Topology¶

This class stores the information about your system’s topology, similarly to the topology file in Gromacs.

API Reference¶

class pmx.forcefield.Topology(filename, is_itp=None, ff=None, assign_types=True, self_contained=False, version='new')¶

Topology class.

Parameters

filename (str) – topology file
is_itp (bool) – whether the topology provided is an itp file. If not provided, this is automatically determined by the file extension (.itp vs .top).
assign_types (bool) – whether to assign types for the atoms in the Topology. Default is True.
self_contained (bool) – Whether the file contains all bonded and non-bonded parameters needed to simulate the system. This can be the case for some small-molecule topologies. If this is set to true, atomtypes are assigned to each atom without looking for a forcefield file.
ff (str, optional) – force field to use. If not provided, it is determined based on the forcefield.itp include statement in the top file. If you are providing an itp file without a reference to the force field, assign_types is True, and self_contained is False, then you have to provide a force field name, so that pmx will know where to look to assign atom and bond types.
version (str?) – what is version? is it still needed?

filename¶

name of the input topology file

Type: str

forcefield¶

forcefield included in the topology file, if present

Type: str

is_itp¶

whether the Topology is an itp file rather than top

Type: bool

include_itps¶

list of itp files included in the topology file, if present

Type: list

nrexcl¶

number of bonds between atoms from which to exclude interactions. See Gromacs manual.

Type: int

atoms¶

list of atoms

Type: list

residues¶

list of residues

Type: list

bonds¶

list of bonds

Type: list

have_constraints¶

whether constraints are present

Type: bool

constrains¶

list of constraints

Type: list

pairs¶

list of pairs

Type: list

cmap¶

list of cmap

Type: list

angles¶

list of angles

Type: list

dihedrals¶

list of dihedrals

Type: list

has_vsites2¶

whether vsites2 are present

Type: bool

has_vsites3¶

whether vsites3 are present

Type: bool

has_vsites4¶

whether vsites4 are present

Type: bool

virtual_sites2¶

list of vsites2

Type: list

virtual_sites3¶

list of vsites3

Type: list

virtual_sites4¶

list of vsites4

Type: list

has_posre¶

whether position restraints are present

Type: bool

posre¶

list of position restraints

Type: list

molecules¶

list of molecules

Type: list

system¶

name of system

Type: str

qA¶

net charge of state A

Type: float

qB¶

net charge of state B

Type: float

Methods

`write`(outfile[, stateBonded, stateTypes, …])	Writes the Topology to file.
`get_qA`()	Returns the total charge of state A.
`get_qB`()	Returns the total charge of state B.
`get_hybrid_qA`()	Returns the charge of state A for hybrid residues only.
`get_hybrid_qB`()	Returns the charge of state B for hybrid residues only.