[med-svn] r1251 - in trunk/packages/mustang/trunk/debian: . patches
mok0-guest at alioth.debian.org
mok0-guest at alioth.debian.org
Fri Feb 1 14:16:00 UTC 2008
Author: mok0-guest
Date: 2008-02-01 14:16:00 +0000 (Fri, 01 Feb 2008)
New Revision: 1251
Added:
trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch
trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch
trunk/packages/mustang/trunk/debian/patches/03-test_zf-cchh.dpatch
Removed:
trunk/packages/mustang/trunk/debian/mustang.1
trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch
trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
Modified:
trunk/packages/mustang/trunk/debian/mustang.manpages
trunk/packages/mustang/trunk/debian/patches/00list
trunk/packages/mustang/trunk/debian/rules
Log:
This commit includes a new patch that incorporates upstream patches.
Furthermore, the pdb files, for testing mustang, is now included
in a separate package. There is a "small" test, that comes with the
mustang binary, consisting of a script "runtest" which will download
two pdb files on the fly and allow the user to test the program.
Deleted: trunk/packages/mustang/trunk/debian/mustang.1
===================================================================
--- trunk/packages/mustang/trunk/debian/mustang.1 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/mustang.1 2008-02-01 14:16:00 UTC (rev 1251)
@@ -1,95 +0,0 @@
-.\" Hey, EMACS: -*- mode: nroff; mode:font-lock -*-
-.TH MUSTANG 1 "June 6, 2007"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.SH NAME
-mustang \- a multiple structural alignment algorithm
-.SH SYNOPSIS
-.B mustang
-.RI [ options ] " files" ...
-.SH DESCRIPTION
-This manual page documents briefly the \fBmustang\fR command.
-
-\fBMustang\fR is a program that implements an algorithm for structural
-alignment of multiple protein structures. Given a set of PDB files, the
-program uses the spatial information in the Calpha atoms of the set to
-produce a sequence alignment. Based on a progressive pairwise heuristic
-the algorithm then proceeds through a number of refinement
-passes. \fBMustang\fR reports the multiple sequence alignment and the
-corresponding superposition of structures.
-
-To keep the command line short the user can write the path and file names
-into a (description) file and supply the description file at the command
-line using the '\-f' option. For example see the file used to test the
-installation: '/usr/share/doc/mustang/examples/test_zf\-CCHH'.
-
-PATH should have a prefix '>'. When the program parses this file, it looks
-for the line starting with '>' symbol (whitespaces are ignored before and
-after the symbol). The PATH containing the PDB files of the structures to
-be aligned should follow. See for example: /usr/share/doc/mustang/examples/test_zf\-CCHH'.
-
-FILENAMES should have a prefix '+' (whitespaces are ignored before and
-after this symbol). If PATH is specified then only the filenames should be
-provided after the '+' symbol. However, if PATH line is NOT provided, then
-the absolute/relative paths of the structure files should be provided.
-
-The description file format is described further under the \fB\-f\fP CmdLine
-option).
-.SH OPTIONS
-A summary of options is included below.
-.TP
-.BI \-p " <path>"
-Path to the directory holding the (PDB) structures
-to be aligned.
-.TP
-.BI \-i " <struct\-1> <struct\-2>" ...
-Input structures to be aligned. Note: if \fB\-p\fR option is used in the
-command line, supply only the file names of the structures; if not give the
-absolute/relative path of each of the input structures.
-.TP
-.BI \-f " <description file>"
-This option is used to AVOID entering the path (\fB\-p\fR) and file name
-(\fB\-i\fR) details in the command line. Instead, to keep the command line
-short, the user can enter the path and file name details in a "description"
-file and supply it in the command line. The format of the "description
-file" is furher discussed in the 'DESCRIPTION' section above. Note: the
-options { \fB\-p\fR , \fB\-i\fR} and {\fB\-f\fR} are mutually exclusive.
-.TP
-.BI \-o " <output identifier>"
-A common identifier for various outputs of the program. Appropriate
-extentions (e.g. \fI<identifier>\fR.html, \fI<identifier>\fR.pdb,
-\fI<identifier>\fR.msf) will be added to this identifier depending on the
-options the user specifies in the command line.
