OAT command line documentation

Align

Aligns each frame in a trajectory to the first frame

usage: oat align [-h] [-p num_cpus] [-i index_file] [-r reference_structure]
                 [-c] [-q]
                 traj outfile

Positional Arguments

traj: The trajectory file to align
outfile: The name of the new trajectory file to write out

Named Arguments

-p, --parallel

(optional) How many cores to use

-i, --index

Align to only a subset of particles from a space-separated list in the provided file

-r, --ref

Align to a provided configuration instead of the first frame.

-c, --nocenter

Don’t center the output. Can avoid errors caused by small boxes.

Default: False

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

ANM parameterize

compute par file for DNA-ANM model

usage: oat anm_parameterize [-h] index_file mean_file trajectory out_file

Positional Arguments

index_file: Index file describing what Bases belong to which Super particle.
mean_file: Reference configuration
trajectory: Trajectory to evaluate
out_file: Output par file name

Backbone flexibility

Computes the deviations in the backbone torsion angles

usage: oat backbone_flexibility [-h] [-p num_cpus] [-o output_file]
                                [-d data_file] [-q]
                                topology trajectory

Positional Arguments

topology: The topology file associated with the trajectory file
trajectory: the trajectory file you wish to analyze

Named Arguments

-p, --parallel

(optional) How many cores to use

-o, --output

(optional) The name of the file to write the graph to

-d, --data

(optional) The name of the file to write the data to

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Bond analysis

Compare the bonds found at each trajectory with the intended design

usage: oat bond_analysis [-h] [-o output_file] [-t trajectory_plot]
                         [-d data_file] [-p num_cpus] [-q]
                         inputfile trajectory designed_pairs

Positional Arguments

inputfile: The inputfile used to run the simulation
trajectory: The trajecotry file to compare against the designed pairs
designed_pairs: The file containing the desired nucleotides pairings in the format a b

Named Arguments

-o, --output

Name of the file to save the output oxView overlay to

-t, --plot

Name of the file to save the trajecotry plot to

-d, --data

If set, save the data used to make the plot to a json file.

-p, --parallel

(optional) How many cores to use

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Centroid

Find the configuration in a trajectory closest to a provided reference configuration

usage: oat centroid [-h] [-p num_cpus] [-o output_file] [-i index_file] [-q]
                    reference_structure trajectory

Positional Arguments

reference_structure: The reference structure to search against
trajectory: the trajectory file you wish to analyze

Named Arguments

-p, --parallel

(optional) How many cores to use

-o, --output

The filename to save the centroid to

-i, --index

Alignment and RMSD based on a subset of particles given in a space-separated list in the provided file

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Clustering

Calculates clusters based on provided order parameters.

usage: oat clustering [-h] [-e EPS] [-m MIN_SAMPLES] [-q] serialized_data

Positional Arguments

serialized_data: The json-formatted input file

Named Arguments

-e, --eps

The epsilon parameter for DBSCAN (maximum distance to be considered a ‘neighbor’)

-m, --min_samples

The min_samples parameter for DBSCAN (number of neighbors which define a point as a central point in a cluster)

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Config

Configure oxDNA_analysis_tools

usage: oat config [-h] [-n CHUNK_SIZE] [-q]

Named Arguments

-n, --chunk_size

Number of configurations to per chunk. Persistent across analyses.

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Contact map

Calculate and display the contact map for a structure

usage: oat contact_map [-h] [-g graph] [-d data] [-p num_cpus] [-q] trajectory

Positional Arguments

trajectory: The file containing the configurations of which the contact map is needed

Named Arguments

-g, --plot

Filename for the plot

-d, --data

The name of the file to save the contact map as a pickle.

-p, --parallel

(optional) How many cores to use

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Decimate

Creates a smaller trajectory only including start/stop/stride frames from the input.

usage: oat decimate [-h] [-s START] [-e STOP] [-d STRIDE] [-q] traj outfile

Positional Arguments

traj: The trajectory file to decimate
outfile: The name of the new trajectory file to write out

Named Arguments

-s, --start

First conf to write to the output file.

