Command Line Tools

ProteinNetPy contains several utility scripts to help work with ProteinNet files.

add_angles_to_proteinnet

Add backbone and dihedral angles to a text ProteinNet data file.

Angles are added under new identifiers [RAMA] and [CHI], each with a final mask row. Backbone angles are in rows ordered omega, phi, psi. Dihedral angles require a local PDB database to query from.

usage: add_angles_to_proteinnet [-h] [--pdb PDB] [--gzip] [--filter] [--rama]
                                [--chi]
                                P

Positional Arguments

P

Input

Named Arguments

--pdb, -p

Path to root of local PDB directory, expects mmCIF to be available

Default: “data/pdb”

--gzip, -g

Local PDB files are gzipped

Default: False

--filter, -f

Dont print records where no structure is found

Default: False

--rama, -r

Calculate ramachandran angles

Default: False

--chi, -c

Calculate chi1 angles

Default: False

filter_proteinnet

Filter a ProteinNet file to include/exclude specific records

usage: filter_proteinnet [-h] [--file FILE] [--exclude] P [I ...]

Positional Arguments

P

Input ProteinNet file

I

IDs list

Named Arguments

--file, -f

File containing one ID per line

--exclude, -e

Exclude IDs

Default: False

proteinnet_to_fasta

Generate a fasta file from a ProteinNet text data file

usage: proteinnet_to_fasta [-h] P

Positional Arguments

P

Input ProteinNet text file