5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD

Classes to read and write DCD binary trajectories, the format used by CHARMM, NAMD, and also LAMMPS. Trajectories can be read regardless of system-endianness as this is auto-detected.

Generally, DCD trajectories produced by any code can be read (with the DCDReader) although there can be issues with the unitcell (simulation box) representation (see Timestep.dimensions). DCDs can also be written but the DCDWriter follows recent NAMD/VMD convention for the unitcell but still writes AKMA time. Reading and writing these trajectories within MDAnalysis will work seamlessly but if you process those trajectories with other tools you might need to watch out that time and unitcell dimensions are correctly interpreted.

Note

The DCD file format is not well defined. In particular, NAMD and CHARMM use it differently. Currently, MDAnalysis tries to guess the correct format for the unitcell representation but it can be wrong. Check the unitcell dimensions, especially for triclinic unitcells (see Issue 187 and Timestep.dimensions). A second potential issue are the units of time which are AKMA for the DCDReader (following CHARMM) but ps for NAMD. As a workaround one can employ the configurable MDAnalysis.coordinates.LAMMPS.DCDReader for NAMD trajectories.

See also

The MDAnalysis.coordinates.LAMMPS module provides a more flexible DCD reader/writer.

The classes in this module are the reference implementations for the Trajectory API.

5.3.1. Classes

class MDAnalysis.coordinates.DCD.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 time is set, then dt will be ignored.
  • time_offset (float, optional) – The starting time from which to calculate time (ps)
  • versionchanged (.) – Added keywords for positions, velocities and forces Can add and remove position/velocity/force information by using the has_* attribute
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
copy()[source]

Make an independent (“deep”) copy of the whole Timestep.

copy_slice(sel)[source]

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 relevant to the selection.

Note

The selection must be a 0 based slice or array of the atom indices in this Timestep

New in version 0.8.

Changed in version 0.11.0: Reworked to follow new Timestep API. Now will strictly only copy official attributes of the Timestep.

dimensions

unitcell dimensions (A, B, C, alpha, beta, gamma)

lengths A, B, C are in the MDAnalysis length unit (Å), and angles are in degrees.

dimensions is read-only because it transforms the actual format of the unitcell (which differs between different trajectory formats) to the representation described here, which is used everywhere in MDAnalysis.

The ordering of the angles in the unitcell is the same as in recent versions of VMD’s DCDplugin (2013), namely the X-PLOR DCD format: The original unitcell is read as [A, gamma, B, beta, alpha, C] from the DCD file (actually, the direction cosines are stored instead of the angles but the underlying C code already does this conversion); if any of these values are < 0 or if any of the angles are > 180 degrees then it is assumed it is a new-style CHARMM unitcell (at least since c36b2) in which box vectors were recorded.

Warning

The DCD format is not well defined. Check your unit cell dimensions carefully, especially when using triclinic boxes. Different software packages implement different conventions and MDAnalysis is currently implementing the newer NAMD/VMD convention and tries to guess the new CHARMM one. Old CHARMM trajectories might give wrong unitcell values. For more details see Issue 187.

Changed in version 0.9.0: Unitcell is now interpreted in the newer NAMD DCD format as [A, gamma, B, beta, alpha, C] instead of the old MDAnalysis/CHARMM ordering [A, alpha, B, beta, gamma, C]. We attempt to detect the new CHARMM DCD unitcell format (see Issue 187 for a discussion).

dt

The time difference in ps between timesteps

Note

This defaults to 1.0 ps in the absence of time data

New in version 0.11.0.

forces

A record of the forces of all atoms in this Timestep

Setting this attribute will add forces to the Timestep if they weren’t originally present.

Returns:

  • A numpy.ndarray of shape (n_atoms, 3) of force data for each
  • atom

Raises:
  • class:MDAnalysis.NoDataError
  • When the Timestep does not contain force information
  • .. versionadded (: 0.11.0) –
from_coordinates(positions=None, velocities=None, forces=None, **kwargs)[source]

Create an instance of this Timestep, from coordinate data

Can pass position, velocity and force data to form a Timestep.

New in version 0.11.0.

from_timestep(other, **kwargs)[source]

Create a copy of another Timestep, in the format of this Timestep

New in version 0.11.0.

has_forces

A boolean of whether this Timestep has force data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

has_positions

A boolean of whether this Timestep has position data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

has_velocities

A boolean of whether this Timestep has velocity data

This can be changed to True or False to allocate space for or remove the data.

