diff -Nru mustang-3.2.3/debian/changelog mustang-3.2.4/debian/changelog --- mustang-3.2.3/debian/changelog 2020-10-30 10:20:06.000000000 +0000 +++ mustang-3.2.4/debian/changelog 2022-12-25 21:30:48.000000000 +0000 @@ -1,3 +1,10 @@ +mustang (3.2.4-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille Sun, 25 Dec 2022 22:30:48 +0100 + mustang (3.2.3-4) unstable; urgency=medium * Standards-Version: 4.5.0 (routine-update) diff -Nru mustang-3.2.3/debian/control mustang-3.2.4/debian/control --- mustang-3.2.3/debian/control 2020-10-30 10:20:06.000000000 +0000 +++ mustang-3.2.4/debian/control 2022-12-25 21:30:48.000000000 +0000 @@ -4,7 +4,7 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13) -Standards-Version: 4.5.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/mustang Vcs-Git: https://salsa.debian.org/med-team/mustang.git Homepage: https://lcb.infotech.monash.edu.au/mustang/ @@ -27,6 +27,7 @@ Architecture: all Depends: ${misc:Depends} Enhances: mustang +Multi-Arch: foreign Description: multiple structural alignment of proteins, test data This package contains a larger set of test data than what comes with the binary package. diff -Nru mustang-3.2.3/debian/patches/cross.patch mustang-3.2.4/debian/patches/cross.patch --- mustang-3.2.3/debian/patches/cross.patch 2020-10-30 10:20:06.000000000 +0000 +++ mustang-3.2.4/debian/patches/cross.patch 2022-12-25 21:30:48.000000000 +0000 @@ -25,7 +25,7 @@ @@ -36,86 +36,86 @@ all: $(ALL) #------------------------------------------------------------------------------ - $(BIN)/mustang-3.2.3: $(OBJECTS) + $(BIN)/mustang-3.2.4: $(OBJECTS) - $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) + $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) diff -Nru mustang-3.2.3/Makefile mustang-3.2.4/Makefile --- mustang-3.2.3/Makefile 2017-01-04 12:21:05.000000000 +0000 +++ mustang-3.2.4/Makefile 2022-10-06 01:53:58.000000000 +0000 @@ -1,5 +1,5 @@ #****************************************************************************** -# TARGETS : ./bin/mustang-3.2.3 +# TARGETS : ./bin/mustang-3.2.4 # AUTHOR : ARUN S KONAGURTHU #****************************************************************************** #directories @@ -28,14 +28,14 @@ $(OBJ)/upgma.o \ $(OBJ)/superpose_on_core.o $(OBJ)/multiple_superposition.o \ $(OBJ)/output_algn.o $(OBJ)/main.o -ALL = $(BIN)/mustang-3.2.3 +ALL = $(BIN)/mustang-3.2.4 #targets all: $(ALL) #------------------------------------------------------------------------------ -$(BIN)/mustang-3.2.3: $(OBJECTS) +$(BIN)/mustang-3.2.4: $(OBJECTS) $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(OBJ)/globals.o: $(SRC)/globals.h $(SRC)/macros.h $(SRC)/globals.cpp diff -Nru mustang-3.2.3/README mustang-3.2.4/README --- mustang-3.2.3/README 2017-01-04 13:32:12.000000000 +0000 +++ mustang-3.2.4/README 2022-10-06 01:51:23.000000000 +0000 @@ -1,13 +1,13 @@ INSTALLATION ON LINUX (or other Unix-based systems with GCC): * Extract the tarball using: - tar -zxvf MUSTANG_v3.2.3.tgz + tar -zxvf MUSTANG_v3.2.4.tgz * then: - cd MUSTANG_v3.2.3 + cd MUSTANG_v3.2.4 * run: make * Test the installation using: - ./bin/mustang-3.2.3 -f ./data/test/test_zf-CCHH + ./bin/mustang-3.2.4 -f ./data/test/test_zf-CCHH This should produce the following files: -- results.html diff -Nru mustang-3.2.3/src/3D_manip_functions.cpp mustang-3.2.4/src/3D_manip_functions.cpp --- mustang-3.2.3/src/3D_manip_functions.cpp 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.4/src/3D_manip_functions.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -207,7 +207,6 @@ */ void coordinate_transformer( float X[4][500],float EX[4][500], int N, int NAT1, int NAT2, int NAT3){ int i,j,k ; - float AX[4][500] ; float T[4][4] ; float Tee[4][4] ; float Tphi[4][4] ; @@ -217,7 +216,7 @@ { sq[k] = X[k][NAT1] ; for( j = 1 ; j <= N ; j++ ) - { AX[k][j] = X[k][j] ; + { X[k][j] -= sq[k] ; } } diff -Nru mustang-3.2.3/src/ew_2.cpp mustang-3.2.4/src/ew_2.cpp --- mustang-3.2.3/src/ew_2.cpp 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.4/src/ew_2.