6.8. GRO file format — MDAnalysis.coordinates.GRO¶
Classes to read and write Gromacs GRO coordinate files; see the notes on the GRO format which includes a conversion routine for the box.
6.8.1. Writing GRO files¶
By default any written GRO files will renumber the atom ids to move sequentially from 1. This can be disabled, and instead the original atom ids kept, by using the reindex=False keyword argument. This is useful when writing a subsection of a larger Universe while wanting to preserve the original identities of atoms.
For example:
>>> u = mda.Universe()`
>>> u.atoms.write('out.gro', reindex=False)
# OR
>>> with mda.Writer('out.gro', reindex=False) as w:
... w.write(u.atoms)
6.8.2. Classes¶
-
class
MDAnalysis.coordinates.GRO.Timestep(n_atoms, **kwargs)[source]¶ Create a Timestep, representing a frame of a trajectory
Parameters: - n_atoms (int) – The total number of atoms this Timestep describes
- positions (bool, optional) – Whether this Timestep has position information [
True] - velocities (bool (optional)) – Whether this Timestep has velocity information [
False] - forces (bool (optional)) – Whether this Timestep has force information [
False] - reader (Reader (optional)) – A weak reference to the owning Reader. Used for when attributes require trajectory manipulation (e.g. dt)
- dt (float (optional)) – The time difference between frames (ps). If
timeis set, then dt will be ignored. - time_offset (float (optional)) – The starting time from which to calculate time (in ps)
Changed in version 0.11.0: Added keywords for positions, velocities and forces. Can add and remove position/velocity/force information by using the
has_*attribute.-
dimensions¶ unitcell dimensions (A, B, C, alpha, beta, gamma)
GRO:
8.00170 8.00170 5.65806 0.00000 0.00000 0.00000 0.00000 4.00085 4.00085
PDB:
CRYST1 80.017 80.017 80.017 60.00 60.00 90.00 P 1 1
XTC: c.trajectory.ts._unitcell:
array([[ 80.00515747, 0. , 0. ], [ 0. , 80.00515747, 0. ], [ 40.00257874, 40.00257874, 56.57218552]], dtype=float32)
-
class
MDAnalysis.coordinates.GRO.GROReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]¶ Reader for the Gromacs GRO structure format.
Note
This Reader will only read the first frame present in a file.
Changed in version 0.11.0: Frames now 0-based instead of 1-based
-
class
MDAnalysis.coordinates.GRO.GROWriter(filename, convert_units=True, n_atoms=None, **kwargs)[source]¶ GRO Writer that conforms to the Trajectory API.
- Will attempt to write the following information from the topology:
- atom name (defaults to ‘X’)
- resnames (defaults to ‘UNK’)
- resids (defaults to ‘1’)
Note
The precision is hard coded to three decimal places
Changed in version 0.11.0: Frames now 0-based instead of 1-based
Changed in version 0.13.0: Now strictly writes positions with 3dp precision. and velocities with 4dp. Removed the convert_dimensions_to_unitcell method, use Timestep.triclinic_dimensions instead. Now now writes velocities where possible.
Changed in version 0.18.0: Added reindex keyword argument to allow original atom ids to be kept.
Set up a GROWriter with a precision of 3 decimal places.
Parameters: - filename (str) – output filename
- n_atoms (int (optional)) – number of atoms
- convert_units (bool (optional)) – units are converted to the MDAnalysis base format; [
True] - reindex (bool (optional)) – By default, all the atoms were reindexed to have a atom id starting
from 1. [
True] However, this behaviour can be turned off by specifying reindex=False.
Note
To use the reindex keyword, user can follow the two examples given below.:
u = mda.Universe()
Usage 1:
u.atoms.write('out.gro', reindex=False)
Usage 2:
with mda.Writer('out.gro', reindex=False) as w: w.write(u.atoms)
-
fmt= {'box_orthorhombic': '{box[0]:10.5f} {box[1]:9.5f} {box[2]:9.5f}\n', 'box_triclinic': '{box[0]:10.5f} {box[4]:9.5f} {box[8]:9.5f} {box[1]:9.5f} {box[2]:9.5f} {box[3]:9.5f} {box[5]:9.5f} {box[6]:9.5f} {box[7]:9.5f}\n', 'n_atoms': '{0:5d}\n', 'xyz': '{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}\n', 'xyz_v': '{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f}\n'}¶ format strings for the GRO file (all include newline); precision of 3 decimal places is hard-coded here.
-
write(obj)[source]¶ Write selection at current trajectory frame to file.
Parameters: obj (AtomGroup or Universe) – Note
The GRO format only allows 5 digits for resid and atom number. If these numbers become larger than 99,999 then this routine will chop off the leading digits.
Changed in version 0.7.6: resName and atomName are truncated to a maximum of 5 characters
Changed in version 0.16.0: frame kwarg has been removed
Deprecated since version 1.0.0: Deprecated calling with Timestep, use AtomGroup or Universe. To be removed in version 2.0.
6.8.3. Developer notes: GROWriter format strings¶
The GROWriter class has a GROWriter.fmt attribute, which is a dictionary of different
strings for writing lines in .gro files. These are as follows:
n_atomsFor the first line of the gro file, supply the number of atoms in the system. E.g.:
fmt['n_atoms'].format(42)
xyzAn atom line without velocities. Requires that the ‘resid’, ‘resname’, ‘name’, ‘index’ and ‘pos’ keys be supplied. E.g.:
fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2, pos=(0.0, 1.0, 2.0))
xyz_v- As above, but with velocities. Needs an additional keyword ‘vel’.
box_orthorhombicThe final line of the gro file which gives box dimensions. Requires the box keyword to be given, which should be the three cartesian dimensions. E.g.:
fmt['box_orthorhombic'].format(box=(10.0, 10.0, 10.0))
box_triclinic- As above, but for a non orthorhombic box. Requires the box keyword, but this time as a length 9 vector. This is a flattened version of the (3,3) triclinic vector representation of the unit cell. The rearrangement into the odd gromacs order is done automatically.