added scripts from http://munk.cis.unimelb.edu.au/~stivalaa/satabsear…

…ch/scripts.tar.gz

scripts/build_betagrasp_query.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# build the tableau + distance matrix for tsrchd_sparse for the 
+# beta-grasp query (as the 4 largest strands and 1 alpha hexli in 
+# ubiquitin structure)
+#
+# $Id: build_betagrasp_query.sh 2908 2009-11-06 05:33:18Z astivala $
+
+# tableaux+distmatrix db file
+TABLEAUX_DB=${HOME}/tableauxdistmatrixdb.ascii
+
+echo "${TABLEAUX_DB}" 
+echo "T T F" # options: type,order,output
+pytableaucreate.py -bf -35 -tdssp -p none -i BGRASP -s2,1,8,5,3 ${HOME}/pdb/d1ubia_.ent  

scripts/build_cops_db.sh

@@ -0,0 +1,65 @@
+#!/bin/sh
+#
+# File:    build_cops_db.sh
+# Author:  Alex Stivala
+# Created: May 2010
+#
+#
+# build_cops_db.sh - build tableaux database for COPS benchmark data set
+#
+# Usage: build_cops_db.sh querydir dbfile
+#
+#         querydir is directory to put query input tableaux into
+#         dbfile   is basename of tableaux database to create, will create
+#                  dbfile.tableaux.pickle, dbfile.distmatrix.pickle and
+#                  dbfile.tableauxdistmatrixdb.ascii
+#
+# Builds tableaux for queries and database for the COPS benchmark data set
+# (Frank et al. 1999 "COPS Benchmark: interactive analysis of database 
+# search methods" Bioinformatics 26(4):574-575) available from
+# http://benchmark.services.came.sbg.ac.at/
+#
+# Requires the buildtableauxdb.py and pytableaucreate.py and convdb2.py
+#  scripts in PATH.
+#
+# WARNING: dbfile and files in querydir are overwritten if they exist.
+#
+# $Id: build_cops_db.sh 3632 2010-05-12 02:07:26Z alexs $
+
+COPS_ROOT=${HOME}/cops-benchmark-2009-6-full
+COPS_PDB_QUERIES=${COPS_ROOT}/queries/pdb
+COPS_PDB_DB=${COPS_ROOT}/database/pdb
+
+if [ $# -ne 2 ]; then
+    echo "Usage: $0 querydir dbfile" >&2
+    exit 1
+fi
+
+QUERYDIR=$1
+DBFILE=$2
+
+OPTIONS="-p none -35 -t dssp"
+
+if [ ! -d $QUERYDIR ]; then
+    mkdir $QUERYDIR
+fi
+
+tableaux_pickle=${DBFILE}.tableaux.pickle
+distmatrix_pickle=${DBFILE}.distmatrix.pickle
+tableauxdb=${DBFILE}.tableauxdb.ascii
+
+for query in ${COPS_PDB_QUERIES}/*.pdb
+do
+  qid=`basename $query .pdb`
+  qfile=${QUERYDIR}/${qid}.input
+  echo $tableauxdb > $qfile
+  echo "T T F" >> $qfile # options: type, order, output
+  pytableaucreate.py -f -b $OPTIONS $query >> $qfile
+done
+
+
+buildtableauxdb.py $OPTIONS $COPS_PDB_DB $tableaux_pickle
+buildtableauxdb.py -d $OPTIONS $COPS_PDB_DB $distmatrix_pickle
+
+convdb2.py $tableaux_pickle $distmatrix_pickle > $tableauxdb
+

