crops-cropstr options¶

Cropping and Renumbering Operations for PDB structure and Sequence files (CROPS) v.1.0.2 This script will remove a number of residues from sequence and structure files in agreement to the intervals and other details supplied.

usage: crops-cropstr [-h] [-o Output_Directory]
                     [-p Oligoseq_ids [Oligoseq_ids ...]] [-i] [-r] [-f]
                     [-t | -u Uniprot_ratio_threshold Sequence_database]
                     [--version]
                     Sequence_filepath Structure_filepath Intervals_database

Positional Arguments¶

`Sequence_filepath`
	Input sequence filepath.
`Structure_filepath`
	Input structure filepath or dir. If a directory is inserted, it will act on all structure files in such directory.
`Intervals_database`
	Input intervals database filepath.

Named Arguments¶

`-o, --outdir`	Set output directory path. If not supplied, default is the one containing the input sequence.
`-p, --preselect`
	From all the sequences in the input sequence file, just print out this preselected subset.
`-i, --individual`
	One separated output fasta file per each sequence. Default: False
`-r, --remove_ligands`
	Remove ligands and water molecules from structure to prevent certain errors during renumbering. Default: False
`-f, --force_alignment`
	Use Needleman-Wunsch algorithm to try to bypass small disagreements between fasta and pdb sequences. Default: False
`-t, --terminals`
	Ignore interval discontinuities and only crop the ends off. Default: False
`-u, --uniprot_threshold`
	Act if SIFTS database is used as intervals source AND % residues from single Uniprot sequence is above threshold. Threshold: [MIN,MAX)=[0,100). Database path: uniclust##_yyyy_mm_consensus.fasta-path or server-only. The latter requires internet connexion.
`--version`	show program’s version number and exit