Default: 0

-e, --stop

Process up to this conf (exclusive). Accepts negative indexes.

Default: -1

-d, --stride

Write out every this many confs (default=10)

Default: 10

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Deviations

Compute the RMSD of each nucleotide from the mean structure produced by compute_mean.py

usage: oat deviations [-h] [-p num_cpus] [-o output_file] [-i index_file]
                      [-r rmsd_plot] [-d rmsd_data] [-q]
                      mean_structure trajectory

Positional Arguments

mean_structure: The mean structure .json file from compute_mean.py
trajectory: the trajectory file you wish to analyze

Named Arguments

-p, --parallel

(optional) How many cores to use

-o, --output

The filename to save the RMSF json file to

-i, --index

Compute mean structure of a subset of particles from a space-separated list in the provided file

-r, --plot

The name of the file to save the RMSD plot to.

-d, --data

The name of the file to save the RMSD data in json format.

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Distance

Finds the ensemble of distances between any two particles in the system

usage: oat distance [-h]
                    [-i input p1 p2 p1 p2...) [input p1 p2 (p1 p2... ...]]
                    [-o output_file] [-f <histogram/trajectory/both>]
                    [-d data_file] [-n names [names ...]] [-p num_cpus] [-c]
                    [-q]

Named Arguments

-i, --input

A trajectory, and a list of particle pairs to compare. Can call -i multiple times to plot multiple datasets.

-o, --output

The name to save the graph file to

-f, --format

Output format for the graphs. Defaults to histogram. Options are “histogram”, “trajectory”, and “both”

-d, --data

If set, the output for the graphs will be dropped as a json to this filename for loading in oxView or your own scripts

-n, --names

Names of the data series. Will default to particle ids if not provided

-p, --parallel

(optional) How many cores to use

-c, --cluster

Run the clusterer on each configuration’s distance?

Default: False

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Dot-bracket to force

Create an external forces file enforcing the current base-pairing arrangement

usage: oat db_to_force [-h] [-o OUTPUT] [-s STIFF] [-r] [-q] db_file

Positional Arguments

db_file: A text file containing dot-bracket notation of the base-pairing arrangement

Named Arguments

-o, --output

Name of the file to write the force list to

-s, --stiff

Stiffness of the mutual trap

-r, --reverse

Reverse the dot-bracket before writing forces

Default: False

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Duplex angle plotter

Finds the ensemble of angles between pairs duplexes defined by nucleotides in the duplexes.

usage: oat duplex_angle_plotter [-h] [-i angle_file [angle_file ...]]
                                [-v INVERT_MASK [INVERT_MASK ...]]
                                [-o output_file]
                                [-f <histogram/trajectory/both>]
                                [-d data_file] [-n names [names ...]] [-q]

Named Arguments

-i, --input

An angle file from duplex_angle_finder.py and a list of particle id pairs found in the duplexes you want to compare. Can call -i multiple times to plot multiple datasets together.

-v, --invert_mask

If 1 invert the i-th vector, if 0, do nothing.

-o, --output

The name to save the graph file to

-f, --format

Output format for the graphs. Defaults to histogram. Options are “histogram”, “trajectory”, and “both”

-d, --data

If set, the output for the graphs will be dropped as a json to this filename for loading in oxView or your own scripts

-n, --names

Names of the data series. Will default to particle ids if not provided

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Duplex finder

Fit vectors to every duplex in the structure

usage: oat duplex_finder [-h] [-p num_cpus] [-o output_file] [-q]
                         input trajectory

Positional Arguments

input: The inputfile used to run the simulation
trajectory: The trajectory file from the simulation

Named Arguments

-p, --parallel

(optional) How many cores to use

-o, --output

name of the file to write the angle list to

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

File info

Prints metadata about trajectories

usage: oat file_info [-h] [-l LABELS [LABELS ...]] [-q]
                     trajectories [trajectories ...]

Positional Arguments

trajectories: One or more trajectories to get information on.