scripts/build_fastscopdominfo_cache.py

@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+###############################################################################
+#
+# build_fastscopdominfo_cache.py - build pickle file for cached SCOP info
+#
+# File:    build_fastscopdominfo_cache.py
+# Author:  Alex Stivala
+# Created: March 2010
+#
+# $Id: scopdominfo.py 3009 2009-12-08 03:01:48Z alexs $
+# 
+###############################################################################
+
+"""
+Build cache (Python pickled dictionary) of information on the folds
+and superfamilies SCOP domain identifiers (sids).
+
+See usage in docstring for main()
+
+SCOP and ASTRAL data is obtained using the Bio.SCOP library (Casbon et
+al 2006 'A high level interface to SCOP and ASTRAL implemented in
+Python' BMC Bioinformatics 7:10) and depends on having the data
+downloaded, in SCOP_DIR (defined below).
+
+Downloaded SCOP files from
+
+http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html
+
+and ASTRAL files (in scopseq-1.73) from
+
+http://astral.berkeley.edu/scopseq-1.73.html
+
+The files downlaoded are:
+
+/local/charikar/SCOP/:
+dir.cla.scop.txt_1.73
+dir.des.scop.txt_1.73
+dir.hie.scop.txt_1.73
+
+/local/charikar/SCOP/scopseq-1.73:
+astral-scopdom-seqres-all-1.73.fa
+astral-scopdom-seqres-sel-gs-bib-95-1.73.id
+
+Other files there are indices built by Bio.SCOP when first used.
+"""
+
+import sys,os
+import pickle
+
+from Bio.SCOP import *
+
+from pathdefs import SCOP_DIR,SCOP_VERSION
+
+#-----------------------------------------------------------------------------
+#
+# Function definitions
+#
+#-----------------------------------------------------------------------------
+
+
+def build_scopdominfo_dict(scop):
+    """
+    Build dictionary with
+    information about superfamily and class of all SCOP domains
+    
+    Parameters:
+      scop - previously built Bio.SCOP Scop instance
+      
+    Return value:
+     dict {sid: (superfamily_sccs, superfamily_description, fold_sccs,fold_description)}
+      where
+     superfamily_sccs is SCOP sccs identifying the superfamily for the domain
+     superamily_description is SCOP dessription of the superfamily
+     fold_description is the SCOP descriptino of the fold the domain is in
+    """
+    scopdominfo_dict = {}
+    for scop_dom in scop.getDomains():
+        sid = scop_dom.sid
+        scop_superfamily = scop_dom.getAscendent('superfamily')
+        scop_fold = scop_dom.getAscendent('fold')
+        scop_class = scop_dom.getAscendent('class')
+        scopdominfo_dict[sid] = (scop_superfamily.sccs,
+                                 scop_superfamily.description,
+                                 scop_fold.sccs,
+                                 scop_fold.description)
+
+    return scopdominfo_dict
+
+
+#-----------------------------------------------------------------------------
+#
+# Main
+#
+#-----------------------------------------------------------------------------
+
+def usage(progname):
+    """
+    Print usage message and exit
+    """
+
+    sys.stderr.write("Usage: " +progname + " cachefile\n")
+    sys.exit(1)
+
+
+def main():
+    """
+    main for scomdominfo.py
+
+    Usage: scomdominfo.py  cachefile
+
+    cachefile is the file to create the pickled domain info dictionary as
+    WARNING: overwritten if it exists
+    """
+    if len(sys.argv) != 2:
+        usage(os.path.basename(sys.argv[0]))
+
+    pickle_filename = sys.argv[1]
+
+    sys.stderr.write("Reading SCOP Data...")
+    scop = Scop(dir_path=SCOP_DIR,version=SCOP_VERSION)
+    sys.stderr.write("done\n")
+
+    sys.stderr.write("Building domain info cache...")
+    scopdominfo_dict = build_scopdominfo_dict(scop)
+    sys.stderr.write("done. Got %d domain descriptions\n" %
+                     len(scopdominfo_dict))
+
+    sys.stderr.write("Writing cache to file %s...\n" % pickle_filename)
+    fh = open(pickle_filename, "w")
+    pickle.dump(scopdominfo_dict, fh)
+    fh.close()
+    sys.stderr.write("done\n")
+
+
+
+if __name__ == "__main__":
+    main()
+

