GromacsGroFile¶
- class 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.
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.
- 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