-DEFAULT output identifier: 'results'
-.TP
-.BI \-F " <fmt>"
-Alignment output format. The choices for \fI<fmt>\fR are: 'html', 'fasta',
- 'pir', 'msf'. DEFAULT format: 'html'
-.TP
-.BI \-D " [CA\-CA diameter]"
-Produce an HTML file where the the residues are reported in lower case with
-grey background when the aligned(superposed) CA\-CA diamter of residues in a
-column of alignment is > the CA\-CA diameter threshold.
-.TP
-.BI \-s " [<ON>/<OFF>]"
-Generate a PDB file containing optimal superposition of all the structures
-based on the alignment. DEFAULT: 'ON'.
-.TP
-.B \-\-help
-display a help message and exits.
-.TP
-.B \-\-version
-output version information and exits.
-
-.SH AUTHORS
-\fBMustang\fR was written by A. S. Konagurthu, using the algorithm of
-A. S. Konagurthu \fIet al.\fR (see reference)
-.PP
-This manual page was written by Morten Kjeldgaard <mok at bioxray.au.dk>.
-
-.SH REFERENCE
-A. S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk, MUSTANG: A
-multiple structural alignment algorithm, \fBProteins, 64(3) 559-574 (2006).\fR
-
-.SH SEE ALSO
-\fBMustang\fR's homepage: http://www.cs.mu.oz.au/~arun/mustang/
Modified: trunk/packages/mustang/trunk/debian/mustang.manpages
===================================================================
--- trunk/packages/mustang/trunk/debian/mustang.manpages 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/mustang.manpages 2008-02-01 14:16:00 UTC (rev 1251)
@@ -1 +1 @@
-debian/mustang.1
+mustang.1
Modified: trunk/packages/mustang/trunk/debian/patches/00list
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/00list 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/patches/00list 2008-02-01 14:16:00 UTC (rev 1251)
@@ -1,2 +1,3 @@
-test_zf-cchh.dpatch
-main.cpp.dpatch
+01-upstream.dpatch
+02-main.cpp.dpatch
+03-test_zf-cchh.dpatch
Added: trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch 2008-02-01 14:16:00 UTC (rev 1251)
@@ -0,0 +1,360 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## upstream.dpatch by Morten Kjeldgaard <mok at bioxray.au.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+# Arun S. Konagurthu
+# 15 January 2008
+#
+diff --recursive -c --new-file src/./CmdLineParser_2.cpp ../old/MUSTANG_v.3/src/./CmdLineParser_2.cpp
+*** foo/src/./CmdLineParser_2.cpp 2008-01-15 13:34:17.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./CmdLineParser_2.cpp 2006-10-19 12:28:31.000000000 -0400
+***************
+*** 387,393 ****
+ static int cntr = 0 ;
+ if( cntr == 0 )
+ {
+! cerr << "MUSTANG v.3 Command Line error!\n" ;
+ }
+
+ cerr << "::" << setw(2) << cntr+1 <<"::" << " invalid option: " << o << endl ;
+--- 387,393 ----
+ static int cntr = 0 ;
+ if( cntr == 0 )
+ {
+! cerr << "MUSTANG vO.2 Command Line error!\n" ;
+ }
+
+ cerr << "::" << setw(2) << cntr+1 <<"::" << " invalid option: " << o << endl ;
+***************