scripts/build_fischer_cm.sh

@@ -0,0 +1,76 @@
+#!/bin/sh
+#
+# File:    build_fischer_cm.sh
+# Author:  Alex Stivala
+# Created: September 2008
+#
+# build_fischer_cm.sh - build contact maps for Fischer data set
+#
+# Usage: build_fischer_cm.sh outdir 
+#
+#   outdir is name of diretory which is created, and each contact map
+#   in ASCII format for use with MSVNS4MaxCMO (Pelta et al 2008) 
+#   or other program using this format of contact matrix is
+#   created as a separate file in that directory, in format for input
+#   for use with msvns4maxcmo_allall.py for example
+#
+# builds contact maps, using pconpy.py,
+# for the Fischer data set (Fischer et al 1996 Pac. Symp. Biocomput. 300-318))
+# This allows all-against-all (including redundant, so for n (=68)
+# there are n*n (=4624) total comparions) with e.g. msvns4maxcmo_allall.py,
+#
+#
+
+# root of divided PDB hierarchy
+PDBROOT=/local/charikar/pdb/pdb
+
+
+# List of probe PDB ids from Fischer 1996 Table I
+# Note several PDB ids obsoleted, so change to the replacments
+FISCHER_S="1mdc 1mup 1npx 1cpc_l 1onc 2ak3_a 1osa 1atn_a 1pfc 1arb 2cmd 2pia 2pna 3rub_l 1bbh_a 2sar_a 1c2r_a 3cd4 1chr_a 1aep 1dxt_b 2mnr 2fbj_l 1lts_d 1gky 2gbp 1hip 1bbt_1 2sas 2mta_c 1fc1_a 1tah_a 2hpd_a 1rcb 1aba 1sac_a 1eaf 1dsb_a 2sga 1stf_i 2hhm_a 2afn_a 1aaj 1fxi_a 5fd1 1bge_b 1isu_a 3hla_b 1gal 3chy 1cau_b 2aza_a 1hom 1cew 1tlk 1cid 2omf 1crl 1lga_a 2sim 1mio_c 1ten 4sbv_a 1tie 8i1b 2snv 1hrh_a 1gp1_a"
+
+
+# List of target fold PDB ids from Fischer 1996 Table I
+# Note several PDB ids obsoleted, so change to the replacments
+# this list corresponds to FISCHER_S ie FISCHER_P[i] is the target fold
+# for probe FISCHER_S[i] for 0 < i < 67
+FISCHER_P="1ifc 1rbp 3grs 1col_a 7rsa 1gky 4cpv 1atr 3hla_b 5ptp 6ldh 1fnb 1sha_a 6xia 2ccy_a 9rnt 1ycc 2rhe 2mnr 256b_a 1hbg 4enl 8fab_b 1bov_a 3adk 2liv 2hip_a 2plv1 2scp_a 1ycc 2fb4_h 1tca 2cpp 2gmf_a 1ego 2ayh 4cla 2trx_a 5ptp 1mol_a 1fbp_a 1aoz_a 1paz 1ubq 1iqz 2gmf_a 2hip_a 2rhe 3cox 2fox 1cau_a 1paz 1lfb 1mol_a 2rhe 2rhe 2por 1ede 2cyp 1nsb_a 2min_b 3hhr_b 2tbv_a 4fgf 4fgf 5ptp 1rnh 2trx_a"
+
+
+# List of 68 probe sequences from Fischer 1996 Table II
+# Note several PDB ids obsoleted, so change to the replacments
+FISCHER_LIST="1dxt_b 1cpc_l 1c2r_a 2mta_c 1bbh_a 1bge_b 1rcb 1aep 1osa 2sas 1hom 1lga_a 2hpd_a 1chr_a 2mnr 3rub_l 1crl 1tah_a 1aba 1dsb_a 1gpl_a 1atn_a 1hrh_a 3chy 2ak3_a 1gky 2cmd 1eaf 2gbp 1mio_c 2pia 1gal 1npx 2hhm_a 1hip 1isu_a 1fc1_a 2fbj_l 1cid 1pfc 1ten 1tlk 3cd4 3hla_b 1aaj 2afn_a 2aza_a 4sbv_a 1bbt_1 1sac_a 1lts_d 1tie 8i1b 1arb 2sga 2snv 1mdc 1mup 2sim 1cau_b 2omf 1fxi_a 1cew 1stf_i 2pna 2sar_a 1onc 5fd1"
+
+if [ $# -ne 1 ]; then
+    echo "Usage: $0  outdir" 2>&1
+    exit 1
+fi
+outdir=$1
+
+if [ ! -d ${outdir} ]; then
+    mkdir ${outdir}
+fi
+
+# pconpy.py options
+threshold=7.0
+pconpyopts="--cmaplist --threshold=${threshold} --seq_separation=2"
+
+for i in $FISCHER_LIST
+do
+    pdb=`echo $i | tr A-Z a-z`
+    if [ `expr index $pdb _` -ne 0 ]; then
+        # get chainid from e.g. 1BYO_B
+        chainid=`expr substr $pdb 6 1`
+        chainopt="--chains=$chainid"
+        pdbid=`expr substr $pdb 1 4`_${chainid}
+    else
+        chainopt=""
+        pdbid=`expr substr $pdb 1 4`
+    fi
+    pdb=`expr substr $pdb 1 4`
+    div=`expr substr $pdb 2 2`
+    pdbfile=${PDBROOT}/${div}/pdb${pdb}.ent.gz
+    pdbid=`echo $pdbid | tr '[a-z]' '[A-Z]'`
+    pconpy.py ${pconpyopts} ${chainopt} --pdb=${pdbfile} --output=${outdir}/${pdbid}.cm_a${threshold}
+done
+