Named Arguments

-l, --labels

Labels for the files if not the filename

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Forces to dot-bracket

Convert a force file to dot-bracket notation

usage: oat forces2db [-h] [-o OUTPUT] [-q] topology force_file

Positional Arguments

topology: Topology file for the structure
force_file: The force file to generate the dot-bracket from

Named Arguments

-o, --output

If set, print the dot-bracket to a file, otherwise to the screen

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Forces to pairs

Convert an external force file to a list of particle pairs

usage: oat forces2pairs [-h] [-o OUTPUT] [-q] force_file

Positional Arguments

force_file: The force file to generate pairs from

Named Arguments

-o, --output

name of the file to write the pair list to

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Generate force

Create an external forces file enforcing the current base-pairing arrangement

usage: oat generate_force [-h] [-o OUTPUT] [-f PAIRS] [-s STIFF] [-q]
                          inputfile configuration

Positional Arguments

inputfile: The inputfile used to run the simulation
configuration: The configuration to generate the forces from

Named Arguments

-o, --output

Name of the file to write the forces to. Defaults to forces.txt

-f, --pairs

Name of the file to write the designed pairs list to

-s, --stiff

Stiffness of the mutual trap

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Mean

Computes the mean structure of a trajectory file

usage: oat mean [-h] [-p num_cpus] [-o output_file] [-d deviation_file]
                [-i index_file] [-a alignment_configuration] [-q]
                trajectory

Positional Arguments

trajectory: The trajectory file you wish to analyze

Named Arguments

-p, --parallel

(optional) How many cores to use

-o, --output

The filename to save the mean structure to

-d, --deviations

Immediately run oat deviations from the output

-i, --index

Compute mean structure of a subset of particles from a space-separated list in the provided file

-a, --align

The id of the configuration to align to, otherwise random

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Minify

Compress given configuration.

usage: oat minify [-h] [-p num_cpus] [-a] [-d DECIMALS] [-q]
                  trajectory outfile

Positional Arguments

trajectory: the trajectory file you wish to analyze
outfile: minified file

Named Arguments

-p, --parallel

(optional) How many cores to use

-a, --no_a

Discard a vectors.

Default: False

-d, --decimals

Round positions and orientations to the specified number of digits.

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Multidimensional scaling mean

Calculate molecular contacts, and assembles an average set of contacts based on MDS

usage: oat multidimensional_scaling_mean [-h] [-o output] [-d dev_file]
                                         [-p num_cpus] [-q]
                                         trajectory

Positional Arguments

trajectory: the trajectory file you wish to analyze

Named Arguments

-o, --output

the name of the .dat file where the mean will be written

-d, --dev_file

the name of the .json file where the devs will be written

-p, --parallel

(optional) How many cores to use

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Output bonds

List all the interactions between nucleotides

usage: oat output_bonds [-h] [-v OUTFILE] [-p num_cpus] [-u UNITS] [-q]
                        inputfile trajectory

Positional Arguments

inputfile: The inputfile used to run the simulation
trajectory: the trajectory file you wish to analyze

Named Arguments

-v, --view

if you want instead average per-particle energy as an oxView JSON

-p, --parallel

(optional) How many cores to use

-u, --units

(optional) The units of the energy (pNnm or oxDNA)

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

oxDNA -> PDB

Convert oxDNA files to PDB. This converter can handle oxDNANM protein simulation files.

usage: oat oxDNA_PDB [-h] [-o OUTPUT] [-d OUTPUT_DIRECTION] [-q] [-H] [-u]
                     [-1] [-r RMSF_BFACTOR]
                     topology configuration direction [pdbfiles ...]

Positional Arguments

topology: the oxDNA topology file for the structure
configuration: the configuration file you wish to convert
direction: the direction of strands in the oxDNA files, either 35 or 53. Most oxDNA files are 3-5.
pdbfiles: PDB files for the proteins present in your structure. The strands in the PDB file(s) must be in the same order as your oxDNA file. If there are multiple of the same protein, you must provide that PDB file that many times.

Named Arguments

-o, --output

The name of the output pdb file. Defaults to name of the configuration+.pdb

-d, --output_direction

Direction to save nucleic acid strands in. Should be “53” or “35”. Defaults to same as input direction.