+*** 786,792 ****
+ cerr << "Try \'mustang --help\' for more information.\n" ;
+ exit(0) ;
+ }
+! //cerr << "MUSTANG v.3: MUltiple STructural Alignment alNGorithm.\n" ;
+ //cerr << "Authors: A.S. Konagurthu, J.C. Whisstock, and P.J. Stuckey, A.M. Lesk\n" ;
+ //cerr << "Written by : A.S. Konagurthu\n" ;
+ exit(0);
+--- 786,792 ----
+ cerr << "Try \'mustang --help\' for more information.\n" ;
+ exit(0) ;
+ }
+! //cerr << "MUSTANG v0.3: MUltiple STructural Alignment alNGorithm.\n" ;
+ //cerr << "Authors: A.S. Konagurthu, J.C. Whisstock, and P.J. Stuckey, A.M. Lesk\n" ;
+ //cerr << "Written by : A.S. Konagurthu\n" ;
+ exit(0);
+diff --recursive -c --new-file src/./ew_2.cpp ../old/MUSTANG_v.3/src/./ew_2.cpp
+*** foo/src/./ew_2.cpp 2008-01-15 13:18:34.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./ew_2.cpp 2005-11-15 19:19:56.000000000 -0500
+***************
+*** 1033,1039 ****
+ int start_pos ;
+
+ //dealing with left-hand terminal
+! if( I > 5 || J > 5 ) // Nterminal- NO cut
+ {
+ start_pos = ( NEQUIV-(2*EXAMINATION_SIZE) ) >= 4 ? 4 : ( NEQUIV-(2*EXAMINATION_SIZE) ) ;
+ CORESIZE = start_pos ;
+--- 1033,1039 ----
+ int start_pos ;
+
+ //dealing with left-hand terminal
+! if( I > 5 || J == 5 ) // Nterminal- NO cut
+ {
+ start_pos = ( NEQUIV-(2*EXAMINATION_SIZE) ) >= 4 ? 4 : ( NEQUIV-(2*EXAMINATION_SIZE) ) ;
+ CORESIZE = start_pos ;
+diff --recursive -c --new-file src/./extended_lib_gen_3.cpp ../old/MUSTANG_v.3/src/./extended_lib_gen_3.cpp
+*** foo/src/./extended_lib_gen_3.cpp 2008-01-15 13:18:34.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./extended_lib_gen_3.cpp 2005-11-15 19:19:56.000000000 -0500
+***************
+*** 32,40 ****
+ #include "macros.h"
+ #include "extended_lib_gen.h"
+ #include "de_alloc_routines.h"
+-
+- int Aminus1, Aminus2, Aminus3, Aminus4, Aplus1, Aplus2, Aplus3, Aplus4 ;
+- int Bmprime1, Bmprime2, Bmprime3, Bmprime4, Bpprime1, Bpprime2, Bpprime3, Bpprime4 ;
+ /* *******************************************
+ * GLOBAL FUNCTION DEFINITION *
+ * ******************************************* */
+--- 32,37 ----
+***************
+*** 213,218 ****
+--- 210,216 ----
+ {
+ float AAA, BBB ;
+ AAA = Edge_Weights[ind][A][B] ;
++ BBB = Edge_Weights[ind][A][B_orig] ;
+
+ /*
+ The paln here is not to extended an arc between A and B thro' C if
+***************
+*** 223,244 ****
+ This helps to stop random drift aways in the final multiple alignment.
+ at the same time allow those that are continuous.
+ */
+! Aminus1 = A-1 ; Aminus2 = A-2 ; Aminus3 = A-3 ; Aminus4 = A-4 ;
+! if(Aminus1>=0) Bmprime1 = merge_trav->mates[0][Aminus1] ; else Bmprime1 = -1 ;
+! if(Aminus2>=0) Bmprime2 = merge_trav->mates[0][Aminus2] ; else Bmprime2 = -1 ;
+! if(Aminus3>=0) Bmprime3 = merge_trav->mates[0][Aminus3] ; else Bmprime3 = -1 ;
+! if(Aminus4>=0) Bmprime4 = merge_trav->mates[0][Aminus4] ; else Bmprime4 = -1 ;
+!
