent, residue_types):
if parent != last_residue_compound:
last_residue_compound = parent
last_residue = top.add_residue(parent.__class__.__name__, last_chain)
last_residue.compound = last_residue_compound
break
else:
if last_chain != default_chain:
last_residue = last_chain_default_residue
else:
last_residue = default_residue
last_residue.compound = last_residue_compound
# Add the actual atoms
try:
elem = get_by_symbol(atom.name)
except KeyError:
elem = get_by_symbol("VS")
at = top.add_atom(atom.name, elem, last_residue)
at.charge = atom.charge
atom_mapping[atom] = at
# Remove empty default residues.
chains_to_remove = [chain for chain in top.chains if chain.n_atoms == 0]
residues_to_remove = [res for res in top.residues if res.n_atoms == 0]
for chain in chains_to_remove:
top._chains.remove(chain)
for res in residues_to_remove:
for chain in top.chains:
try:
chain._residues.remove(res)
except ValueError: # Already gone.
pass
for atom1, atom2 in self.bonds():
# Ensure that both atoms are part of the compound. This becomes an
# issue if you try to convert a sub-compound to a topology which is
# bonded to a different subcompound.
if all(a in atom_mapping.keys() for a in [atom1, atom2]):
top.add_bond(atom_mapping[atom1], atom_mapping[atom2])
return top示例11: load_hoomdxml
def load_hoomdxml(filename, top=None):
"""Load a single conformation from an HOOMD-Blue XML file.
For more information on this file format, see:
http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
Notably, all node names and attributes are in all lower case.
HOOMD-Blue does not contain residue and chain information explicitly.
For this reason, chains will be found by looping over all the bonds and
finding what is bonded to what.
Each chain consisists of exactly one residue.
Parameters
----------
filename : string
The path on disk to the XML file
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object, with corresponding
Topology.
Notes
-----
This function requires the NetworkX python package.
"""
from mdtraj.core.trajectory import Trajectory
from mdtraj.core.topology import Topology
topology = Topology()
tree = cElementTree.parse(filename)
config = tree.getroot().find('configuration')
position = config.find('position')
bond = config.find('bond')
atom_type = config.find('type') # MDTraj calls this "name"
box = config.find('box')
box.attrib = dict((key.lower(), val) for key, val in box.attrib.items())
# be generous for case of box attributes
lx = float(box.attrib['lx'])
ly = float(box.attrib['ly'])
lz = float(box.attrib['lz'])
try:
xy = float(box.attrib['xy'])
xz = float(box.attrib['xz'])
yz = float(box.attrib['yz'])
except:
xy = 0.0
xz = 0.0
yz = 0.0
unitcell_vectors = np.array([[[lx, xy*ly, xz*lz],
[0.0, ly, yz*lz],
[0.0, 0.0, lz ]]])
positions, types = [], {}
for pos in position.text.splitlines()[1:]:
positions.append((float(pos.split()[0]),
float(pos.split()[1]),
float(pos.split()[2])))
for idx, atom_name in enumerate(atom_type.text.splitlines()[1:]):
types[idx] = str(atom_name.split()[0])
if len(types) != len(positions):
raise ValueError('Different number of types and positions in xml file')
# ignore the bond type
bonds = [(int(b.split()[1]), int(b.split()[2])) for b in bond.text.splitlines()[1:]]
chains = _find_chains(bonds)
ions = [i for i in range(len(types)) if not _in_chain(chains, i)]
# add chains, bonds and ions (each chain = 1 residue)
for chain in chains:
t_chain = topology.add_chain()
t_residue = topology.add_residue('A', t_chain)
for atom in chain:
topology.add_atom(types[atom], 'U', t_residue)
for ion in ions:
t_chain = topology.add_chain()
t_residue = topology.add_residue('A', t_chain)
topology.add_atom(types[atom], 'U', t_residue)
for bond in bonds:
atom1, atom2 = bond[0], bond[1]
topology.add_bond(topology.atom(atom1), topology.atom(atom2))
traj = Trajectory(xyz=np.array(positions), topology=topology)
traj.unitcell_vectors = unitcell_vectors
return traj示例12: load_mol2
def load_mol2(filename):
"""Load a TRIPOS mol2 file from disk.
Parameters
----------
filename : str
Path to the prmtop file on disk.
Returns
-------
traj : md.Trajectory
The resulting topology, as an md.Topology object.
Notes
-----
This function should work on GAFF and sybyl style MOL2 files, but has
been primarily tested on GAFF mol2 files.
This function does NOT accept multi-structure MOL2 files!!!
The elements are guessed using GAFF atom types or via the atype string.
