diff --recursive -c --new-file MUSTANG_v3.2.3/Makefile MUSTANG_v3.2.4/Makefile *** MUSTANG_v3.2.3/Makefile 2017-01-04 23:21:05.000000000 +1100 --- MUSTANG_v3.2.4/Makefile 2022-10-06 12:53:58.000000000 +1100 *************** *** 1,5 **** #****************************************************************************** ! # TARGETS : ./bin/mustang-3.2.3 # AUTHOR : ARUN S KONAGURTHU #****************************************************************************** #directories --- 1,5 ---- #****************************************************************************** ! # TARGETS : ./bin/mustang-3.2.4 # AUTHOR : ARUN S KONAGURTHU #****************************************************************************** #directories *************** *** 28,41 **** $(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 #targets all: $(ALL) #------------------------------------------------------------------------------ ! $(BIN)/mustang-3.2.3: $(OBJECTS) $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(OBJ)/globals.o: $(SRC)/globals.h $(SRC)/macros.h $(SRC)/globals.cpp --- 28,41 ---- $(OBJ)/upgma.o \ $(OBJ)/superpose_on_core.o $(OBJ)/multiple_superposition.o \ $(OBJ)/output_algn.o $(OBJ)/main.o ! ALL = $(BIN)/mustang-3.2.4 #targets all: $(ALL) #------------------------------------------------------------------------------ ! $(BIN)/mustang-3.2.4: $(OBJECTS) $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(OBJ)/globals.o: $(SRC)/globals.h $(SRC)/macros.h $(SRC)/globals.cpp diff --recursive -c --new-file MUSTANG_v3.2.3/README MUSTANG_v3.2.4/README *** MUSTANG_v3.2.3/README 2017-01-05 00:32:12.000000000 +1100 --- MUSTANG_v3.2.4/README 2022-10-06 12:51:23.000000000 +1100 *************** *** 1,13 **** INSTALLATION ON LINUX (or other Unix-based systems with GCC): * Extract the tarball using: ! tar -zxvf MUSTANG_v3.2.3.tgz * then: ! cd MUSTANG_v3.2.3 * run: make * Test the installation using: ! ./bin/mustang-3.2.3 -f ./data/test/test_zf-CCHH This should produce the following files: -- results.html --- 1,13 ---- INSTALLATION ON LINUX (or other Unix-based systems with GCC): * Extract the tarball using: ! tar -zxvf MUSTANG_v3.2.4.tgz * then: ! cd MUSTANG_v3.2.4 * run: make * Test the installation using: ! ./bin/mustang-3.2.4 -f ./data/test/test_zf-CCHH This should produce the following files: -- results.html diff --recursive -c --new-file MUSTANG_v3.2.3/src/3D_manip_functions.cpp MUSTANG_v3.2.4/src/3D_manip_functions.cpp *** MUSTANG_v3.2.3/src/3D_manip_functions.cpp 2014-07-08 16:48:20.000000000 +1000 --- MUSTANG_v3.2.4/src/3D_manip_functions.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 207,213 **** */ 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] ; --- 207,212 ---- *************** *** 217,223 **** { sq[k] = X[k][NAT1] ; for( j = 1 ; j <= N ; j++ ) ! { AX[k][j] = X[k][j] ; X[k][j] -= sq[k] ; } } --- 216,222 ---- { sq[k] = X[k][NAT1] ; for( j = 1 ; j <= N ; j++ ) ! { X[k][j] -= sq[k] ; } } diff --recursive -c --new-file MUSTANG_v3.2.3/src/ew_2.cpp MUSTANG_v3.2.4/src/ew_2.cpp *** MUSTANG_v3.2.3/src/ew_2.cpp 2014-07-08 16:48:20.000000000 +1000 --- MUSTANG_v3.2.4/src/ew_2.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 214,221 **** 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] ; 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++ ) --- 214,221 ---- Coords_Set_moving[i] = new float [3] ; } float RMSD; ! 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++ ) *************** *** 270,283 **** 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 --- 270,275 ---- diff --recursive -c --new-file MUSTANG_v3.2.3/src/extended_lib_gen_3.cpp MUSTANG_v3.2.4/src/extended_lib_gen_3.cpp *** MUSTANG_v3.2.3/src/extended_lib_gen_3.cpp 2014-07-08 16:48:20.000000000 +1000 --- MUSTANG_v3.2.4/src/extended_lib_gen_3.