scripts/build_fischer_db.sh

@@ -0,0 +1,85 @@
+#!/bin/sh
+#
+# File:    build_fischer_db.sh
+# Author:  Alex Stivala
+# Created: September 2008
+#
+# build_fischer_db.sh - build tableaux database for Fischer data set
+#
+# Usage: build_fischer_db.sh outdir 
+#
+#   outdir is name of diretory which is created, and each tableau 
+#   in ASCII format for use with tsrchd_sparse etc. is
+#   created as a separate file in that directory, in format for input
+#   for use with qptabmatch_allpairs.py for example
+#
+#   To stdout is written the ASCII format db of all the tableaux+dist matrices
+#   (just all the ones written to outdir concatenated together with
+#   blank line between each). 
+#  
+# builds database of tableaux, using pytableaycreate.py,
+# for the Fischer data set (Fischer et al 1996 Pac. Symp. Biocomput. 300-318))
+# This allows all-against-all (including redundant, so for n (=68)
+# there are n*n (=4624) total comparions) with e.g. qptabmatch_allall.py,
+#
+#
+
+# root of divided PDB hierarchy
+PDBROOT=/local/charikar/pdb/pdb
+
+
+# List of probe PDB ids from Fischer 1996 Table I
+# Note several PDB ids obsoleted, so change to the replacments
+FISCHER_S="1mdc 1mup 1npx 1cpc_l 1onc 2ak3_a 1osa 1atn_a 1pfc 1arb 2cmd 2pia 2pna 3rub_l 1bbh_a 2sar_a 1c2r_a 3cd4 1chr_a 1aep 1dxt_b 2mnr 2fbj_l 1lts_d 1gky 2gbp 1hip 1bbt_1 2sas 2mta_c 1fc1_a 1tah_a 2hpd_a 1rcb 1aba 1sac_a 1eaf 1dsb_a 2sga 1stf_i 2hhm_a 2afn_a 1aaj 1fxi_a 5fd1 1bge_b 1isu_a 3hla_b 1gal 3chy 1cau_b 2aza_a 1hom 1cew 1tlk 1cid 2omf 1crl 1lga_a 2sim 1mio_c 1ten 4sbv_a 1tie 8i1b 2snv 1hrh_a 1gp1_a"
+
+
+# List of target fold PDB ids from Fischer 1996 Table I
+# Note several PDB ids obsoleted, so change to the replacments
+# this list corresponds to FISCHER_S ie FISCHER_P[i] is the target fold
+# for probe FISCHER_S[i] for 0 < i < 67