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

-H, --hydrogen

if you want to include hydrogen atoms in the output PDB file

Default: True

-u, --uniform-residue-names

if you want to use uniform residue names in the output PDB file

Default: False

-1, --one_file_per_strand

if you want to have one PDB file per strand

Default: False

-r, --rmsf-file

A RMSF file from deviations. Will be used to fill the b-factors field in the output PDB (only for D(R)NA)

Pairs to dot-bracket

Convert a pair file to dot-bracket notation

usage: oat pairs2db [-h] [-o OUTPUT] [-q] topology pair_file

Positional Arguments

topology: Topology file for the structure
pair_file: The pair file to generate the dot-bracket from

Named Arguments

-o, --output

If set, print the dot-bracket to a file, otherwise to the screen

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

PDB -> oxDNA

Convert a PDB file to oxDNA

usage: oat PDB_oxDNA [-h] [-o output_file] [-b] [-q] pdb_file

Positional Arguments

pdb_file: The pdb file you wish to convert

Named Arguments

-o, --output

The filename to save the output oxDNA files to

-b, --backward

Use the old topology format? (strands will be listed 3’-5’)

Default: False

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Persistence Length

Calculates persistence length and contour length of a paired sequence of DNA.

usage: oat persistence_length [-h] [-p num_cpus] [-d data_file] [-n PLOT_NAME]
                              [-q]
                              traj_file input nucid_1 nucid_2

Positional Arguments

traj_file: The trajectory file to analyze
input: The input file associated with the trajectory
nucid_1: Nucleotide ID to start the calculation at
nucid_2: Nucleotide ID to stop the calculation at

Named Arguments

-p, --parallel

(optional) How many cores to use

-d, --data

If set, the correlations will be written to a txt file in the format offset correlation

-n, --plot_name

Name to save the plot showing the fit of persistence length to correlations. Defaults to persistence_length.png

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Plot energy

Plot oxDNA energy files

usage: oat plot_energy [-h] [-o output_file] [-f <histogram/trajectory/both>]
                       [-q]
                       energy [energy ...]

Positional Arguments

energy: Energy files to plot

Named Arguments

-o, --output

The name to save the graph file to

-f, --format

Output format for the graphs. Defaults to histogram. Options are “histogram”, “trajectory”, and “both”

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Principal component analysis

Calculates a principal component analysis of nucleotide deviations over a trajectory

usage: oat pca [-h] [-p num_cpus] [-c] [-n num_components] [-q]
               trajectory meanfile outfile

Positional Arguments

trajectory: the trajectory file you wish to analyze
meanfile: The mean structure from oat mean
outfile: the name of the oxView .json overlay file where the PCs will be written

Named Arguments

-p, --parallel

(optional) How many cores to use

-c, --cluster

Run the clusterer on each configuration’s position in PCA space?

Default: False

-n, --view_comps

(optional) Print the first N components as oxView overlay files (defaults to 1)

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Subset trajectory

Extracts parts of a structure into separate trajectories

usage: oat subset_trajectory [-h] [-i index outfile] [-p num_cpus] [-f] [-q]
                             trajectory topology

Positional Arguments

trajectory: The trajectory file to subset
topology: The topology file corresponding to the trajectory

Named Arguments

-i, --index

A space separated index file and the associated output file name. This can be called multiple times

-p, --parallel

(optional) How many cores to use

-f, --old_format

Use the old 3’-5’ topology format?

Default: False

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False

Superimpose

superimposes one or more structures sharing a topology to a reference structure

usage: oat superimpose [-h] [-i index_files) [index_file(s ...]]
                       [-o output_names [output_names ...]] [-q]
                       reference victims [victims ...]

Positional Arguments

reference: The reference configuration to superimpose to
victims: The configurations to superimpose on the reference

Named Arguments

-i, --index

Align to only a subset of particles from a space-separated list in the provided file. If 1 file provided, the indexing is applied to all structures. Otherwise an equal number of indexes and configurations must be provided.

-o, --output

The names of the output files (defaults to inputname_a.dat)

-q, --quiet

Don’t print ‘INFO’ messages to stderr

Default: False