+ int cntm = 0;
+ if( Bmprime1 == B-1 ) cntm++ ;
+ if( Bmprime2 == B-2 ) cntm++ ;
+ if( Bmprime3 == B-3 ) cntm++ ;
+ if( Bmprime4 == B-4 ) cntm++ ;
+! Aplus1 = A+1 ; Aplus2 = A+2 ; Aplus3 = A+3 ; Aplus4 = A+4 ;
+! if(Aplus1<merge_trav->sizes[0]) Bpprime1 = merge_trav->mates[0][Aplus1] ; else Bpprime1 = -1 ;
+! if(Aplus2<merge_trav->sizes[0]) Bpprime2 = merge_trav->mates[0][Aplus2] ; else Bpprime2 = -1 ;
+! if(Aplus3<merge_trav->sizes[0]) Bpprime3 = merge_trav->mates[0][Aplus3] ; else Bpprime3 = -1 ;
+! if(Aplus4<merge_trav->sizes[0]) Bpprime4 = merge_trav->mates[0][Aplus4] ; else Bpprime4 = -1 ;
+ int cntp = 0;
+ if( Bpprime1 == B+1 ) cntp++ ;
+ if( Bpprime2 == B+2 ) cntp++ ;
+--- 221,241 ----
+ This helps to stop random drift aways in the final multiple alignment.
+ at the same time allow those that are continuous.
+ */
+! int Aminus1 = A-1 ; int Aminus2 = A-2 ; int Aminus3 = A-3 ; int Aminus4 = A-4 ;
+! int Bmprime1 = merge_trav->mates[0][Aminus1] ;
+! int Bmprime2 = merge_trav->mates[0][Aminus2] ;
+! int Bmprime3 = merge_trav->mates[0][Aminus3] ;
+! int Bmprime4 = merge_trav->mates[0][Aminus4] ;
+ int cntm = 0;
+ if( Bmprime1 == B-1 ) cntm++ ;
+ if( Bmprime2 == B-2 ) cntm++ ;
+ if( Bmprime3 == B-3 ) cntm++ ;
+ if( Bmprime4 == B-4 ) cntm++ ;
+! int Aplus1 = A+1 ; int Aplus2 = A+2 ; int Aplus3 = A+3 ; int Aplus4 = A+4 ;
+! int Bpprime1 = merge_trav->mates[0][Aplus1] ;
+! int Bpprime2 = merge_trav->mates[0][Aplus2] ;
+! int Bpprime3 = merge_trav->mates[0][Aplus3] ;
+! int Bpprime4 = merge_trav->mates[0][Aplus4] ;
+ int cntp = 0;
+ if( Bpprime1 == B+1 ) cntp++ ;
+ if( Bpprime2 == B+2 ) cntp++ ;
+***************
+*** 263,274 ****
+ //if( B_orig != -99 || merge_trav->mates[1][B] != -99 || cntm >= 3 ||cntp >=3 )
+ if( extend_flag == YES )
+ {
+
+! if( Extended_Edge_Weights[ind][A][B] >= 0 )
+ Extended_Edge_Weights[ind][A][B] ++ ;
+ else
+ Extended_Edge_Weights[ind][A][B] = 1 ;
+ }
+ }
+ temp_merge_trav_CB= temp_merge_trav_CB->link ;
+ }
+--- 260,321 ----
+ //if( B_orig != -99 || merge_trav->mates[1][B] != -99 || cntm >= 3 ||cntp >=3 )
+ if( extend_flag == YES )
+ {
++ float min = AAA < BBB ? AAA : BBB ;
+
+! if( Extended_Edge_Weights[ind][A][B] >= BBB && BBB >= 0 )
+ Extended_Edge_Weights[ind][A][B] ++ ;
++ else if( BBB >= 0 )
++ {
++ Extended_Edge_Weights[ind][A][B] =
++ Edge_Weights[ind][A][B_orig]+1 ;
++ }
+ else
+ Extended_Edge_Weights[ind][A][B] = 1 ;
+ }
++
++ /*
++ int ZZZ_ind1 , ZZZ_ind2;
++ if( intermediate > I)
++ ZZZ_ind1 = (NSTRUCTS-1)*I + intermediate - ( I*(I+1)/2+1);
++ else
++ ZZZ_ind1 = (NSTRUCTS-1)*intermediate + I - ( intermediate*(intermediate+1)/2+1);
++ if( intermediate > J)
++ ZZZ_ind2 = (NSTRUCTS-1)*J + intermediate - ( J*(J+1)/2+1);
++ else
++ ZZZ_ind2 = (NSTRUCTS-1)*intermediate + J - ( intermediate*(intermediate+1)/2+1);
++ */
++
++ /*
++ AAA = (intermediate > I) ?
