cath-ssap

Description

============
cath-ssap v0.14.1-0-gbb6e6a3 [2017-05-31]
============

Run a SSAP pairwise structural alignment
[algorithm devised by C A Orengo and W R Taylor, see --citation-help]

Build
-----
   May 31 2017 08:33:21
   Clang version 3.6.2 (branches/release_36)
   GNU libstdc++ version 20160726
   Boost 1_57

Usage

Usage: cath-ssap [options] <protein1> <protein2>

Run a SSAP pairwise structural alignment
[algorithm devised by C A Orengo and W R Taylor, see --citation-help]

cath-ssap uses two types of structural comparison:
  1. Fast SSAP: a quick secondary-structure based SSAP alignment
  2. Slow SSAP: residue alignment only

If both structures have more than one SS element, a fast SSAP is run first. If the fast SSAP score isn't good, another fast SSAP is run with looser cutoffs. If the (best) fast SSAP score isn't good, a slow SSAP is run. Only the best of these scores is output. These behaviours can be configured using the parameters below.)

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

Standard SSAP options:
  --debug                                  Output debugging information
  -o [ --outfile ] <file>                  [DEPRECATED] Output scores to <file> rather than to stdout
  --clique-file <file>                     Read clique from <file>
  --domin-file <file>                      Read domin from <file>
  --max-score-to-fast-rerun <score> (=65)  Run a second fast SSAP with looser cutoffs if the first fast SSAP's score falls below <score>
  --max-score-to-slow-rerun <score> (=75)  Perform a slow SSAP if the (best) fast SSAP score falls below <score>
  --slow-ssap-only                         Don't try any fast SSAPs; only use slow SSAP
  --local-ssap-score                       [DEPRECATED] Normalise the SSAP score over the length of the smallest domain rather than the largest
  --all-scores                             [DEPRECATED] Output all SSAP scores from fast and slow runs, not just the highest
  --prot-src-files <set> (=PDB)            Read the protein data from the set of files <set>, of available sets:
                                           PDB, PDB_DSSP, PDB_DSSP_SEC, WOLF_SEC
  --supdir <dir>                           [DEPRECATED] Output a superposition to directory <dir>
  --aligndir <dir> (=".")                  Write alignment to directory <dir>
  --min-score-for-files <score> (=0)       Only output alignment/superposition files if the SSAP score exceeds <score>
  --min-sup-score <score> (=-0.25)         [DEPRECATED] Calculate superposition based on the residue-pairs with scores greater than <score>
  --rasmol-script                          [DEPRECATED] Write a rasmol superposition script to load and colour the superposed structures
  --xmlsup                                 [DEPRECATED] Write a small xml superposition file, from which a larger superposition file can be reconstructed

Conversion between a protein's name and its data files:
  --pdb-path <path> (=.)                   Search for PDB files using the path <path>
  --dssp-path <path> (=.)                  Search for DSSP files using the path <path>
  --wolf-path <path> (=.)                  Search for wolf files using the path <path>
  --sec-path <path> (=.)                   Search for sec files using the path <path>
  --pdb-prefix <pre>                       Prepend the prefix <pre> to a protein's name to form its PDB filename
  --dssp-prefix <pre>                      Prepend the prefix <pre> to a protein's name to form its DSSP filename
  --wolf-prefix <pre>                      Prepend the prefix <pre> to a protein's name to form its wolf filename
  --sec-prefix <pre>                       Prepend the prefix <pre> to a protein's name to form its sec filename
  --pdb-suffix <suf>                       Append the suffix <suf> to a protein's name to form its PDB filename
  --dssp-suffix <suf> (=.dssp)             Append the suffix <suf> to a protein's name to form its DSSP filename
  --wolf-suffix <suf> (=.wolf)             Append the suffix <suf> to a protein's name to form its wolf filename
  --sec-suffix <suf> (=.sec)               Append the suffix <suf> to a protein's name to form its sec filename

Detailed help:
  --alignment-help                         Help on alignment format
  --citation-help                          Help on SSAP authorship & how to cite it
  --scores-help                            Help on scores format

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