Classes for reading and writing of Gromacs TRR trajectories together with supporting code.
Note
Users should access classes from MDAnalysis.coordinates.TRR.
See also
MDAnalysis.coordinates.xdrfile.libxdrfile2 for low-level bindings to the Gromacs trajectory file formats
Timestep for a Gromacs TRR trajectory.
The Timestep can be initialized with arg being
- an integer (the number of atoms)
- another Timestep instance, in which case a copy is made; attention: loss of attributes that do not exist within the TRR Timestep may occur;
- a numpy.ndarray of shape (numatoms, 3) (for positions only) or (numatoms, 9) (for positions, velocities, and forces): positions = arg[:,:3], velocities = arg[:,3:6], and forces = arg[:,6:].
The constructor also takes the named arguments has_x, has_v, and has_f, which are used to set the Timestep flags has_x, has_v, and has_f, described below. Depending on the arg use-case above, the defaults set for these flags will vary:
- when arg is an integer has_x defaults to True and has_v and has_f to False.
- when arg is another Timestep instance the flags will default to being copied from the passed Timestep. If that instance has no ‘has_*’ flags the behavior is to assign them to True depending on the existence of _velocities and _forces (_pos is assumed to always be there, so in this case has_x defaults to True).
- when arg is a numpy array, the default flags will reflect what information is passed in the array.
TRR Timestep objects are now fully aware of the existence or not of coordinate/velocity/force information in frames, reflected in the has_x, has_v, and has_f flags. Accessing either kind of information while the corresponding flag is set to False wil raise a NoDataError. Internally, however, the arrays are always populated, even when the flags are False; upon creation of a Timestep they are zero-filled, but this might not always be the case later on for properties flagged as False if the same Timestep instance is used to read from a TRR frame.
When doing low-level writing to _pos, _velocities, or The TRR :class:`Timestep constructor allows for the named boolean arguments has_x, has_v, and has_f to be passed for automatic setting of the corresponding flag. An exception to this is assignment to the full property array thus:
ts = MDAnalysis.coordinates.TRR.Timestep(N) # N being the number of atoms
ts._velocities = vel_array # Where vel_array is an existing array of shape (N, DIM)
# This will also automatically set 'has_v' to True.
Attempting to populate the array instead will, however, raise a NoDataError exception:
ts = MDAnalysis.coordinates.TRR.Timestep(N) # N being the number of atoms
ts._velocities[:] = vel_array # This will fail if 'has_v' hasn't been set to True.
Changed in version 0.8.0: TRR Timestep objects are now fully aware of the existence or not of coordinate/velocity/force information in frames.
Make a new Timestep containing a subset of the original Timestep.
ts.copy_slice(slice(start, stop, skip)) ts.copy_slice([list of indices])
Returns: | A Timestep object of the same type containing all header information and all atom information relevent to the selection. |
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Note
The selection must be a 0 based slice or array of the atom indices in this Timestep
New in version 0.8.
unitcell dimensions (A, B, C, alpha, beta, gamma)
volume of the unitcell
Read a Gromacs TRR trajectory.
Changed in version 0.8.0: Timestep objects returned from TRR files now have has_x, has_v, and has_f flags reflecting whether coordinates/velocities/forces were read. Attempting to access such data when the corresponding flag is set to False will raise a NoDataError.
Arguments: |
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Keywords: |
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Changed in version 0.9.0: New keyword refresh_offsets
Returns a writer appropriate for filename.
Sets the default keywords start, step and delta (if available). numatoms is always set from Reader.numatoms.
See also
Reader.Writer() and MDAnalysis.Writer()
Returns a Gromacs TrjWriter for filename with the same parameters as this trajectory.
All values can be changed through keyword arguments.
Arguments: |
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Keywords: |
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Returns: | appropriate TrjWriter |
Close xdr trajectory file if it was open.
Specific implementation of trajectory closing.
In-place conversion of forces array force from native units to base units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
In-place conversion of force array force from base units to native units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
In-place conversion of coordinate array x from native units to base units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Conversion of coordinate array x from base units to native units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Convert time t from native units to base units.
By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Convert time t from base units to native units.
By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
In-place conversion of velocities array v from native units to base units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
In-place conversion of coordinate array v from base units to native units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
Time step length in ps.
The result is computed from the trajectory and cached. If for any reason the trajectory cannot be read then 0 is returned.
Time between two trajectory frames in picoseconds.
Frame number of the current time step.
This is a simple short cut to Timestep.frame.
Loads current trajectory offsets from pickled filename.
Checks if ctime and size of trajectory file matches that stored in pickled filename. If either one does not match (and check == True) then the offsets are not loaded. This is intended to conservatively avoid loading out-of-date offsets.
Arguments: |
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Keywords: |
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Raises: | IOError if the file cannot be read (see open()). |
Forward one step to next frame.
The number of publically available atoms that this reader will store in the timestep.
If ‘sub’ was not given in the ctor, then this value will just be the actual number of atoms in the underlying trajectory file. If however ‘sub’ was given, then this value is the number specified by the ‘sub’ sub-selection.
If for any reason the trajectory cannot be read then a negative value is returned.
Read the number of frames from the trajectory.
The result is cached. If for any reason the trajectory cannot be read then 0 is returned.
This takes a long time because the frames are counted by iterating through the whole trajectory. If the trajectory was previously loaded and saved offsets exist, then loading will be significantly faster.
See also
TrjReader.load_offsets() and TrjReader.save_offsets()
Open xdr trajectory file.
Returns: | pointer to XDRFILE (and sets self.xdrfile) |
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Raises: | IOError with code EALREADY if file was already opened or ENOENT if the file cannot be found |
Position at beginning of trajectory
Saves current trajectory offsets into filename, as a pickled object.
Along with the offsets themselves, the ctime and file size of the trajectory file are also saved. These are used upon load as a check to ensure the offsets still match the trajectory they are being applied to.
Arguments: |
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Time of the current frame in MDAnalysis time units (typically ps).
time = Timestep.frame * Reader.dt
Total length of the trajectory numframes * dt.
Write a Gromacs TRR trajectory.
Create a new TrjWriter
Arguments: |
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Keywords: |
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Changed in version 0.8.0: The TRR writer is now able to write TRRs without coordinates/velocities/forces, depending on the properties available in the Timestep objects passed to write().
Specific implementation of trajectory closing.
Read dimensions from timestep ts and return Gromacs box vectors
In-place conversion of forces array force from native units to base units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
In-place conversion of force array force from base units to native units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
In-place conversion of coordinate array x from native units to base units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Conversion of coordinate array x from base units to native units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Convert time t from native units to base units.
By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
Convert time t from base units to native units.
By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
In-place conversion of velocities array v from native units to base units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
In-place conversion of coordinate array v from base units to native units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
Returns True if all values are within limit values of their formats.
Due to rounding, the test is asymmetric (and min is supposed to be negative):
min < x <= max
Arguments: |
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Returns: | boolean |