Examples
--------
>>> traj = md.load_mol2('mysystem.mol2')
"""
from mdtraj.core.trajectory import Trajectory
from mdtraj.core.topology import Topology, Single, Double, Triple, Aromatic, Amide
atoms, bonds = mol2_to_dataframes(filename)
atoms_mdtraj = atoms[["name", "resName"]].copy()
atoms_mdtraj["serial"] = atoms.index
#Figure out 1 letter element names
# IF this is a GAFF mol2, this line should work without issues
atoms_mdtraj["element"] = atoms.atype.map(gaff_elements)
# If this is a sybyl mol2, there should be NAN (null) values
if atoms_mdtraj.element.isnull().any():
# If this is a sybyl mol2, I think this works generally.
# Argument x is being passed as a list with only one element.
def to_element(x):
if isinstance(x, (list, tuple)):
assert len(x) == 1
x = x[0]
if '.' in x: # orbital-hybridizations in SYBL
return x.split('.')[0]
try:
# check if we can convert the whole str to an Element,
# if not, we only pass the first letter.
from mdtraj.core.element import Element
Element.getBySymbol(x)
except KeyError:
return to_element(x[0])
return x
atoms_mdtraj["element"] = atoms.atype.apply(to_element)
atoms_mdtraj["resSeq"] = np.ones(len(atoms), 'int')
atoms_mdtraj["chainID"] = np.ones(len(atoms), 'int')
bond_type_map = {
'1': Single,
'2': Double,
'3': Triple,
'am': Amide,
'ar': Aromatic
}
if bonds is not None:
bonds_mdtraj = bonds[["id0", "id1"]].values
offset = bonds_mdtraj.min() # Should this just be 1???
bonds_mdtraj -= offset
# Create the bond augment information
n_bonds = bonds_mdtraj.shape[0]
bond_augment = np.zeros([n_bonds, 2], dtype=float)
# Add bond type information
bond_augment[:, 0] = [float(bond_type_map[str(bond_value)]) for bond_value in bonds["bond_type"].values]
# Add Bond "order" information, this is not known from Mol2 files
bond_augment[:, 1] = [0.0 for _ in range(n_bonds)]
# Augment array, dtype is cast to minimal representation of float
bonds_mdtraj = np.append(bonds_mdtraj, bond_augment, axis=-1)
else:
bonds_mdtraj = None
top = Topology.from_dataframe(atoms_mdtraj, bonds_mdtraj)
xyzlist = np.array([atoms[["x", "y", "z"]].values])
xyzlist /= 10.0 # Convert from angstrom to nanometer
traj = Trajectory(xyzlist, top)
return traj示例13: __init__
def __init__(self, topology, use_chains=None):
if use_chains is None:
use_chains = range(len(topology._chains))
self._ref_topology = topology.copy()
# Build new topology
newTopology = Topology()
new_atm_idx = 0
res_idx = 1
prev_ca = None
ca_idxs = []
self._sidechain_idxs = []
self._sidechain_mass = []
self._chain_indices = []
for chain_count, chain in enumerate(topology._chains):
if chain_count in use_chains:
newChain = newTopology.add_chain()
for residue in chain._residues:
#resSeq = getattr(residue, 'resSeq', None) or residue.index
newResidue = newTopology.add_residue(residue.name, newChain, res_idx)
# map CA
new_ca = newTopology.add_atom('CA', md.core.element.get_by_symbol('C'),
newResidue, serial=new_atm_idx)
self._chain_indices.append(chain_count)
if prev_ca is None:
prev_ca = new_ca
else:
# only bond atoms in the same chain.
if new_ca.residue.chain.index == prev_ca.residue.chain.index:
newTopology.add_bond(prev_ca, new_ca)
prev_ca = new_ca
try:
ca_idxs.append([[ atm.index for atm in residue.atoms if \
(atm.name == "CA") ][0], new_atm_idx ])
except:
print(residue)
print(chain)
for atm in residue.atoms:
atm.name
raise
new_atm_idx += 1
if residue.name == 'GLY':
self._sidechain_idxs.append([])
self._sidechain_mass.append([])
else:
# map CB
cb_name = "CB%s" % atom_types.residue_code[residue.name]
new_cb = newTopology.add_atom(cb_name, md.core.element.get_by_symbol('C'),
newResidue, serial=new_atm_idx)
self._chain_indices.append(chain_count)
newTopology.add_bond(new_cb, new_ca)
self._sidechain_idxs.append([[ atm.index for atm in residue.atoms if \
(atm.is_sidechain) and (atm.element.symbol != "H") ], new_atm_idx ])
self._sidechain_mass.append(np.array([ atm.element.mass for atm in residue.atoms if \
(atm.is_sidechain) and (atm.element.symbol != "H") ]))
new_atm_idx += 1
res_idx += 1
self._ca_idxs = np.array(ca_idxs)
self.topology = newTopology
assert self.topology.n_atoms == len(self._chain_indices)