# 7.1. Trajectory Readers and Writers — `MDAnalysis.coordinates`

The coordinates submodule contains code to read, write and store coordinate information, either single frames (e.g., the `GRO` format) or trajectories (such as the `DCD` format); see the Table of supported coordinate formats for all formats.

MDAnalysis calls the classes that read a coordinate trajectory and make the data available “Readers”. Similarly, classes that write out coordinates are called “Writers”. Readers and Writers provide a common interface to the underlying coordinate data. This abstraction of coordinate access through an object-oriented interface is one of the key capabilities of MDAnalysis.

## 7.1.1. Readers

All Readers are based on a `ProtoReader` class that defines a common Trajectory API and allows other code to interface with all trajectory formats in the same way, independent of the details of the trajectory format itself.

The `Universe` contains the API entry point attribute `Universe.trajectory` that points to the actual `ProtoReader` object; all Readers are accessible through this entry point in the same manner (”duck typing”).

There are four types of base Reader which act as starting points for each specific format. These are:

`ReaderBase`

  A standard multi frame Reader which allows iteration over a single file to provide multiple frames of data. This is used by formats such as TRR and DCD.

`SingleFrameReaderBase`

  A simplified Reader which reads a file containing only a single frame of information. This is used with formats such as GRO and CRD

`StreamReaderBase`

  A specialized Reader for continuous data streams such as live simulation feeds. Unlike standard readers, streaming readers cannot randomly access frames, rewind, or determine total length. This is used for real-time trajectory data from simulations via IMD connections.

`ChainReader`

  An advanced Reader designed to read a sequence of files, to provide iteration over all the frames in each file seamlessly. This Reader can also provide this functionality over a sequence of files in different formats.

Normally, one does not explicitly need to select a reader. This is handled automatically when creating a `Universe` and the appropriate reader for the file type is selected (typically by the file extension but this choice can be overriden with the `format` argument to `Universe`).

If additional simulation data is available, it may be added to and read alongside a trajectory using `add_auxiliary()` as described in the Auxiliary API.

## 7.1.2. Writers

In order to write coordinates, a factory function is provided (`MDAnalysis.coordinates.core.writer()`, which is also made available as `MDAnalysis.Writer()`) that returns a Writer appropriate for the desired file format (as indicated by the filename suffix). Furthermore, a trajectory `ProtoReader` can also have a method `Writer()` that returns an appropriate `WriterBase` for the file format of the trajectory.

In analogy to `MDAnalysis.coordinates.core.writer()`, there is also a `MDAnalysis.coordinates.core.reader()` function available to return a trajectory `ProtoReader` instance although this is often not needed because the `Universe` class can choose an appropriate reader automatically.

A typical approach is to generate a new trajectory from an old one, e.g., to only keep the protein:

    u = MDAnalysis.Universe(PDB, XTC)
    protein = u.select_atoms("protein")
    with MDAnalysis.Writer("protein.xtc", protein.n_atoms) as W:
        for ts in u.trajectory:
            W.write(protein)

Using the `with()` statement will automatically close the trajectory when the last frame has been written.

## 7.1.3. Timesteps

Both Readers and Writers use Timesteps as their working object. A `Timestep` represents all data for a given frame in a trajectory. The data inside a `Timestep` is often accessed indirectly through a `AtomGroup` but it is also possible to manipulate Timesteps directly.

The current `Timestep` can be accessed through the `ts` attribute of the trajectory attached to the active `Universe`:

    ts = u.trajectory.ts
    ts.positions  # returns a numpy array of positions

Most individual formats have slightly different data available in each Timestep due to differences in individual simulation packages, but all share in common a broad set of basic data, detailed in Timestep API

## 7.1.4. Supported coordinate formats

The table below lists the coordinate file formats understood by MDAnalysis. The emphasis is on formats that are used in popular molecular dynamics codes. By default, MDAnalysis figures out formats by looking at the extension. Thus, a DCD file always has to end with “.dcd” to be recognized as such unless the format is explicitly specified with the format keyword to `Universe` or `load_new()`. A number of files are also recognized when they are compressed with gzip or bzip2 such as “.xyz.bz2”.

