cath-refine-align.ubuntu-20.04

Description

============
cath-refine-align v0.16.10-0-g99edb28 [2021-04-20]
============

Iteratively refine an existing alignment by attempting to optimise SSAP score

Build
-----
   Apr 20 2021 13:24:46
   GNU C++ version 10.2.0
   GNU libstdc++ version 20200808
   Boost 1_71

Usage

Usage: cath-refine-align alignment_source protein_file_source [superposition_outputs]

Iteratively refine an existing alignment by attempting to optimise SSAP score

Please specify:
 * at most one alignment (default: --do-the-ssaps)
 * one method of reading proteins (number of proteins currently restricted to 2)

PyMOL is started if no alignment or superposition output option is specified

Miscellaneous:
  -h [ --help ]                      Output help message
  -v [ --version ]                   Output version information

Input:

Alignment source:
  --res-name-align                   Align residues by simply matching their names (numbers+insert)
                                     (for multiple models of the same structure)
  --fasta-aln-infile <file>          Read FASTA alignment from file <file>
  --ssap-aln-infile <file>           Read SSAP alignment from file <file>
  --cora-aln-infile <file>           Read CORA alignment from file <file>
  --ssap-scores-infile <file>        Glue pairwise alignments together using SSAP scores in file <file>
                                     Assumes all .list alignment files in same directory
  --do-the-ssaps [=<dir>(="")]       Do the required SSAPs in directory <dir>; use results as with --ssap-scores-infile
                                     Use a suitable temp directory if none is specified

Alignment refining:
  --align-refining <refn> (=HEAVY)   Apply <refn> refining to the alignment, one of available values:
                                        NO    - Don't refine the alignment
                                        LIGHT - Refine any alignments with few entries; glue alignments one more entry at a time
                                        HEAVY - Perform heavy (slow) refining on the alignment, including when gluing alignments together
                                     This can change the method of gluing alignments under --ssap-scores-infile and --do-the-ssaps

ID options:
  --id arg                           Structure ids

PDB files source:
  --pdb-infile <pdbfile>             Read PDB from file <pdbfile> (may be specified multiple times)
  --pdbs-from-stdin                  Read PDBs from stdin (separated by line: "END   ")

Regions:
  --align-regions <regions>          Handle region(s) <regions> as the alignment part of the structure.
                                     May be specified multiple times, in correspondence with the structures.
                                     Format is: D[5inwB02]251-348:B,408-416A:B
                                     (Put <regions> in quotes to prevent the square brackets confusing your shell ("No match"))

Output:

Alignment output:
  --aln-to-cath-aln-file arg         [EXPERIMENTAL] Write the alignment to a CATH alignment file
  --aln-to-cath-aln-stdout           [EXPERIMENTAL] Print the alignment to stdout in CATH alignment format
  --aln-to-fasta-file arg            Write the alignment to a FASTA file
  --aln-to-fasta-stdout              Print the alignment to stdout in FASTA format
  --aln-to-ssap-file arg             Write the alignment to a SSAP file
  --aln-to-ssap-stdout               Print the alignment to stdout as SSAP
  --aln-to-html-file arg             Write the alignment to a HTML file
  --aln-to-html-stdout               Print the alignment to stdout as HTML

Superposition output:
  --sup-to-pdb-file arg              Write the superposed structures to a single PDB file arg, separated using faked chain codes
  --sup-to-pdb-files-dir arg         Write the superposed structures to separate PDB files in directory arg
  --sup-to-stdout                    Print the superposed structures to stdout, separated using faked chain codes
  --sup-to-pymol                     Start up PyMOL for viewing the superposition
  --pymol-program arg (="pymol")     Use arg as the PyMOL executable for viewing; may optionally include the full path
  --sup-to-pymol-file arg            Write the superposition to a PyMOL script arg
                                     (Recommended filename extension: .pml)
  --sup-to-json-file arg             Write the superposition to JSON superposition file
                                     (Recommended filename extension: .sup_json)

Viewer (eg PyMOL, Jmol etc) options:
  --viewer-colours <colrs>           Use <colrs> to colour successive entries in the viewer
                                     (format: colon-separated list of comma-separated triples of RGB values between 0 and 1)
                                     (will wrap-around when it runs out of colours)
  --gradient-colour-alignment        Colour the length of the alignment with a rainbow gradient (blue -> red)
  --show-scores-if-present           Show the alignment scores
                                     (use with gradient-colour-alignment)
  --scores-to-equivs                 Show the alignment scores to equivalent positions, which increases relative scores where few entries are aligned
                                     (use with --gradient-colour-alignment and --show-scores-if-present)
  --normalise-scores                 When showing scores, normalise them to the highest score in the alignment
                                     (use with --gradient-colour-alignment and --show-scores-if-present)

Please tell us your cath-tools bugs/suggestions : https://github.com/UCLOrengoGroup/cath-tools/issues/new