+FISCHER_P="1ifc 1rbp 3grs 1col_a 7rsa 1gky 4cpv 1atr 3hla_b 5ptp 6ldh 1fnb 1sha_a 6xia 2ccy_a 9rnt 1ycc 2rhe 2mnr 256b_a 1hbg 4enl 8fab_b 1bov_a 3adk 2liv 2hip_a 2plv1 2scp_a 1ycc 2fb4_h 1tca 2cpp 2gmf_a 1ego 2ayh 4cla 2trx_a 5ptp 1mol_a 1fbp_a 1aoz_a 1paz 1ubq 1iqz 2gmf_a 2hip_a 2rhe 3cox 2fox 1cau_a 1paz 1lfb 1mol_a 2rhe 2rhe 2por 1ede 2cyp 1nsb_a 2min_b 3hhr_b 2tbv_a 4fgf 4fgf 5ptp 1rnh 2trx_a"
+
+
+# List of 68 probe sequences from Fischer 1996 Table II
+# Note several PDB ids obsoleted, so change to the replacments
+FISCHER_LIST="1dxt_b 1cpc_l 1c2r_a 2mta_c 1bbh_a 1bge_b 1rcb 1aep 1osa 2sas 1hom 1lga_a 2hpd_a 1chr_a 2mnr 3rub_l 1crl 1tah_a 1aba 1dsb_a 1gpl_a 1atn_a 1hrh_a 3chy 2ak3_a 1gky 2cmd 1eaf 2gbp 1mio_c 2pia 1gal 1npx 2hhm_a 1hip 1isu_a 1fc1_a 2fbj_l 1cid 1pfc 1ten 1tlk 3cd4 3hla_b 1aaj 2afn_a 2aza_a 4sbv_a 1bbt_1 1sac_a 1lts_d 1tie 8i1b 1arb 2sga 2snv 1mdc 1mup 2sim 1cau_b 2omf 1fxi_a 1cew 1stf_i 2pna 2sar_a 1onc 5fd1"
+
+if [ $# -ne 1 ]; then
+    echo "Usage: $0  outdir" 2>&1
+    exit 1
+fi
+outdir=$1
+
+if [ ! -d ${outdir} ]; then
+    mkdir ${outdir}
+fi
+
+# pytableaucreate.py options
+tabopts="-35 -f -t dssp -p none"
+
+first=1
+for i in $FISCHER_LIST
+do
+    pdb=`echo $i | tr A-Z a-z`
+    if [ `expr index $pdb _` -ne 0 ]; then
+        # get chainid from e.g. 1BYO_B
+        chainid=`expr substr $pdb 6 1`
+        chainopt="-c $chainid"
+        pdbid=`expr substr $pdb 1 4`_${chainid}
+    else
+        chainopt=""
+        pdbid=`expr substr $pdb 1 4`
+    fi
+    pdb=`expr substr $pdb 1 4`
+    div=`expr substr $pdb 2 2`
+    pdbfile=${PDBROOT}/${div}/pdb${pdb}.ent.gz
+    if [ $first -eq 0 ]; then
+        echo
+    else
+        first=0
+    fi
+    pytableaucreate.py ${tabopts} ${chainopt} ${pdbfile} | tee ${outdir}/${pdbid}.tableaudistmatrix 
+    # append distance matrix, removing identifier on first line
+    pytableaucreate.py -d ${tabopts} ${chainopt} ${pdbfile} | awk 'NR > 1'| tee -a ${outdir}/${pdbid}.tableaudistmatrix 
+done
+