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       0     CYS        0
1       1  CH3       C       0     CYS        0
2       2   H2       H       0     CYS        0
3       3   H3       H       0     CYS        0
4       4    C       C       0     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       0     CYSS        0
1       1  CH3       C       0     CYSS        0
2       2   H2       H       0     CYSS        0
3       3   H3       H       0     CYSS        0
4       4    C       C       0     CYSS        0
>>> t2 = md.Topology.from_dataframe(table, bonds)

Attributes

`chains`	Iterator over all Chains in the Topology.
`residues`	Iterator over all Residues in the Topology.
`atoms`	Iterator over all Atoms in the Topology.

__init__()¶: Create a new Topology object

Methods

`__init__`()	Create a new Topology object
`add_atom`(name, element, residue)	Create a new Atom and add it to the Topology.
`add_bond`(atom1, atom2)	Create a new bond and add it to the Topology.
`add_chain`()	Create a new Chain and add it to the Topology.
`add_residue`(name, chain[, resSeq])	Create a new Residue and add it to the Topology.
`atom`(index)	Get a specific atom by index.
`chain`(index)	Get a specific chain by index.
`copy`()	Return a copy of the topology
`create_disulfide_bonds`(positions)	Identify disulfide bonds based on proximity and add them to the Topology.
`create_standard_bonds`()	Create bonds based on the atom and residue names for all standard residue types.
`from_dataframe`(atoms[, bonds])	Create a mdtraj topology from a pandas data frame
`from_openmm`(value)	Create a mdtraj topology from an OpenMM topology
`join`(other)	Join two topologies together
`residue`(index)	Get a specific residue by index.
`subset`(atom_indices)	Create a new Topology from a subset of the atoms in an existing topology.
`to_dataframe`()	Convert this topology into a pandas dataframe
`to_openmm`()	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_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.

copy()¶

Return a copy of the topology

Returns:

out : Topology

A copy of this topology

join(other)¶

Join two topologies together

Parameters:

other : Topology

Another topology object

Returns:

out : Topology

A joint topology, with all of the atoms/residues/chains/bonds in each of the individual topologies

to_openmm()¶

Convert this topology into OpenMM topology

Returns:

topology : simtk.openmm.app.Topology

This topology, as an OpenMM topology

classmethod from_openmm(value)¶

Create a mdtraj topology from an OpenMM topology

Parameters:

value : simtk.openmm.app.Topology

An OpenMM topology that you wish to convert to a mdtraj topology.

to_dataframe()¶

Convert this topology into a pandas dataframe

Returns:

atoms : pandas.DataFrame

The atoms in the topology, represented as a data frame.

bonds : np.ndarray

The bonds in this topology, represented as an n_bonds x 2 array of the indices of the atoms involved in each bond.

classmethod from_dataframe(atoms, bonds=None)¶

Create a mdtraj topology from a pandas data frame

Parameters:

atoms : pandas.DataFrame

The atoms in the topology, represented as a data frame. This data frame should have columns “serial” (atom index), “name” (atom name), “element” (atom’s element), “resSeq” (index of the residue) “resName” (name of the residue), “chainID” (index of the chain), following the same conventions as wwPDB 3.0 format.

bonds : np.ndarray, shape=(n_bonds, 2), dtype=int, optional

The bonds in the topology, represented as an n_bonds x 2 array of the indices of the atoms involved in each bond. Specifiying bonds here is optional. To create standard protein bonds, you can use create_standard_bonds to “fill in” the bonds on your newly created Topology object