Table of supported coordinate formats
Name | extension | IO | remarks
--- | --- | --- | ---
CHARMM, NAMD | dcd | r/w | standard CHARMM binary trajectory; endianness is autodetected. Fixed atoms may not be handled correctly (requires testing). Module `MDAnalysis.coordinates.DCD`
LAMMPS | dcd | r/w | CHARMM-style binary trajectory; endianness is autodetected. Units are appropriate for LAMMPS. Module `MDAnalysis.coordinates.LAMMPS`
LAMMPS [1] | data | r | Single frame of coordinates read from .data files
LAMMPS [1] | lammpsdump | r | Ascii trajectory in atom style
Gromacs | xtc | r/w | Compressed (lossy) xtc trajectory format. Module `MDAnalysis.coordinates.XTC`
Gromacs | trr | r/w | Full precision trr trajectory. Coordinates and velocities are processed. Module `MDAnalysis.coordinates.TRR`
Gromacs | tpr | r | Coordinates and velocities are read in. Module `MDAnalysis.coordinates.TPR`
Gromacs | tng | r | Variable precision tng trajectory. Coordinates, velocities and forces are processed along with any additional tng block data requested for reading. Uses the PyTNG package for tng file reading. Module `MDAnalysis.coordinates.TNG`
XYZ [1] | xyz | r/w | Generic white-space separate XYZ format; can be compressed (gzip or bzip2). Module `MDAnalysis.coordinates.XYZ`
TXYZ [1] | txyz, arc | r | Tinker XYZ format. Module `MDAnalysis.coordinates.TXYZ`
HOOMD [1] | gsd | r | HOOMD GSD format (using `gsd.hoomd`). Module `MDAnalysis.coordinates.GSD`
GAMESS | gms, log, out | r | Generic semi-formatted GAMESS output log; can be compressed (gzip or bzip2). Module `MDAnalysis.coordinates.GMS`
AMBER | trj, mdcrd | r | formatted (ASCII) trajectories; the presence of a periodic box is autodetected (experimental). Module `MDAnalysis.coordinates.TRJ`
AMBER | inpcrd, restrt | r | formatted (ASCII) coordinate/restart file Module `MDAnalysis.coordinates.INPCRD`
AMBER | ncdf, nc | r/w | binary (NetCDF) trajectories are fully supported with optional netcdf4-python module (coordinates and velocities). Module `MDAnalysis.coordinates.TRJ`
Brookhaven [1] | pdb/ent | r/w | a relaxed PDB format (as used in MD simulations) is read by default; Multiple frames (MODEL) are supported but require the multiframe keyword. Module `MDAnalysis.coordinates.PDB`
XPDB | pdb | r | Extended PDB format (can use 5-digit residue numbers). To use, specify the format “XPBD” explicitly: `Universe(..., format="XPDB")`. Module `MDAnalysis.coordinates.PDB`
PDBQT [1] | pdbqt | r/w | file format used by AutoDock with atom types t and partial charges q. Module: `MDAnalysis.coordinates.PDBQT`
PQR [1] | pqr | r/w | PDB-like but whitespace-separated files with charge and radius information. Module `MDAnalysis.coordinates.PQR`
GROMOS96 [1] | gro | r/w | basic GROMOS96 format (velocities as well). Only the first frame present will be read. Module `MDAnalysis.coordinates.GRO`
GROMOS11 | trc | r | Basic GROMOS11 trajectory format. Can read positions, box-sizes and timesteps. Module `MDAnalysis.coordinates.TRC`
CHARMM CARD [1] | crd | r/w | “CARD” coordinate output from CHARMM; deals with either standard or EXTended format. Module `MDAnalysis.coordinates.CRD`
DESRES [1] | dms | r | DESRES Molecular Structure file format reader. Module `MDAnalysis.coordinates.DMS`
IBIsCO/YASP | trz | r/w | Binary IBIsCO or YASP trajectories Module `MDAnalysis.coordinates.TRZ`
MOL2 | mol2 | r/w | Text-based Tripos molecular structure format `MDAnalysis.coordinates.MOL2`
DL_Poly [1] | config | r | DL_Poly ascii config file `MDAnalysis.coordinates.DLPOLY`
DL_Poly [1] | history | r | DL_Poly ascii history file `MDAnalysis.coordinates.DLPOLY`
MMTF [1] | mmtf | r | Macromolecular Transmission Format `MDAnalysis.coordinates.MMTF`
NAMD | coor, namdbin | r/w | NAMD binary file format for coordinates `MDAnalysis.coordinates.NAMDBIN`
FHIAIMS | in | r/w | FHI-AIMS file format for coordinates `MDAnalysis.coordinates.FHIAIMS`
H5MD | h5md | r | H5MD file format for coordinates `MDAnalysis.coordinates.H5MD`
chemfiles library | CHEMFILES | r/w | interface to chemfiles, see the list of chemfiles file formats and `MDAnalysis.coordinates.chemfiles`
IMD | imd:// <host>: <port> | r | Receive simulation trajectory data using interactive molecular dynamics version 3 (IMDv3) by configuring a socket address to a NAMD, GROMACS, or LAMMPS simulation. `MDAnalysis.coordinates.IMD`

