Command Line Interface

Usage

usage: 
            Minimal use: enzymm -i query.pdb -o result.tsv
            
            Recommended use: enzymm -l query_pdbs.list -o results.tsv -v --pdbs pdb_folder --include-query

Named Arguments

-V, --version

show program’s version number and exit

-j, --jobs

The number of threads to spawn for jobs in parallel. Pass 0 to select all cores. Negative numbers: leave this many cores free.

Default: 2

Mandatory Parameters

-o, --output: Output tsv file to which results should get written

Inputs - Use either or combine

-i, --input

File path to a PDB or mmCIF file to use as query

Default: []

-l, --list

File containing a list of PDB or mmCIF files to read

Optional Arguments

--pdbs

Output directory to which results should get written

-p, --parameters

Fixed Jess parameters for all templates. Jess space seperated parameters rmsd, distance, max_dynamic_distance

-t, --template-dir

Path to directory containing jess templates. This directory will be recursively searched.

-c, --conservation-cutoff

Atoms with a value in the B-factor column below this cutoff will be excluded form matching to the templates. Useful for predicted structures.

Default: 0

Flags

-v, --verbose

If process information and time progress should be printed to the command line

Default: False

-w, --warn

If warings about bad template processing or suspicous and missing annotations should be raised

Default: False

-q, --include-query

Include the query structure together with the hits in the pdb output

Default: False

--include-template

Include the template structure together with the hits in the pdb output

Default: False

-u, --unfiltered

If set, matches which logistic regression predicts as false based on RMSD and resdiue orientation will be retained. By default, matches predicted as false are removed.

Default: False

--transform

If set, one pdb file per matched template pdb with will be written in the coordinate system of that template

Default: False

--save-transformations

If set, save the 4x4 tansformation matrix in homogeneous coordinates needed to align the query with the template residues as a numpy .npz file.

Default: False

--skip-smaller-hits

If set, will not search with smaller templates if larger templates have already found hits.

Default: False

--match-small-templates

If set, templates with less then 3 defined sidechain residues will still be matched.

Default: False

--skip-annotation

If set, M-CSA derived templates will NOT be annotated with extra information.

Default: False

--simple-results

If set, a simpler version of the results table will be returned instead

Default: False

--per-residue-results

If set, an additional table with residue mappings betwen query, template and refrence will be returned too.

Default: False

--write-parquet

If set, all results tables will be written in parquet format instead of .tsv format. Requires polars!

Default: False