stacker.file_manipulation module

stacker.file_manipulation module#

Filter Trajectory Files

This module contains functions for manipulating trajectory files. This includes filtering a trajectory to desired atoms, converting trajectory filetype, and outputting Python trajectories to other filetypes (eg. prmtop, mdcrd, pdb)

filter_traj(trj_file, top_file, residues={}, atoms={})[source]#

Filters an input trajectory to only the specified atoms and residues

Filteres an input trajectory that contains all of the atoms in a topology to only the desired atoms at the desired residues (eg. the atoms necessary to find the center of geometry of a residue). If residues or atoms are empty, all residues or atoms are included respectively.

Parameters:
trj_filestr

filepath of the trajectory

top_filestr

filepath of the topology of the molecule

residuesset or str

1-indexed residue numbers of residues to keep in the trajectory. Accepts smart-indexed str representing a list of residues (e.g ‘1-5,6,39-48’). If Empty, include all residues.

atomsset

atomnames to keep in the trajectory. If Empty, include all atoms.

Returns:
filtered_trajectorymdtraj.Trajectory

a trajectory object representing the filtered structure across all frames

See also

filter_traj_to_pdb

Filters an input trajectory to only the specified atoms and residues and outputs to pdb

mdtraj.Trajectory

The Trajectory object in mdtraj package

Notes

Inputed trajectory should have 1-indexed Residue Indices, Outputed trajectory object will be 0-indexed.

Examples

>>> import stacker as st
>>> filtered_traj = st.filter_traj('stacker/testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd', 
...                             'stacker/testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop', 
...                             residues = {426,427}, 
...                             atoms = {'C2','C4','C6'})
WARNING: Residue Indices are expected to be 1-indexed
Reading trajectory...
Reading topology...
Filtering trajectory...
WARNING: Output filtered traj atom, residue, and chain indices are zero-indexed
>>> table, bonds = filtered_traj.topology.to_dataframe()
>>> print(table)
serial name element  resSeq resName  chainID segmentID
0   None   C6       C     425       G        0          
1   None   C2       C     425       G        0          
2   None   C4       C     425       G        0          
3   None   C6       C     426       C        0          
4   None   C4       C     426       C        0          
5   None   C2       C     426       C        0

Residue Number support SmartIndexing

>>> import stacker as st
>>> filtered_traj = st.filter_traj('../testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd', 
...                             '../testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop', 
...                              residues = '1-16,25,50-57', 
...                              atoms = {'C2','C4','C6'})
WARNING: Residue Indices are expected to be 1-indexed
Reading trajectory...
Reading topology...
Filtering trajectory...
WARNING: Output filtered traj atom, residue, and chain indices are zero-indexed
>>> filtered_traj
<mdtraj.Trajectory with 10 frames, 75 atoms, 25 residues, without unitcells at 0x1156c3ed0>
filter_traj_to_pdb(trj_file, top_file, pdb, residues={}, atoms={})[source]#

Filters an input trajectory to only the specified atoms and residues and outputs to pdb

Filteres an input trajectory that contains all of the atoms in a trajectory to only the desired atoms at the desired residues (eg. the atoms necessary to find the center of geometry of a residue) and writes the output to a specified pdb file. If residues or atomnames are empty, all residues or atoms are included respectively.

Parameters:
trj_filestr

path to file of the concatenated trajectory. Should be resampled to the 1 in 50 frames sampled trajectories for each replicate.

top_filestr

path to file of the topology of the molecule

pdbstr

path to the output pdb file

residuesset or str

1-indexed residue numbers of residues to keep in the trajectory. Accepts smart-indexed str representing a list of residues (e.g ‘1-5,6,39-48’) If Empty, include all residues.

atomnamesset

atomnames to keep in the trajectory

Returns:
None

See also

filter_traj

Filters an input trajectory to only the specified atoms and residues

Notes

Inputed trajectory should have 1-indexed Residue Indices, Outputed trajectory object will be 0-indexed.

file_convert(trj_file, top_file, outfile)[source]#

Converts a trajectory input file to a new output type.

The output file type is determined by the outfile extension. Uses mdtraj.save() commands to convert trajectory files to various file types such as mdtraj.save_mdcrd(), mdtraj.save_pdb(), mdtraj.save_xyz(), etc.

Parameters:
trj_filestr

Path to the file of the concatenated trajectory (eg. .mdcrd file).

top_filestr

Path to the file of the topology of the molecule (.prmtop file).

outfilestr

Output filename (include .mdcrd, .pdb, etc.).

Returns:
None

See also

mdtraj.load

Load trajectory files

mdtraj.save

Save md.Trajectory to file

mdtraj.load_xyz

Load a .xyz trajectory file

Notes

Output filetype determined from file extension of output_file parameter.

Examples

>>> import stacker as st
>>> import mdtraj as md
>>> st.file_convert('stacker/testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.mdcrd', 
...                 'stacker/testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop', 
...                 'stacker/testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.xyz')
WARNING: Output file atom, residue, and chain indices are zero-indexed
Trajectory written to: stacker/testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.xyz
>>> md.load_xyz('stacker/testing/first10_5JUP_N2_tUAG_aCUA_+1GCU_nowat.xyz', 
...             top='stacker/testing/5JUP_N2_tUAG_aCUA_+1GCU_nowat.prmtop')
<mdtraj.Trajectory with 10 frames, 12089 atoms, 494 residues, without unitcells at 0x10bb75cd0>
class SmartIndexingAction(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None, deprecated=False)[source]#

Bases: Action

Custom argparse action to handle smart indexing of frame numbers.

Parses a comma-separated list of frame numbers with optional ranges (e.g., ‘1-20, 34, 25, 50-100’) and generates a list of individual frame numbers. Modifies the namespace by setting the attribute specified by the ‘dest’ parameter to the list of individual frame numbers.

Parameters:
parser: argparse.ArgumentParser

The argparse parser object.

namespace: argparse.Namespace

The argparse namespace.

values: str

The input string containing frame numbers and ranges.

option_string: str, default=None

The option string.

Attributes:
deststr

The attribute name in the namespace where the parsed list will be stored.

Methods

__call__(parser, namespace, values, option_string=None)

Parses the provided string of values into a sorted list of integers and sets it as an attribute in the namespace.

Examples

>>> parser = argparse.ArgumentParser()
>>> parser.add_argument("-fl", "--frame_list", metavar="FRAME_LIST", help="Smart-indexed list of 1-indexed Frame Numbers within trajectory to analyze", required=False, action=SmartIndexingAction)
>>> args = parser.parse_args(["-fl", "1-20,34,25,50-100"])
>>> print(args.frame_list)
[1, 2, ..., 20, 34, 25, 50, 51, ..., 100]
static parse_smart_index(value)[source]#

Checks that an inputted variable is a list that can be smart indexed and indexes it if necessary.

Parameters:
value{str, set, list}

The input string containing ranges (e.g., “1-5,10,15-20”) or a set of integers.

Returns:
set

A set of integers parsed from the input.

Raises:
ValueError

If the input is not a string or set.

Examples

>>> import stacker as st
>>> st.SmartIndexingAction.parse_smart_index('1-5,8,12-17')
{1, 2, 3, 4, 5, 8, 12, 13, 14, 15, 16, 17}
__init__(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None, deprecated=False)#
_get_args()#
_get_kwargs()#
format_usage()#