[1] (1,2,3,4,5,6,7,8,9,10,11,12,13,14)

This format can also be used to provide basic topology information (i.e. the list of atoms); it is possible to create a full `Universe` by simply providing a file of this format: `u = Universe(filename)`

## 7.1.5. Trajectory API

The Trajectory API defines how classes have to be structured that allow reading and writing of coordinate files. By following the API it is possible to seamlessly enhance the I/O capabilities of MDAnalysis. The actual underlying I/O code can be written in C or python or a mixture thereof.

Typically, each format resides in its own module, named by the format specifier (and using upper case by convention).

Reader and Writer classes are derived from base classes in `MDAnalysis.coordinates.base`.

### 7.1.5.1. Registry

In various places, MDAnalysis tries to automatically select appropriate formats (e.g. by looking at file extensions). In order to allow it to choose the correct format, all I/O classes must subclass either `MDAnalysis.coordinates.base.ReaderBase`, `MDAnalysis.coordinates.base.SingleFrameReaderBase`, or `MDAnalysis.coordinates.base.WriterBase` and set the `format` attribute with a string defining the expected suffix. To assign multiple suffixes to an I/O class, a list of suffixes can be given.

In addition to this, a Reader may define a `_format_hint` staticmethod, which returns a boolean of if it can process a given object. E.g. the `MDAnalysis.coordinates.memory.MemoryReader` identifies itself as capable of reading numpy arrays. This functionality is used in `MDAnalysis.core._get_readers.get_reader_for()` when figuring out how to read an object (which was usually supplied to mda.Universe).

To define that a Writer can write multiple trajectory frames, set the multiframe attribute to `True`. The default is `False`. To define that a Writer does not support single frame writing the singleframe attribute can be set to `False`. This is `True` by default, ie we assume all Writers can also do a single frame.

### 7.1.5.2. Timestep class

A Timestep instance holds data for the current frame. It is updated whenever a new frame of the trajectory is read.

Timestep classes are derived from `MDAnalysis.coordinates.timestep.Timestep`, which is the primary implementation example (and used directly for the DCDReader).

The discussion on this format is detailed in Issue 250

#### 7.1.5.2.1. Methods

`__init__(n_atoms, positions=True, velocities=False, forces=False)`

  Define the number of atoms this Timestep will hold and whether or not it will have velocity and force information

`__eq__`

  Compares a Timestep with another

`__getitem__(atoms)`

  position(s) of atoms; can be a slice or numpy array and then returns coordinate array

`__len__()`

  number of coordinates (atoms) in the frame

`__iter__()`

  iterator over all coordinates

`copy()`

  deep copy of the instance

`_init_unitcell`

  hook that returns empty data structure for the unitcell representation of this particular file format; called from within `__init__()` to initialize `Timestep._unitcell`.

