[med-svn] [Git][med-team/mustang][master] 8 commits: New upstream version 3.2.4
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Dec 25 21:32:05 GMT 2022
Andreas Tille pushed to branch master at Debian Med / mustang
Commits:
810aa249 by Andreas Tille at 2022-10-14T20:35:59+02:00
New upstream version 3.2.4
- - - - -
d96c1fe8 by Andreas Tille at 2022-10-14T20:35:59+02:00
routine-update: New upstream version
- - - - -
f49f513c by Andreas Tille at 2022-10-14T20:36:00+02:00
Update upstream source from tag 'upstream/3.2.4'
Update to upstream version '3.2.4'
with Debian dir 8d04def1b23ac3fd8be52b26d584cc199a029b47
- - - - -
8152609d by Andreas Tille at 2022-10-14T20:36:00+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
33a4dc84 by Andreas Tille at 2022-10-14T20:36:58+02:00
Apply multi-arch hints.
+ mustang-testdata: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
06b55f43 by Andreas Tille at 2022-12-25T22:25:52+01:00
Standards-Version: 4.6.2
- - - - -
3f1f5518 by Andreas Tille at 2022-12-25T22:30:37+01:00
Update patches
- - - - -
400bb1ae by Andreas Tille at 2022-12-25T22:31:14+01:00
Upload to unstable
- - - - -
14 changed files:
- Makefile
- README
- debian/changelog
- debian/control
- debian/patches/cross.patch
- + src/.primary_lib_gen.cpp.swp
- src/3D_manip_functions.cpp
- src/ew_2.cpp
- src/extended_lib_gen_3.cpp
- src/macros.h
- src/neighbour_joining.cpp
- src/pdb_ripper_2.cpp
- src/primary_lib_gen.cpp
- src/refine_pairalgn_2.cpp
Changes:
=====================================
Makefile
=====================================
@@ -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 @@ OBJECTS = $(OBJ)/globals.o $(OBJ)/CmdLineParser.o $(OBJ)/distmat.o $(OBJ)/sse_RK
$(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
=====================================
README
=====================================
@@ -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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+mustang (3.2.4-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 25 Dec 2022 22:30:48 +0100
+
mustang (3.2.3-4) unstable; urgency=medium
* Standards-Version: 4.5.0 (routine-update)
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
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 @@ Package: mustang-testdata
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.
=====================================
debian/patches/cross.patch
=====================================
@@ -25,7 +25,7 @@ Description: use standard variable for the c++ compiler
@@ -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)
=====================================
src/.primary_lib_gen.cpp.swp
=====================================
Binary files /dev/null and b/src/.primary_lib_gen.cpp.swp differ
=====================================
src/3D_manip_functions.cpp
=====================================
@@ -207,7 +207,6 @@ void compute_dihedral_angle( float A[3], float B[3], float C[3], float D[3], flo
*/
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 @@ void coordinate_transformer( float X[4][500],float EX[4][500], int N, int NAT1,
{
sq[k] = X[k][NAT1] ;
for( j = 1 ; j <= N ; j++ )
- { AX[k][j] = X[k][j] ;
+ {
X[k][j] -= sq[k] ;
}
}
=====================================
src/ew_2.cpp
=====================================
@@ -214,8 +214,8 @@ void CALCULATE_EDGE_WEIGHTS( int a , int b , float ***edge_weights )
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 @@ void CALCULATE_EDGE_WEIGHTS( int a , int b , float ***edge_weights )
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
=====================================
src/extended_lib_gen_3.cpp
=====================================
@@ -216,9 +216,6 @@ void EXTENDED_LIBRARY_GENERATION()
//*/
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
=====================================
src/macros.h
=====================================
@@ -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
=====================================
src/neighbour_joining.cpp
=====================================
@@ -180,7 +180,7 @@ void UPDATE_TREE_INFO_AND_DISTMAT( float **raw_distmat , float R[] , int *t_inde
}
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];
=====================================
src/pdb_ripper_2.cpp
=====================================
@@ -50,7 +50,6 @@ int CHECK_NCHAINS_IN_PDB( char *fname )
{
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 @@ int CHECK_NCHAINS_IN_PDB( char *fname )
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' &&
=====================================
src/primary_lib_gen.cpp
=====================================
@@ -92,14 +92,14 @@ void GLOBAL_LIBRARY_GENERATION()
{
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 ;
}
=====================================
src/refine_pairalgn_2.cpp
=====================================
@@ -658,8 +658,8 @@ void REFINE_PAIRWISE_ALIGNMENT( int a , int b , float **edge_weights )
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-- ;
}
View it on GitLab: https://salsa.debian.org/med-team/mustang/-/compare/b410ebdd82b713812c9e73d1cb1cd6d9981f3ec7...400bb1ae603a95af193ea495664f88329df72d13
--
View it on GitLab: https://salsa.debian.org/med-team/mustang/-/compare/b410ebdd82b713812c9e73d1cb1cd6d9981f3ec7...400bb1ae603a95af193ea495664f88329df72d13
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