mdtraj.formats.GroTrajectoryFile

class mdtraj.formats.GroTrajectoryFile(filename, mode='r', force_overwrite=True, top=None)

Interface for reading and writing to GROMACS GRO files.

Parameters

filenamepath-like

The filename to open. A path to a file on disk.

mode{‘r’, ‘w’}

The mode in which to open the file, either ‘r’ for read or ‘w’ for write.

force_overwritebool

If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

topmdtraj.core.Topology, default=None

if you give a topology as input the topology won’t be parsed from the gro file it saves time if you have to parse a big number of files

See also

load_gro

High-level wrapper that returns a md.Trajectory

Attributes

n_atomsint

The number of atoms in the file

topologymd.Topology

The topology. TODO(rmcgibbo) note about chain

Methods

close()	Close the file
read([n_frames, stride, atom_indices])	Read data from a molecular dynamics trajectory in the GROMACS GRO format.
read_as_traj([n_frames, stride, atom_indices])	Read a trajectory from a gro file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(coordinates, topology[, time, …])	Write one or more frames of a molecular dynamics trajectory to disk in the GROMACS GRO format.

__init__(filename, mode='r', force_overwrite=True, top=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(filename[, mode, force_overwrite, top])	Initialize self.
close()	Close the file
read([n_frames, stride, atom_indices])	Read data from a molecular dynamics trajectory in the GROMACS GRO format.
read_as_traj([n_frames, stride, atom_indices])	Read a trajectory from a gro file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(coordinates, topology[, time, …])	Write one or more frames of a molecular dynamics trajectory to disk in the GROMACS GRO format.

Attributes

distance_unit