Extension: | .edr |
---|
EDR files store per-frame information for gromacs trajectories. Examples of properties obtainable from EDR files are:
- temperature
- pressure
- density
- potential energy
- total energy
- etc.
To know which quantities are available in a certain edr file you can access the feature ‘avail quantity’:
>>> datafile('ener.edr').read('avail quantities')
['Temperature', 'Pressure', 'Potential', ...]
To get the frame information for a certain quantity you may use the “quantity” property passing the quantity as additional argument, this will return two arrays, the first is an array of times in ps and the second are the corrisponding quantities:
>>> time, temp = datafile('ener.edr').read('quantity', 'Temperature')
Features
Return an array of times in ps and the corresponding quantities at that times.
Return the available quantities in the file.
Return a dictionary where the keys are the quantities and the value are the units in which that quantity is expressed.
Return a dictionary where the keys are the quantities and the value are the units in which that quantity is expressed.
Extension: | .gro |
---|
Handler for .gro file format. Example at http://manual.gromacs.org/online/gro.html.
Features
Read the gro file and return a System instance. It also add the following exporting informations:
Write the syst System instance to disk. The export arrays should have the groname and grotype entries as specified in the read("system") method.
Example
Export informations for water SPC:
Molecule([
Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.033, 0.094, 0.0],export={'grotype':'HW2'})],
export={'groname': 'SOL'})
Extension: | .pdb |
---|
Starting implementation of a PDB file parser.
Note
This handler was developed as an example. If you like to contribute by implementing it you can write an email to the mailing list.
Features
Read the pdb file as a huge Molecule.
Read the pdb file as a System, where each residue is a molecule.
Extension: | .xtc |
---|
Reader for GROMACS XTC trajectories.
Features
Read the frames from the file and returns the trajectory as an array of times and an array of atomic positions:
>>> times, positions = datafile('traj.xtc').read('trajectory')
[t1, t2, t3], [pos1, pos2, ...]
positions is a list of np.ndarray(n_atoms, 3).
Extension: | .xyz |
---|