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-- ;
}