#### 7.1.5.2.2. Attributes

`n_atoms`

  number of atoms in the frame

`frame`

  current frame number (0-based)

`_frame`

  The native frame number of the trajectory. This can differ from `frame` as that will always count sequentially from 0 on iteration, whilst `_frame` is taken directly from the trajectory.

`time`

  The current system time in ps. This value is calculated either from a time set as the Timestep attribute, or from frame * dt. Either method allows allows an offset to be applied to the time.

`dt`

  The change in system time between different frames. This can be set as an attribute, but defaults to 1.0 ps.

`data`

  A dictionary containing all miscellaneous information for the current Timestep.

`positions`

  A numpy array of all positions in this Timestep, otherwise raises a `NoDataError`

`velocities`

  If present, returns a numpy array of velocities, otherwise raises a `NoDataError`

`forces`

  If present, returns a numpy array of forces, otherwise raises a `NoDataError`

`has_positions`

  Boolean of whether position data is available

`has_velocities`

  Boolean of whether velocity data is available

`has_forces`

  Boolean of whether force data is available

`dimensions`

  system box dimensions (x, y, z, alpha, beta, gamma) Also comes with a setter that takes a MDAnalysis box so that one can do

      Timestep.dimensions = [A, B, C, alpha, beta, gamma]

  which then converts automatically to the underlying representation and stores it in `Timestep._unitcell`.

`volume`

  system box volume (derived as the determinant of the box vectors of `dimensions`)

`aux`

  namespace for the representative values of any added auxiliary data.

#### 7.1.5.2.3. Private attributes

These attributes are set directly by the underlying trajectory readers. Normally the user should not have to directly access those, but instead should use the attribute above.

`_pos`

  raw coordinates, a `numpy.float32` array; `X = _pos[:,0], Y = _pos[:,1], Z = _pos[:,2]`

`_velocities`

  raw velocities, a `numpy.float32` array containing velocities (similar to `_pos`)

`_forces`

  forces, similar to velocities above.

`_unitcell`

  native unit cell description; the format depends on the underlying trajectory format. A user should use the `dimensions` attribute to access the data in a canonical format instead of accessing `Timestep._unitcell` directly.

  The method `Timestep._init_unitcell()` is a hook to initialize this attribute.

### 7.1.5.3. Trajectory Reader class

Trajectory readers are derived from `MDAnalysis.coordinates.base.ReaderBase` (or from `MDAnalysis.coordinates.base.ProtoReader` if they do not required `Reader.__del__()` method). A special case are SingleFrame readers for formats that contain only a single coordinate frame. These readers are derived from a subclass of `ProtoReader` named `MDAnalysis.coordinates.base.SingleFrameReaderBase`.

Typically, many methods and attributes are overriden but the ones listed below must be implemented.

See also

See the section on Readers in `MDAnalysis.coordinates.base` for implementation details.

#### 7.1.5.3.1. Methods

The `MDAnalysis.coordinates.DCD.DCDReader` class is the primary implementation example.

Mandatory methods

The following methods must be implemented in a Reader class.

`__init__(filename, **kwargs)`

  open filename; other kwargs are processed as needed and the Reader is free to ignore them. Typically, when MDAnalysis creates a Reader from `MDAnalysis.Universe` it supplies as much information as possible in kwargs; at the moment the following data are supplied:

  - n_atoms: the number of atoms from the supplied topology. This is

      not required for all readers and can be ignored if not required.

