GromacsGroFile

class simtk.openmm.app.gromacsgrofile.GromacsGroFile(file)

GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it.

A .gro file also contains some topological information, such as elements and residue names, but not enough to construct a full Topology object. This information is recorded and stored in the object’s public fields.

__init__(file)

Load a .gro file.

The atom positions can be retrieved by calling getPositions().

Parameters:file (string) – the name of the file to load

Methods

__init__(file)	Load a .gro file.
getNumFrames()	Get the number of frames stored in the file.
getPeriodicBoxVectors([frame])	Get the vectors defining the periodic box.
getPositions([asNumpy, frame])	Get the atomic positions.
getUnitCellDimensions([frame])	Get the dimensions of the crystallographic unit cell.

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__

getNumFrames()

Get the number of frames stored in the file.

getPositions(asNumpy=False, frame=0)

Get the atomic positions.

Parameters:

• asNumpy (boolean=False) – if true, the values are returned as a numpy array instead of a list of Vec3s
• frame (int=0) – the index of the frame for which to get positions

getPeriodicBoxVectors(frame=0)

Get the vectors defining the periodic box.

Parameters:frame (int=0) – the index of the frame for which to get the box vectors

getUnitCellDimensions(frame=0)

Get the dimensions of the crystallographic unit cell.

Parameters:frame (int=0) – the index of the frame for which to get the unit cell dimensions