New in version 0.11.0.

n_atoms

A read only view of the number of atoms this Timestep has

Changed in version 0.11.0: Changed to read only property

positions

A record of the positions of all atoms in this Timestep

Setting this attribute will add positions to the Timestep if they weren’t originally present.

Returns:

  • A numpy.ndarray of shape (n_atoms, 3) of position data for each
  • atom

Raises:
  • class:MDAnalysis.exceptions.NoDataError
  • If the Timestep has no position data

Changed in version 0.11.0: Now can raise NoDataError when no position data present

time

The time in ps of this timestep

This is calculated as:

time = ts.data['time_offset'] + ts.time

Or, if the trajectory doesn’t provide time information:

time = ts.data['time_offset'] + ts.frame * ts.dt

New in version 0.11.0.

triclinic_dimensions

The unitcell dimensions represented as triclinic vectors

Returns:
Return type:A (3, 3) numpy.ndarray of unit cell vectors

Examples

The unitcell for a given system can be queried as either three vectors lengths followed by their respective angle, or as three triclinic vectors.

>>> ts.dimensions
array([ 13.,  14.,  15.,  90.,  90.,  90.], dtype=float32)
>>> ts.triclinic_dimensions
array([[ 13.,   0.,   0.],
       [  0.,  14.,   0.],
       [  0.,   0.,  15.]], dtype=float32)

Setting the attribute also works:

>>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]]
>>> ts.dimensions
array([ 15.        ,  15.81138802,  16.58312416,  67.58049774,
        72.45159912,  71.56504822], dtype=float32)

New in version 0.11.0.

velocities

A record of the velocities of all atoms in this Timestep

Setting this attribute will add velocities to the Timestep if they weren’t originally present.

Returns:

  • A numpy.ndarray of shape (n_atoms, 3) of velocity data for each
  • atom

Raises:
  • class:MDAnalysis.exceptions.NoDataError
  • When the Timestep does not contain velocity information

New in version 0.11.0.

volume

volume of the unitcell

class MDAnalysis.coordinates.DCD.DCDReader(dcdfilename, **kwargs)[source]

Reads from a DCD file

Data:
ts

Timestep object containing coordinates of current frame

``dcd = DCD(dcdfilename)``

open dcd file and read header

``len(dcd)``

return number of frames in dcd

``for ts in dcd

`` iterate through trajectory

``for ts in dcd[start

stop:skip]:`` iterate through a trajectory

``dcd[i]``

random access into the trajectory (i corresponds to frame number)

``data = dcd.timeseries(...)``

retrieve a subset of coordinate information for a group of atoms

``data = dcd.correl(...)``

populate a MDAnalysis.core.Timeseries.Collection object with computed timeseries

Note

The DCD file format is not well defined. In particular, NAMD and CHARMM use it differently. Currently, MDAnalysis tries to guess the correct format for the unitcell representation but it can be wrong. Check the unitcell dimensions, especially for triclinic unitcells (see Issue 187 and Timestep.dimensions). A second potential issue are the units of time (TODO).

Changed in version 0.9.0: The underlying DCD reader (written in C and derived from the catdcd/molfile plugin code of VMD) is now reading the unitcell in NAMD ordering: [A, B, C, sin(gamma), sin(beta), sin(alpha)]. See Issue 187 for further details.

Changed in version 0.11.0: Frames now 0-based instead of 1-based Native frame number read into ts._frame Removed skip keyword and functionality

OtherWriter(filename, **kwargs)

Returns a writer appropriate for filename.

Sets the default keywords start, step and dt (if available). n_atoms is always set from Reader.n_atoms.

See also

Reader.Writer() and MDAnalysis.Writer()

Writer(filename, **kwargs)[source]

Returns a DCDWriter for filename with the same parameters as this DCD.

All values can be changed through keyword arguments.

Parameters:

*filename* – filename of the output DCD trajectory

Keywords:
n_atoms

number of atoms

start

number of the first recorded MD step

step

indicate that step MD steps (!) make up one trajectory frame

delta

MD integrator time step (!), in AKMA units

dt

Override step and delta so that the DCD records that dt ps lie between two frames. (It sets step = 1 and delta = AKMA(dt).) The default is None, in which case step and delta are used.

remarks

string that is stored in the DCD header [XXX – max length?]

Returns:

DCDWriter

Note

The keyword arguments set the low-level attributes of the DCD according to the CHARMM format. The time between two frames would be delta * step !

