👾 Command Line Interface¶
You can access the Ensemblify Command Line Interface (CLI) using the ensemblify command.
(ensemblify_env) $ ensemblify [options]
ensemblify help¶
Access information about the available Ensemblify modules.
(ensemblify_env) $ ensemblify help
usage: ensemblify {modelling, generation, conversion, analysis, reweighting, clash_checking, help} [module options]
Command-line tool to access the modules of the Ensemblify Python library.
positional arguments:
help (h) Show this message and exit.
modelling (m, mod) Access the modelling module.
generation (g, gen) Access the generation module.
conversion (c, con) Access the conversion module.
analysis (a, ana) Access the analysis module.
reweighting (r, rew) Access the reweighting module.
clash_checking (cch) Access the clash checking module.
ensemblify modelling --help¶
Access information about the Ensemblify modelling module.
(ensemblify_env) $ ensemblify modelling --help
usage: ensemblify {modelling, mod, m} [options]
The modelling module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-f, --fastas Path(s) to FASTA file(s) containing the sequences of all protein domains (folded + disordered) to be fused, in order from N- to C-terminal.
-p, --pdbs Path(s) to PDB file(s) containing the structures of folded protein domains to be fused, in order from N- to C-terminal.
-i, --id Name for the output fused PDB file (without extension).
-o, --output_dir (Optional) Directory where the output fused PDB file will be saved. Defaults to current working directory.
ensemblify generation --help¶
Access information about the Ensemblify generation module.
(ensemblify_env) $ ensemblify generation --help
usage: ensemblify {generation, gen, g} [options]
The generation module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-p, --parameters (Optional) Path to parameters file for ensemble generation (.yml). Incompatible with --suggest_targets.
-st, --suggest_targets (Optional) UniProt accession to query MobiDB, TED and AFDB. Incompatible with --parameters.
ensemblify conversion --help¶
Access information about the Ensemblify conversion module.
(ensemblify_env) $ ensemblify conversion --help
usage: ensemblify {conversion, con, c} [options]
The conversion module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-e, --ensembledir Path to directory where ensemble files (.pdb) are located. Defaults to current working directory.
-t, --trajectorydir Path to directory where trajectory file (.xtc) will be created. Defaults to current working directory.
-i, --trajectoryid Prefix for created trajectory file (.xtc). Defaults to None.
-s, --size (Optional) Number of .pdb files to use for trajectory creation. Defaults to all .pdb files in the ensemble directory.
ensemblify analysis --help¶
Access information about the Ensemblify analysis module.
(ensemblify_env) $ ensemblify analysis --help
usage: ensemblify {analysis, ana, a} [options]
The analysis module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-trj, --trajectory Path(s) to trajectory file(s) (.xtc).
-top, --topology Path(s) to topology file(s) (.pdb).
-tid, --trajectoryid Prefix identifier(s) for trajectory file(s).
-out, --outputdir (Optional) Path to output directory. Defaults to current working directory.
-ram, --ramachandran (Optional) Whether to calculate a dihedral angles matrix. Defaults to True.
-dmx, --distancematrix (Optional) Whether to calculate a distance matrix. Defaults to True.
-cmx, --contactmatrix (Optional) Whether to calculate a contact matrix. Defaults to True.
-ssf, --ssfrequency (Optional) Whether to calculate a secondary structure assignment frequency matrix. Defaults to True.
-rgy, --radiusgyration (Optional) Whether to calculate a radius of gyration distribution. Defaults to True.
-mxd, --maxdist (Optional) Whether to calculate a maximum distance distribution. Defaults to True.
-eed, --endtoend (Optional) Whether to calculate an end-to-end distance distribution. Defaults to True.
-cmd, --centermassdist (Optional) Pair(s) of MDAnalysis selection strings for which to calculate a center of mass distance distribution. Defaults to None.
-cls, --colors (Optional) List of color hexcodes to use, one for each analyzed trajectory. Defaults to colorblind friendly color palette.
ensemblify reweighting --help¶
Access information about the Ensemblify reweighting module.
(ensemblify_env) $ ensemblify reweighting --help
usage: ensemblify {reweighting, rew, r} [options]
The reweighting module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-trj, --trajectory Path to trajectory file (.xtc).
-top, --topology Path to topology file (.pdb).
-tid, --trajectoryid Name to give reweighted trajectory file(s) in created reweighting figures.
-exp, --expdata Path to experimental data file (.dat).
-expt, --exptype (Optional) Type of provided experimental data. Required if not specified in experimental data file.
-out, --outputdir (Optional) Path to output directory. Defaults to current working directory.
-tht, --theta (Optional) List of values to try as the theta parameter in BME. Defaults to [1, 10, 20, 50, 75, 100, 200, 400, 750, 1000, 5000, 10000].
-csaxs, --calcsaxs (Optional) Path to file (.dat) with calculated SAXS profiles for each conformer in the ensemble. Defaults to None.
-cmx, --contactmatrix (Optional) Path to calculated contact matrix file (.csv). Defaults to None.
-dmx, --distancematrix (Optional) Path to calculated distance matrix file (.csv). Defaults to None.
-ssf, --ssfrequency (Optional) Path to calculated secondary structure frequency matrix file (.csv). Defaults to None.
-met, --metrics (Optional) Path to calculated structural metrics file (.csv). Defaults to None.
-rgy, --compare_rg (Optional) Whether to calculate and compare uniform/reweighted radius of gyration distributions. Defaults to True.
-mxd, --compare_dmax (Optional) Whether to calculate and compare uniform/reweighted maximum distance distributions. Defaults to True.
-eed, --compare_eed (Optional) Whether to calculate and compare uniform/reweighted end-to-end distance distributions. Defaults to True.
-cmd, --compare_cmdist (Optional) Pair(s) of MDAnalysis selection strings for which to calculate and compare uniform/reweighted center of mass distance distributions. Defaults to None.
-pso, --pepsi_saxs_opt (Optional) Additional command line options that will be passed onto Pepsi-SAXS invocation. Defaults to None.
ensemblify clash_checking --help¶
Access information about the Ensemblify clash_checking module.
(ensemblify_env) $ ensemblify clash_checking --help
usage: ensemblify {clash_checking, cch} [options]
The clash checking module of the Ensemblify Python library.
options:
-h, --help show this help message and exit
-e, --ensembledir Path to directory where ensemble .pdb structures are stored. Defaults to current working directory.
-s, --samplingtargets (Optional) Path to file (.yml) with sampling targets: mapping of chain letters to residue ranges. Defaults to None.
-i, --inputstructure (Optional) Path to input structure (.pdb) used to generate the ensemble. Defaults to None.