++ ((Edge_Weights[ZZZ_ind1][A][C]*tot_max)/
++ max_edge_weights[ZZZ_ind1]) :
++ ((Edge_Weights[ZZZ_ind1][C][A]*tot_max)/
++ max_edge_weights[ZZZ_ind1]) ;
++ BBB = (intermediate < J) ?
++ ((Edge_Weights[ZZZ_ind2][C][B]*tot_max)/
++ max_edge_weights[ZZZ_ind2]) :
++ ((Edge_Weights[ZZZ_ind2][B][C]*tot_max)/
++ max_edge_weights[ZZZ_ind2]) ;
++ float min = AAA < BBB ? AAA : BBB ;
++ Extended_Edge_Weights[ind][A][B]+=min ;
++ */
++ /*
++ if( B_orig != -99 )
++ {
++ //AAA = ((Edge_Weights[ind][A][B_orig]*tot_max)/
++ // max_edge_weights[ZZZ_ind1]) ;
++ //BBB = ((Edge_Weights[ind][A][B]*tot_max)/
++ // max_edge_weights[ZZZ_ind1]) ;
++ //float min = AAA < BBB ? AAA : BBB ;
++ //float max = AAA > BBB ? AAA : BBB ;
++ Extended_Edge_Weights[ind][A][B] ++ ;
++ }
++ else
++ Extended_Edge_Weights[ind][A][B] ++ ;
++ //Extended_Edge_Weights[ind][A][B] +=
++ // ((Edge_Weights[ind][A][B]*tot_max)/
++ // max_edge_weights[ZZZ_ind1]);
++ */
+ }
+ temp_merge_trav_CB= temp_merge_trav_CB->link ;
+ }
+diff --recursive -c --new-file src/./main.cpp ../old/MUSTANG_v.3/src/./main.cpp
+*** foo/src/./main.cpp 2008-01-15 13:35:04.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./main.cpp 2006-10-19 12:39:45.000000000 -0400
+***************
+*** 65,71 ****
+ {
+ cout << "\n" ;
+ cout << "\t\t\t\t\033[0;37;1;41m";
+! cout << " MUSTANG (v.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ;
+ //cout << "\033[0;49m" ;
+ cout << "\t\t\t\t\033[1;33;4;1;46m";
+ cout << "Authors: " ;
+--- 65,71 ----
+ {
+ cout << "\n" ;
+ cout << "\t\t\t\t\033[0;37;1;41m";
+! cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ;
+ //cout << "\033[0;49m" ;
+ cout << "\t\t\t\t\033[1;33;4;1;46m";
+ cout << "Authors: " ;
+***************
+*** 421,427 ****
+ DE_ALLOC_MERGE_LIB();
+ DE_ALLOC_2D( ALGN , NSTRUCTS ) ;
+ DE_ALLOC_2D( I_ALGN , NSTRUCTS ) ;
+! DE_ALLOC_2D( ALGN_QUALITY , NSTRUCTS ) ;
+ DE_ALLOC_1D( STRUCT_PATH ) ;
+ DE_ALLOC_2D( struct_names, NSTRUCTS ) ;
+ DE_ALLOC_2D( struct_paths, NSTRUCTS ) ;
+--- 421,427 ----
+ DE_ALLOC_MERGE_LIB();
+ DE_ALLOC_2D( ALGN , NSTRUCTS ) ;
+ DE_ALLOC_2D( I_ALGN , NSTRUCTS ) ;
+! if(param_D_flag) DE_ALLOC_2D( ALGN_QUALITY , NSTRUCTS ) ;
+ DE_ALLOC_1D( STRUCT_PATH ) ;
+ DE_ALLOC_2D( struct_names, NSTRUCTS ) ;
+ DE_ALLOC_2D( struct_paths, NSTRUCTS ) ;
+diff --recursive -c --new-file src/./output_algn.cpp ../old/MUSTANG_v.3/src/./output_algn.cpp
+*** foo/src/./output_algn.cpp 2008-01-15 13:39:07.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./output_algn.cpp 2005-11-15 19:19:57.000000000 -0500
+***************
+*** 331,337 ****
+ outfile2 << "<PRE>\n" ;
+ // Header starts
+ outfile2 << "################################################################################################\n" ;
+! outfile2 << "# Program: <font color=\"Red\">MUSTANG v.3: A Multiple structural alignment algorithm</font>\n";
