mdtraj.formats.GroTrajectoryFile

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

Interface for reading and writing to GROMACS GRO files.

Parameters:
  • filename (path-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_overwrite (bool) – If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?

  • top (mdtraj.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

n_atoms

The number of atoms in the file

Type:

int

topology

The topology. TODO(rmcgibbo) note about chain

Type:

md.Topology

See also

load_gro

High-level wrapper that returns a md.Trajectory

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)[source]

Methods

__init__(filename[, mode, force_overwrite, top])

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