Topology

Topology definition

Topology([molecules, numbers, cell])	A topology is a combination of molecules and unit cell.
Atom([name])	An atom is a particle in simulation.
Molecule([name])	A molecule is defined as atoms and the connectivity between them.
Residue([name])	A residue is a group of consecutive atoms, e.g.
UnitCell([box])	UnitCell represents the periodic boundary condition of simulation system.

Connectivity

Bond(atom1, atom2[, order])	A bond between two atoms.
Angle(atom1, atom2, atom3)	A angle between three atoms.
Dihedral(atom1, atom2, atom3, atom4)	A dihedral between four atoms.
Improper(atom1, atom2, atom3, atom4)	An improper between four atoms.

Virtual site

VirtualSite()	Base class for virtual site definitions.
TIP4PSite(parents, parameters)	A virtual site used in TIP4P model.

Topology parser

Psf(file, **kwargs)	Generate Topology from NAMD-variant (space-delimited instead of column-based) PSF file.
LammpsData(file[, improper_center])	Generate topology from Lammps data file.
Pdb(file, **kwargs)	Generate Topology from PDB file.
Zmat(file, **kwargs)	Generate Topology from ZMAT file.
Smi(file, **kwargs)	Generate Topology from SMI file.
GroTopology(file, **kwargs)	Generate Topology from GRO file.
XyzTopology(file, **kwargs)	Generate Topology from XYZ file.