+ outfile2 << "# Authors: <font color=\"Red\">A. S. Konagurthu, J. C. Whisstock, and P. J. Stuckey, A. M. Lesk</font>\n";
+
+ outfile2 << "# Rundate: <font color=\"Brown\">" << asctime(localtime(&rundate)) << "</font>";
+--- 331,337 ----
+ outfile2 << "<PRE>\n" ;
+ // Header starts
+ outfile2 << "################################################################################################\n" ;
+! outfile2 << "# Program: <font color=\"Red\">MUSTANG v0.3: A Multiple structural alignment algorithm</font>\n";
+ outfile2 << "# Authors: <font color=\"Red\">A. S. Konagurthu, J. C. Whisstock, and P. J. Stuckey, A. M. Lesk</font>\n";
+
+ outfile2 << "# Rundate: <font color=\"Brown\">" << asctime(localtime(&rundate)) << "</font>";
+***************
+*** 576,582 ****
+ }
+
+ outfile_ps << "\%!PS-Adobe-\n" ;
+! outfile_ps << "\%\%Creator: MUSTANG v.3\n" ;
+ outfile_ps << "\%\%CreationDate:" << asctime(localtime(&rundate)) << "\n" ;
+ outfile_ps << "\%\%EndComments\n\n\n" ;
+
+--- 576,582 ----
+ }
+
+ outfile_ps << "\%!PS-Adobe-\n" ;
+! outfile_ps << "\%\%Creator: MUSTANG v0.3\n" ;
+ outfile_ps << "\%\%CreationDate:" << asctime(localtime(&rundate)) << "\n" ;
+ outfile_ps << "\%\%EndComments\n\n\n" ;
+
+***************
+*** 610,616 ****
+
+ pscolor_indx = 3 ;
+ line_cont = YES ;
+! strcpy(strbuffer , "MUSTANG v.3: A Multiple structural alignment algorithm") ;
+ PSPRINT( strbuffer , bold_boolean, pscolor_indx , line_cntr++ , outfile_ps , line_cont ) ;
+
+
+--- 610,616 ----
+
+ pscolor_indx = 3 ;
+ line_cont = YES ;
+! strcpy(strbuffer , "MUSTANG-Lite v0.3: A Multiple structural alignment algorithm") ;
+ PSPRINT( strbuffer , bold_boolean, pscolor_indx , line_cntr++ , outfile_ps , line_cont ) ;
+
+
+diff --recursive -c --new-file src/./pairwise_global_structalgn.cpp ../old/MUSTANG_v.3/src/./pairwise_global_structalgn.cpp
+*** foo/src/./pairwise_global_structalgn.cpp 2008-01-15 13:18:34.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./pairwise_global_structalgn.cpp 2005-11-15 19:19:57.000000000 -0500
+***************
+*** 56,62 ****
+ //cout << "Exe_Time:" << (end -start) << endl ;
+ //exit(0);
+ void COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( int , int , float ** ) ;
+! //COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( a , b, edge_weights ) ;
+ //if( gibberish )
+ if( 0 )
+ {
+--- 56,62 ----
+ //cout << "Exe_Time:" << (end -start) << endl ;
+ //exit(0);
+ void COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( int , int , float ** ) ;
+! COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( a , b, edge_weights ) ;
+ //if( gibberish )
+ if( 0 )
+ {
+diff --recursive -c --new-file src/./pdb_ripper_2.cpp ../old/MUSTANG_v.3/src/./pdb_ripper_2.cpp
+*** foo/src/./pdb_ripper_2.cpp 2008-01-15 13:18:34.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./pdb_ripper_2.cpp 2005-11-15 19:19:57.000000000 -0500
+***************
+*** 598,602 ****
+ pdb_trav -> occupancy = temp_occupancy ;
