mdtraj.Topology

class mdtraj.Topology

Topology stores the topological information about a system.

The structure of a Topology object is similar to that of a PDB file. It consists of a set of Chains (often but not always corresponding to polymer chains). Each Chain contains a set of Residues, and each Residue contains a set of Atoms. In addition, the Topology stores a list of which atom pairs are bonded to each other.

Atom and residue names should follow the PDB 3.0 nomenclature for all molecules for which one exists.

Examples

>>> topology = md.load('example.pdb').topology
>>> print(topology)
<mdtraj.Topology with 1 chains, 3 residues, 22 atoms, 21 bonds at 0x105a98e90>
>>> table, bonds = topology.to_dataframe()
>>> print(table.head())
   serial name element  resSeq resName  chainID
0       0   H1       H       1     CYS        0
1       1  CH3       C       1     CYS        0
2       2   H2       H       1     CYS        0
3       3   H3       H       1     CYS        0
4       4    C       C       1     CYS        0
>>> # rename residue "CYS" to "CYSS"
>>> table[table['residue'] == 'CYS']['residue'] = 'CYSS'
>>> print(table.head())
   serial name element  resSeq resName   chainID
0       0   H1       H       1     CYSS        0
1       1  CH3       C       1     CYSS        0
2       2   H2       H       1     CYSS        0
3       3   H3       H       1     CYSS        0
4       4    C       C       1     CYSS        0
>>> t2 = md.Topology.from_dataframe(table, bonds)

Attributes

chainsgenerator

Iterator over all Chains in the Topology.

residuesgenerator

Iterator over all Residues in the Topology.

atomsgenerator

Iterator over all Atoms in the Topology.

bondsgenerator

Iterator over all bonds (each represented as a tuple of two Atoms) in the Topology.

Methods

add_atom(self, name, element, residue[, serial])	Create a new Atom and add it to the Topology.
add_bond(self, atom1, atom2[, type, order])	Create a new bond and add it to the Topology.
add_chain(self)	Create a new Chain and add it to the Topology.
add_residue(self, name, chain[, resSeq, …])	Create a new Residue and add it to the Topology.
atom(self, index)	Get a specific atom by index.
atoms_by_name(self, name)	Iterator over all Atoms in the Topology with a specified name
chain(self, index)	Get a specific chain by index.
copy(self)	Return a copy of the topology
create_disulfide_bonds(self, positions)	Identify disulfide bonds based on proximity and add them to the Topology.
create_standard_bonds(self)	Create bonds based on the atom and residue names for all standard residue types.
delete_atom_by_index(self, index)	Delete an Atom from the topology.
find_molecules(self)	Identify molecules based on bonds.
from_dataframe(atoms[, bonds])	Create a mdtraj topology from a pandas data frame
from_openmm(value)	Create a mdtraj topology from an OpenMM topology
guess_anchor_molecules(self)	Guess anchor molecules for imaging
insert_atom(self, name, element, residue[, …])	Create a new Atom and insert it into the Topology at a specific position.
join(self, other)	Join two topologies together
residue(self, index)	Get a specific residue by index.
select(self, selection_string)	Execute a selection against the topology
select_atom_indices(self[, selection])	Get the indices of biologically-relevant groups by name.
select_expression(self, selection_string)	Translate a atom selection expression into a pure python expression.
select_pairs(self[, selection1, selection2])	Generate unique pairs of atom indices.
subset(self, atom_indices)	Create a new Topology from a subset of the atoms in an existing topology.
to_bondgraph(self)	Create a NetworkX graph from the atoms and bonds in this topology
to_dataframe(self)	Convert this topology into a pandas dataframe
to_fasta(self[, chain])	Convert this topology into FASTA string
to_openmm(self[, traj])	Convert this topology into OpenMM topology

__init__(self)

Create a new Topology object

Methods

__init__(self)	Create a new Topology object
add_atom(self, name, element, residue[, serial])	Create a new Atom and add it to the Topology.
add_bond(self, atom1, atom2[, type, order])	Create a new bond and add it to the Topology.
add_chain(self)	Create a new Chain and add it to the Topology.
add_residue(self, name, chain[, resSeq, …])	Create a new Residue and add it to the Topology.
atom(self, index)	Get a specific atom by index.
atoms_by_name(self, name)	Iterator over all Atoms in the Topology with a specified name
chain(self, index)	Get a specific chain by index.
copy(self)	Return a copy of the topology
create_disulfide_bonds(self, positions)	Identify disulfide bonds based on proximity and add them to the Topology.
create_standard_bonds(self)	Create bonds based on the atom and residue names for all standard residue types.
delete_atom_by_index(self, index)	Delete an Atom from the topology.
find_molecules(self)	Identify molecules based on bonds.
from_dataframe(atoms[, bonds])	Create a mdtraj topology from a pandas data frame
from_openmm(value)	Create a mdtraj topology from an OpenMM topology
guess_anchor_molecules(self)	Guess anchor molecules for imaging
insert_atom(self, name, element, residue[, …])	Create a new Atom and insert it into the Topology at a specific position.
join(self, other)	Join two topologies together
residue(self, index)	Get a specific residue by index.
select(self, selection_string)	Execute a selection against the topology
select_atom_indices(self[, selection])	Get the indices of biologically-relevant groups by name.
select_expression(self, selection_string)	Translate a atom selection expression into a pure python expression.
select_pairs(self[, selection1, selection2])	Generate unique pairs of atom indices.
subset(self, atom_indices)	Create a new Topology from a subset of the atoms in an existing topology.
to_bondgraph(self)	Create a NetworkX graph from the atoms and bonds in this topology
to_dataframe(self)	Convert this topology into a pandas dataframe
to_fasta(self[, chain])	Convert this topology into FASTA string
to_openmm(self[, traj])	Convert this topology into OpenMM topology

Attributes

atoms	Iterator over all Atoms in the Topology.
bonds	Iterator over all bonds (each represented as a tuple of two Atoms) in the Topology.
chains	Iterator over all Chains in the Topology.
n_atoms	Get the number of atoms in the Topology
n_bonds	Get the number of bonds in the Topology
n_chains	Get the number of chains in the Topology
n_residues	Get the number of residues in the Topology.
residues	Iterator over all Residues in the Topology.