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 216,224 **** //*/ 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 --- 216,221 ---- diff --recursive -c --new-file MUSTANG_v3.2.3/src/macros.h MUSTANG_v3.2.4/src/macros.h *** MUSTANG_v3.2.3/src/macros.h 2017-01-04 23:22:47.000000000 +1100 --- MUSTANG_v3.2.4/src/macros.h 2022-10-06 12:51:45.000000000 +1100 *************** *** 29,35 **** #ifndef MACROS_H #define MACROS_H ! #define VERSION "v3.2.3" /* OUTPUT CONTROLS*/ #define TRUE 1 --- 29,35 ---- #ifndef MACROS_H #define MACROS_H ! #define VERSION "v3.2.4" /* OUTPUT CONTROLS*/ #define TRUE 1 diff --recursive -c --new-file MUSTANG_v3.2.3/src/neighbour_joining.cpp MUSTANG_v3.2.4/src/neighbour_joining.cpp *** MUSTANG_v3.2.3/src/neighbour_joining.cpp 2014-07-08 16:48:20.000000000 +1000 --- MUSTANG_v3.2.4/src/neighbour_joining.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 180,186 **** } temp_list[size-2] = *t_index ; //copy_back the temp_list to current_list ! for( int i = 0 ; i < size-1 ; i ++ ) current_nodes[i] = temp_list[i] ; //updating raw_distmat float **temp_distmat = new float* [size]; --- 180,186 ---- } temp_list[size-2] = *t_index ; //copy_back the temp_list to current_list ! for( int i = 0 ; i < size-1 ; i++ ) current_nodes[i] = temp_list[i] ; //updating raw_distmat float **temp_distmat = new float* [size]; diff --recursive -c --new-file MUSTANG_v3.2.3/src/pdb_ripper_2.cpp MUSTANG_v3.2.4/src/pdb_ripper_2.cpp *** MUSTANG_v3.2.3/src/pdb_ripper_2.cpp 2014-07-08 16:48:21.000000000 +1000 --- MUSTANG_v3.2.4/src/pdb_ripper_2.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 50,56 **** { int NCHAINS = 0 ; int chain_flag = OFF ; - int chain_id = -1; char buffer[90]; ifstream pdb( fname , ios::in ) ; if( !pdb ) --- 50,55 ---- *************** *** 69,75 **** 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' && --- 68,73 ---- diff --recursive -c --new-file MUSTANG_v3.2.3/src/primary_lib_gen.cpp MUSTANG_v3.2.4/src/primary_lib_gen.cpp *** MUSTANG_v3.2.3/src/primary_lib_gen.cpp 2014-07-08 16:48:21.000000000 +1000 --- MUSTANG_v3.2.4/src/primary_lib_gen.cpp 2022-10-06 16:02:01.000000000 +1100 *************** *** 92,105 **** { if(!meditate) { ! cout << setw(4) << pair_cntr << " of " << setw(4) << tot_pairs << flush ; } PAIRWISE_GLOBAL_STRUCTURAL_ALIGNMENT( I , J ); if(!meditate) { ! for( int i = 0 ; i < 12 ; i++ ) cout << "\b" ; cout << flush ; } --- 92,105 ---- { if(!meditate) { ! cout << setw(8) << pair_cntr << " of " << setw(8) << tot_pairs << flush ; } PAIRWISE_GLOBAL_STRUCTURAL_ALIGNMENT( I , J ); if(!meditate) { ! for( int i = 0 ; i < 20 ; i++ ) cout << "\b" ; cout << flush ; } Binary files MUSTANG_v3.2.3/src/.primary_lib_gen.cpp.swp and MUSTANG_v3.2.4/src/.primary_lib_gen.cpp.swp differ diff --recursive -c --new-file MUSTANG_v3.2.3/src/refine_pairalgn_2.cpp MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp *** MUSTANG_v3.2.3/src/refine_pairalgn_2.cpp 2014-07-08 16:48:21.000000000 +1000 --- MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp 2022-10-06 12:50:29.000000000 +1100 *************** *** 658,665 **** 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 ; } pos1-- ; } --- 658,665 ---- int Y = A2I_hash[1][pos1] ; if(X!= -99 && Y!= -99) edge_weights[ X ][ Y ] = -1 ; ! if (X != -99) Global_Library[g_index].mates[0][X] = -99 ; ! if (Y != -99) Global_Library[g_index].mates[1][Y] = -99 ; } pos1-- ; }