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -214,8 +214,8 @@ Coords_Set_moving[i] = new float [3] ; } float RMSD; - float ROTATION_MAT[3][3] , prev_ROTMAT[3][3]; - double CM_stationary[3] , CM_moving[3] ; double prev_CM_S[3] , prev_CM_M[3] ; + float ROTATION_MAT[3][3]; + double CM_stationary[3] , CM_moving[3] ; for( int I = 0 ; I < PROT_SIZES[a] - MIN_CP_WINDOW_SIZE + 1; I++ ) for( int J = 0 ; J < PROT_SIZES[b] - MIN_CP_WINDOW_SIZE + 1 ; J++ ) @@ -270,14 +270,6 @@ prev_rmsd = RMSD ; if( tmp_ind < 4 ) prev_rmsds[tmp_ind++] = RMSD ; - //copy ROTATION_MAT to prev_ROTMAT, CM_stationary -> prev_CM_S , and CM_moving -> prev_CM_M - for( int i = 0 ; i < 3 ; i++ ) - { - for( int j = 0 ; j < 3; j++ ) - prev_ROTMAT[i][j] = ROTATION_MAT[i][j] ; - prev_CM_S[i] = CM_stationary[i] ; - prev_CM_M[i] = CM_moving[i] ; - } } //cout << I << " " << J << " " << RMSD << " " << prev_rmsd << endl ; // find similarity score of this maximal fragment diff -Nru mustang-3.2.3/src/extended_lib_gen_3.cpp mustang-3.2.4/src/extended_lib_gen_3.cpp --- mustang-3.2.3/src/extended_lib_gen_3.cpp 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.4/src/extended_lib_gen_3.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -216,9 +216,6 @@ //*/ else if( B!= -99 && B_orig == -99 && merge_trav->mates[1][B] == -99 ) { - float AAA ; - AAA = Edge_Weights[ind][A][B] ; - /* The paln here is not to extended an arc between A and B thro' C if A and B are both unmatched in the pairwise alignment. However if diff -Nru mustang-3.2.3/src/macros.h mustang-3.2.4/src/macros.h --- mustang-3.2.3/src/macros.h 2017-01-04 12:22:47.000000000 +0000 +++ mustang-3.2.4/src/macros.h 2022-10-06 01:51:45.000000000 +0000 @@ -29,7 +29,7 @@ #ifndef MACROS_H #define MACROS_H -#define VERSION "v3.2.3" +#define VERSION "v3.2.4" /* OUTPUT CONTROLS*/ #define TRUE 1 diff -Nru mustang-3.2.3/src/neighbour_joining.cpp mustang-3.2.4/src/neighbour_joining.cpp --- mustang-3.2.3/src/neighbour_joining.cpp 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.4/src/neighbour_joining.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -180,7 +180,7 @@ } temp_list[size-2] = *t_index ; //copy_back the temp_list to current_list - for( int i = 0 ; i < size-1 ; i ++ ) + for( int i = 0 ; i < size-1 ; i++ ) current_nodes[i] = temp_list[i] ; //updating raw_distmat float **temp_distmat = new float* [size]; diff -Nru mustang-3.2.3/src/pdb_ripper_2.cpp mustang-3.2.4/src/pdb_ripper_2.cpp --- mustang-3.2.3/src/pdb_ripper_2.cpp 2014-07-08 06:48:21.000000000 +0000 +++ mustang-3.2.4/src/pdb_ripper_2.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -50,7 +50,6 @@ { int NCHAINS = 0 ; int chain_flag = OFF ; - int chain_id = -1; char buffer[90]; ifstream pdb( fname , ios::in ) ; if( !pdb ) @@ -69,7 +68,6 @@ if( buffer[0] == 'A' && buffer[1] == 'T' && buffer[2] == 'O' && buffer[3] == 'M' && chain_flag == OFF ) { chain_flag = ON ; - chain_id = buffer[ 21 ] ; } if( chain_flag == ON && buffer[0] == 'T' && buffer[1] == 'E' && diff -Nru mustang-3.2.3/src/primary_lib_gen.cpp mustang-3.2.4/src/primary_lib_gen.cpp --- mustang-3.2.3/src/primary_lib_gen.cpp 2014-07-08 06:48:21.000000000 +0000 +++ mustang-3.2.4/src/primary_lib_gen.cpp 2022-10-06 05:02:01.000000000 +0000 @@ -92,14 +92,14 @@ { if(!meditate) { - cout << setw(4) << pair_cntr << " of " << setw(4) << tot_pairs << flush ; + cout << setw(8) << pair_cntr << " of " << setw(8) << tot_pairs << flush ; } PAIRWISE_GLOBAL_STRUCTURAL_ALIGNMENT( I , J ); if(!meditate) { - for( int i = 0 ; i < 12 ; i++ ) cout << "\b" ; + for( int i = 0 ; i < 20 ; i++ ) cout << "\b" ; cout << flush ; } Binary files /tmp/tmp0_qc21r7/prLmRhKjdO/mustang-3.2.3/src/.primary_lib_gen.cpp.swp and /tmp/tmp0_qc21r7/8gavfNJwJ9/mustang-3.2.4/src/.primary_lib_gen.cpp.swp differ diff -Nru mustang-3.2.3/src/refine_pairalgn_2.cpp mustang-3.2.4/src/refine_pairalgn_2.cpp --- mustang-3.2.3/src/refine_pairalgn_2.cpp 2014-07-08 06:48:21.000000000 +0000 +++ mustang-3.2.4/src/refine_pairalgn_2.cpp 2022-10-06 01:50:29.000000000 +0000 @@ -658,8 +658,8 @@ int Y = A2I_hash[1][pos1] ; if(X!= -99 && Y!= -99) edge_weights[ X ][ Y ] = -1 ; - Global_Library[g_index].mates[0][X] = -99 ; - Global_Library[g_index].mates[1][Y] = -99 ; + if (X != -99) Global_Library[g_index].mates[0][X] = -99 ; + if (Y != -99) Global_Library[g_index].mates[1][Y] = -99 ; } pos1-- ; }