See also

DCDWriter has detailed argument description

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
check_slice_indices(start, stop, step)

Check frame indices are valid and clip to fit trajectory

Parameters:stop, step (start,) – Values representing the slice indices. Can use None to use defaults of (0, -1, and 1) respectively.
Returns:start, stop, step – Integers representing the slice
Return type:int
convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned.

New in version 0.7.5.

correl(timeseries, start=0, stop=-1, skip=1)[source]

Populate a TimeseriesCollection object with timeseries computed from the trajectory

Parameters:
dt

Time between two trajectory frames in picoseconds.

frame

Frame number of the current time step.

This is a simple short cut to Timestep.frame.

next()

Forward one step to next frame.

rewind()

Position at beginning of trajectory

time

Time of the current frame in MDAnalysis time units (typically ps).

This is either read straight from the Timestep, or calculated as time = Timestep.frame * Timestep.dt

timeseries(asel, start=0, stop=-1, skip=1, format=u'afc')[source]

Return a subset of coordinate data for an AtomGroup

Parameters:
  • *asel*AtomGroup object
  • stop, skip* (*start,) – range of trajectory to access, start and stop are inclusive
  • *format* – the order/shape of the return data array, corresponding to (a)tom, (f)rame, (c)oordinates all six combinations of ‘a’, ‘f’, ‘c’ are allowed ie “fac” - return array where the shape is (frame, number of atoms, coordinates)
totaltime

Total length of the trajectory n_frames * dt.

class MDAnalysis.coordinates.DCD.DCDWriter(filename, n_atoms, start=0, step=1, delta=20.45482949774598, dt=None, remarks=u'Created by DCDWriter', convert_units=None)[source]

Writes to a DCD file

Typical usage:

with DCDWriter("new.dcd", u.atoms.n_atoms) as w:
    for ts in u.trajectory
        w.write_next_timestep(ts)

Keywords are available to set some of the low-level attributes of the DCD.

``d = DCDWriter(dcdfilename, n_atoms, start, step, delta, remarks)``

Note

The Writer will write the unit cell information to the DCD in a format compatible with NAMD and older CHARMM versions, namely the unit cell lengths in Angstrom and the angle cosines (see Timestep). Newer versions of CHARMM (at least c36b2) store the matrix of the box vectors. Writing this matrix to a DCD is currently not supported (although reading is supported with the DCDReader); instead the angle cosines are written, which might make the DCD file unusable in CHARMM itself. See Issue 187 for further information.

The writing behavior of the DCDWriter is identical to that of the DCD molfile plugin of VMD with the exception that by default it will use AKMA time units.

Create a new DCDWriter

Arguments:
filename

name of output file

n_atoms

number of atoms in dcd file

start

starting timestep

step

skip between subsequent timesteps (indicate that step MD integrator steps (!) make up one trajectory frame); default is 1.

delta

timestep (MD integrator time step (!), in AKMA units); default is 20.45482949774598 (corresponding to 1 ps).

remarks

comments to annotate dcd file

dt

Override step and delta so that the DCD records that dt ps lie between two frames. (It sets step = 1 and delta = AKMA(dt).) The default is None, in which case step and delta are used.

convert_units

units are converted to the MDAnalysis base format; None selects the value of MDAnalysis.core.flags [‘convert_lengths’]. (see Flags)

Note

The keyword arguments set the low-level attributes of the DCD according to the CHARMM format. The time between two frames would be delta * step ! For convenience, one can alternatively supply the dt keyword (see above) to just tell the writer that it should record “There are dt ps between each frame”.

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
close()[source]

Close trajectory and flush buffers.

convert_dimensions_to_unitcell(ts, _ts_order=[0, 2, 5, 4, 3, 1])[source]

Read dimensions from timestep ts and return appropriate native unitcell.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned.

New in version 0.7.5.

has_valid_coordinates(criteria, x)

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
Parameters:
  • *criteria* – dictionary containing the max and min values in native units
  • *x*np.ndarray of (x, y, z) coordinates of atoms selected to be written out.
Returns:

boolean

write(obj)

Write current timestep, using the supplied obj.

The argument should be a AtomGroup or a Universe or a Timestep instance.

Note

The size of the obj must be the same as the number of atom provided when setting up the trajectory.

write_next_timestep(ts=None)[source]

write a new timestep to the dcd file

ts - timestep object containing coordinates to be written to dcd file

Changed in version 0.7.5: Raises ValueError instead of generic Exception if wrong number of atoms supplied and NoDataError if no coordinates to be written.