+ pdb_trav -> B_factor = temp_bfactor ;
+ }
+- pdb.close() ;
+ }
+--- 598,601 ----
+diff --recursive -c --new-file src/./superpose_on_core_2.cpp ../old/MUSTANG_v.3/src/./superpose_on_core_2.cpp
+*** foo/src/./superpose_on_core_2.cpp 2008-01-15 13:41:23.000000000 -0500
+--- ../old/MUSTANG_v.3/src/./superpose_on_core_2.cpp 2006-10-19 12:37:57.000000000 -0400
+***************
+*** 139,146 ****
+ // Fill Headers
+ transf.unsetf(ios::left);
+ transf.unsetf(ios::right);
+! transf << "REMARK Produced by MUSTANG v.3" << "\n" ;
+! transf << "REMARK Authors: A S Konagurthu, J C Whisstock, P J Stuckey, and A M Lesk\n" ;
+ transf << "REMARK\n" ;
+ transf << "REMARK Structures: ";
+ int temp_cntr = 0 ;
+--- 139,146 ----
+ // Fill Headers
+ transf.unsetf(ios::left);
+ transf.unsetf(ios::right);
+! transf << "REMARK Produced by MUSTANG_Lite VER. 0.2" << "\n" ;
+! transf << "REMARK Authors: A S Konagurthu, P J Stuckey, J C Whisstock, and A M Lesk\n" ;
+ transf << "REMARK\n" ;
+ transf << "REMARK Structures: ";
+ int temp_cntr = 0 ;
Property changes on: trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch 2008-02-01 14:16:00 UTC (rev 1251)
@@ -0,0 +1,34 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## main.cpp.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: beautify output of initial advertisement
+
+ at DPATCH@
+
+--- mustang-3.0/src/main.cpp 2006-10-19 18:39:45.000000000 +0200
++++ mustang-3.0.orig/src/main.cpp 2007-08-22 17:13:17.000000000 +0200
+@@ -64,17 +64,17 @@
+ if(!meditate)
+ {
+ cout << "\n" ;
+- cout << "\t\t\t\t\033[0;37;1;41m";
+- cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ;
++ cout << "\033[0;37;1;41m";
++ cout << " MUSTANG (v0.3): A MUltiple STructural AligNment alGorithm. \033[0;0m\n" ;
+ //cout << "\033[0;49m" ;
+- cout << "\t\t\t\t\033[1;33;4;1;46m";
++ cout << "\033[1;33;4;1;46m";
+ cout << "Authors: " ;
+ cout << "\033[0;1;37;4;1;46m" ;
+- cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk.\033[0m\n";
++ cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk. \033[0m\n";
+ //cout << "\033[0m" ;
+- cout << "\t\t\t\t\033[0;33;4;1;46m";
++ cout << "\033[0;33;4;1;46m";
+ cout << "(Mis)Coding: " ; cout << "\033[0;37;4;1;46m" ;
+- cout << " A S Konagurthu. \033[0m\n";
++ cout << " A S Konagurthu. \033[0m\n";
+ cout << "\033[0m" ;
+ cout << "\n\n" ;
+ }
Property changes on: trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mustang/trunk/debian/patches/03-test_zf-cchh.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/03-test_zf-cchh.dpatch (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/03-test_zf-cchh.dpatch 2008-02-01 14:16:00 UTC (rev 1251)
@@ -0,0 +1,30 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## test_zf_cchh by Morten Kjeldgaard <mok at bioxray.dk>
+##
+## DP: Fix the test command file so it makes use of the pdb entries
+## DP: that have been downloaded.