`__iter__()`

  allow iteration from beginning to end:

      for ts in trajectory:
          print(ts.frame)

  Readers will automatically rewind the trajectory to before the initial frame (often by re-opening the file) before starting the iteration. Multi frame readers (see Readers) will also rewind the trajectory after the iteration so that the current trajectory frame is set to the first trajectory frame. Single frame readers do not explicitly rewind after iteration but simply remain on the one frame in the trajectory.

`close()`

  close the file and cease I/O

`next()`

  advance to next time step or raise `IOError` when moving past the last frame

`rewind()`

  reposition to first frame

`__entry__()`

  entry method of a Context Manager (returns self)

`__exit__()`

  exit method of a Context Manager, should call `close()`.

Note

a `__del__()` method should also be present to ensure that the trajectory is properly closed. However, certain types of Reader can ignore this requirement. These include the `SingleFrameReaderBase` (file reading is done within a context manager and needs no closing by hand) and the `ChainReader` (it is a collection of Readers, each already with its own `__del__` method).

Optional methods

Not all trajectory formats support the following methods, either because the data are not available or the methods have not been implemented. Code should deal with missing methods gracefully.

`__len__()`

  number of frames in trajectory

`__getitem__(arg)`

  advance to time step arg = frame and return `Timestep`; or if arg is a slice, then return an iterable over that part of the trajectory.

  The first functionality allows one to randomly access frames in the trajectory:

      universe.trajectory[314]

  would load frame 314 into the current `Timestep`.

  Using slices allows iteration over parts of a trajectory

      for ts in universe.trajectory[1000:2000]:
          process_frame(ts)   # do some analysis on ts

  or skipping frames

      for ts in universe.trajectory[1000::100]:
          process_frame(ts)   # do some analysis on ts

  The last example starts reading the trajectory at frame 1000 and reads every 100th frame until the end.

  A sequence of indices or a mask of booleans can also be provided to index a trajectory.

  The performance of the `__getitem__()` method depends on the underlying trajectory reader and if it can implement random access to frames. All readers in MDAnalysis should support random access.

  For external custom readers this may not be easily (or reliably) implementable and thus one is restricted to sequential iteration. If the Reader is not able to provide random access to frames then it should raise `TypeError` on indexing. It is possible to partially implement `__getitem__` (as done on `MDAnalysis.coordinates.base.ProtoReader.__getitem__` where slicing the full trajectory is equivalent to `MDAnalysis.coordinates.base.ProtoReader.__iter__` (which is always implemented) and other slices raise `TypeError`.

  When indexed with a slice, a sequence of indices, or a mask of booleans, the return value is an instance of `FrameIteratorSliced` or `FrameIteratorIndices`. See FrameIterators for more details.

`parse_n_atoms(filename, **kwargs)`

  Provide the number of atoms in the trajectory file, allowing the Reader to be used to provide an extremely minimal Topology. Must be implemented as either a staticmethod or a classmethod.

`Writer(filename, **kwargs)`

  returns a `WriterBase` which is set up with the same parameters as the trajectory that is being read (e.g. time step, length etc), which facilitates copying and simple on-the-fly manipulation.

  If no Writer is defined then a `NotImplementedError` is raised.

  The kwargs can be used to customize the Writer as they are typically passed through to the init method of the Writer, with sensible defaults filled in; the actual keyword arguments depend on the Writer.

`timeseries(atomGroup, [start[,stop[,skip[,format]]]])`

  returns a subset of coordinate data

#### 7.1.5.3.2. Attributes

`filename`

  filename of the trajectory

`n_atoms`

  number of atoms (coordinate sets) in a frame (constant)

`n_frames`

  total number of frames (if known) – `None` if not known

`ts`

  the `Timestep` object; typically customized for each trajectory format and derived from `timestep.Timestep`.

`units`

  dictionary with keys time, length, speed, force and the appropriate unit (e.g. ‘AKMA’ and ‘Angstrom’ for Charmm dcds, ‘ps’ and ‘nm’ for Gromacs trajectories, `None` and ‘Angstrom’ for PDB). Any field not used should be set to `None`.

