# Trajectory Reference

Loading molecular dynamics trajectories is easy with MDTraj.

    >>> import mdtraj as md
    >>> t = md.load('trajectory.pdb')

The function `mdtraj.load()` will automatically detect the appropriate format based on the filename extension. The supported formats are all listed below in the format-specific loaders. The return value of `mdtraj.load()` is an `mdtraj.Trajectory` object.

While `mdtraj.load()` will read an entire trajectory into memory, other functions like `mdtraj.iterload()` and `mdtraj.open()` are available for working with trajectories in chunks, without loading them entirely into memory all at once.

## Internal representation

`Trajectory`(xyz, topology[, time, ...]) | Container object for a molecular dynamics trajectory
`Topology`() | Topology stores the topological information about a system.

## Format-agnostic loading functions

`load`(filename_or_filenames[, ...]) | Load a trajectory from one or more files on disk.
`iterload`(filename[, chunk]) | An iterator over a trajectory from one or more files on disk, in fragments
`load_frame`(filename, index[, top, atom_indices]) | Load a single frame from a trajectory file
`open`(filename[, mode, force_overwrite]) | Open a trajectory file-like object
`join`(trajs[, check_topology, ...]) | Concatenate multiple trajectories into one long trajectory

## Format-specific loading functions

`load_lh5`(filename[, top, stride, ...]) | Load an deprecated MSMBuilder2 LH5 trajectory file.
`load_pdb`(filename[, stride, atom_indices, ...]) | Load a RCSB Protein Data Bank file from disk.
`load_xml`(filename[, top]) | Load a single conformation from an OpenMM XML file.
`load_arc`(filename[, stride, atom_indices, ...]) | Load a TINKER .arc file from disk.
`load_dcd`(filename[, top, stride, ...]) | Load an DCD file from disk.
`load_dtr`(filename[, top, stride, ...]) | Load a dtr file from disk.
`load_hdf5`(filename[, stride, atom_indices, ...]) | Load an MDTraj hdf5 trajectory file from disk.
`load_netcdf`(filename[, top, stride, ...]) | Load an AMBER NetCDF file.
`load_trr`(filename[, top, stride, ...]) | Load a Gromacs TRR file from disk.
`load_xtc`(filename[, top, stride, ...]) | Load a Gromacs XTC file from disk.
`load_prmtop`(filename[, standard_names]) | Load an AMBER prmtop topology file from disk.
`load_xyz`(filename[, top, stride, ...]) | Load a xyz trajectory file.
`load_lammpstrj`(filename[, top, stride, ...]) | Load a LAMMPS trajectory file.
`load_hoomdxml`(filename[, top]) | Load a single conformation from an HOOMD-Blue XML file.