+
+ at DPATCH@
+diff -urNad mustang~/data/test/test_zf-CCHH mustang/data/test/test_zf-CCHH
+--- mustang~/data/test/test_zf-CCHH 2008-01-31 17:10:54.000000000 +0100
++++ mustang/data/test/test_zf-CCHH 2008-02-01 15:01:14.000000000 +0100
+@@ -16,8 +16,7 @@
+ ## symbols to show that the whitespaces are ignored ##
+ ###############################################################################################
+
+-
+- > ./data/test/pdbs
++> /usr/share/doc/mustang-testdata/examples/pdbs
+
+ +1ard.pdb
+ +1bboN.pdb
+@@ -37,6 +36,7 @@
+ +2drp2.pdb
+ +3znf.pdb
+
++
+ +5znf.pdb
+-#+test1.pdb
+-#+test2.pdb
+++test1.pdb
+++test2.pdb
Property changes on: trunk/packages/mustang/trunk/debian/patches/03-test_zf-cchh.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/patches/main.cpp.dpatch 2008-02-01 14:16:00 UTC (rev 1251)
@@ -1,34 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## main.cpp.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: beautify output of initial advertisement
-
- at DPATCH@
-
---- mustang-3.0/src/main.cpp 2006-10-19 18:39:45.000000000 +0200
-+++ mustang-3.0.orig/src/main.cpp 2007-08-22 17:13:17.000000000 +0200
-@@ -64,17 +64,17 @@
- if(!meditate)
- {
- cout << "\n" ;
-- cout << "\t\t\t\t\033[0;37;1;41m";
-- cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ;
-+ cout << "\033[0;37;1;41m";
-+ cout << " MUSTANG (v0.3): A MUltiple STructural AligNment alGorithm. \033[0;0m\n" ;
- //cout << "\033[0;49m" ;
-- cout << "\t\t\t\t\033[1;33;4;1;46m";
-+ cout << "\033[1;33;4;1;46m";
- cout << "Authors: " ;
- cout << "\033[0;1;37;4;1;46m" ;
-- cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk.\033[0m\n";
-+ cout << " A S Konagurthu, J Whisstock, and P J Stuckey, A M Lesk. \033[0m\n";
- //cout << "\033[0m" ;
-- cout << "\t\t\t\t\033[0;33;4;1;46m";
-+ cout << "\033[0;33;4;1;46m";
- cout << "(Mis)Coding: " ; cout << "\033[0;37;4;1;46m" ;
-- cout << " A S Konagurthu. \033[0m\n";
-+ cout << " A S Konagurthu. \033[0m\n";
- cout << "\033[0m" ;
- cout << "\n\n" ;
- }
Deleted: trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/patches/test_zf-cchh.dpatch 2008-02-01 14:16:00 UTC (rev 1251)
@@ -1,18 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## test_zf_cchh by Morten Kjeldgaard <mok at bioxray.au.dk>
-##
-## DP: Fix the test command file so it makes use of the pdb entries
-## DP: in the right directory
-
- at DPATCH@
-
-diff -urNad mustang-3.0.orig~/data/test/test_zf-CCHH mustang-3.0.orig/data/test/test_zf-CCHH
---- mustang-3.0.orig~/data/test/test_zf-CCHH 2007-08-18 02:39:49.000000000 +0200
-+++ mustang-3.0.orig/data/test/test_zf-CCHH 2007-08-18 02:40:05.000000000 +0200
-@@ -17,7 +17,7 @@
- ###############################################################################################
-
-
-- > ./data/test/pdbs
-+ > /usr/share/doc/mustang/examples/pdbs
-
Modified: trunk/packages/mustang/trunk/debian/rules
===================================================================
--- trunk/packages/mustang/trunk/debian/rules 2008-02-01 14:13:02 UTC (rev 1250)
+++ trunk/packages/mustang/trunk/debian/rules 2008-02-01 14:16:00 UTC (rev 1251)
@@ -21,7 +21,7 @@
get-orig-source:
wget http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz -O ../mustang_3.0.orig.tar.gz
-build: build-arch build-indep
+build: patch-stamp build-arch build-indep
build-arch: build-arch-stamp
build-arch-stamp:
@@ -29,7 +29,7 @@
# Compile Mustang:
$(MAKE) CPPFLAGS="$(CPPFLAGS)"
-
+ cp mustang mustang.1
touch $@
build-indep: build-indep-stamp
@@ -39,7 +39,7 @@
build-indep-stamp:
-clean:
+clean: unpatch
dh_testdir
dh_testroot
rm -f build-arch-stamp build-indep-stamp
@@ -47,6 +47,7 @@
# Clean up after the build process.
rm -f obj/*.o
rm -f bin/MUSTANG_v.3
+ rm -f mustang.1
dh_clean
install: install-indep install-arch
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