`format`

  string that identifies the file format, e.g. “DCD”, “PDB”, “CRD”, “XTC”, “TRR”; this is typically the file extension in upper case.

`dt`

  time between frames in ps; a managed attribute (read only) that computes on the fly `skip_timestep * delta` and converts to the MDAnalysis base unit for time (pico seconds by default)

`totaltime`

  total length of the trajectory = `n_frames * dt`

`time`

  time of the current time step, in MDAnalysis time units (ps)

`frame`

  frame number of the current time step (0-based)

`aux_list`

  list of the names of any added auxiliary data.

`_auxs`

  dictionary of the `AuxReader` instances for any added auxiliary data.

Optional attributes

`delta`

  integrator time step (in native units); hence the “length” of a trajctory frame is `skip_timestep*delta` time units

`compressed`

  string that identifies the compression (e.g. “gz” or “bz2”) or `None`.

`fixed`

  bool, saying if there are fixed atoms (e.g. dcds)

`periodic`

  boolean saying if contains box information for periodic boundary conditions unit cell information is stored in attribute dimensions

`skip_timestep`

  number of integrator steps between frames + 1 (i.e. the stride at which the MD simulation was sampled)

### 7.1.5.4. Trajectory Writer class

Trajectory writers are derived from `MDAnalysis.coordinates.base.WriterBase`. They are used to write multiple frames to a trajectory file. Every time the `write()` method is called, another frame is appended to the trajectory.

Typically, many methods and attributes are overriden.

Signature:

    with TrajectoryWriter(filename, n_atoms, **kwargs) as w:
        w.write(Universe)    # write a whole universe

or:

    w.write(AtomGroup)  # write a selection of Atoms from Universe

See also

See the section on Writers in `MDAnalysis.coordinates.base` for implementation details.

#### 7.1.5.4.1. Methods

`__init__(filename, n_atoms, **kwargs)`

  Set-up the reader. This may open file filename and may write content to it such as headers immediately but the writer is allowed to delay I/O up to the first call of `write()`.

  Any `**kwargs` that are not processed by the writer must be silently ignored.

`write(obj)`

  write Timestep data in obj

`convert_dimensions_to_unitcell(timestep)`

  take the dimensions from the timestep and convert to the native unitcell representation of the format

`close()`

  close file and finish I/O

`__del__()`

  ensures that close() is called

#### 7.1.5.4.2. Attributes

`filename`

  name of the trajectory file

`units`

  dictionary with keys time, length, speed, force and the appropriate unit (e.g. ‘AKMA’ and ‘Angstrom’ for Charmm dcds, ‘ps’ and ‘nm’ for Gromacs trajectories, `None` and ‘Angstrom’ for PDB). Any field not used should be set to `None`.

`format`

  string that identifies the file format, e.g. “DCD”, “PDB”, “CRD”, “XTC”, “TRR”

Optional

`ts`

  `Timestep` instance

### 7.1.5.5. Single Frame Writer class

A single frame writer is a special case of a trajectory writer in that it writes only a single coordinate frame to a file, for instance, a pdb or gro file. Unlike trajectory formats, which only contains coordinates, single frame formats contain much more information (e.g. atom and residue names and numbers) and hence it is possible to write selections of atoms in a meaningful way.

Signature:

    W = FrameWriter(filename, **kwargs)
    W.write(AtomGroup)
    W.write(Universe)

The blanket kwargs is required so that one can pass the same kind of arguments (filename and n_atoms) as for the Trajectory writers. In this way, the simple `writer()` factory function can be used for all writers.

#### 7.1.5.5.1. Methods

`__init__(filename, **kwargs)`

  opens filename for writing; kwargs are typically ignored

`write(obj)`

  writes the object obj, containing a `AtomGroup` group of atoms (typically obtained from a selection) or `Universe` to the file and closes the file

Note

Trajectory and Frame writers can be used in almost exactly the same manner with the one difference that Frame writers cannot deal with raw `Timestep` objects.