[med-svn] r5086 - trunk/packages/autodocksuite/trunk/debian/patches
Steffen Möller
moeller at alioth.debian.org
Sun Aug 1 19:41:48 UTC 2010
Author: moeller
Date: 2010-08-01 19:41:41 +0000 (Sun, 01 Aug 2010)
New Revision: 5086
Added:
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
Modified:
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch
trunk/packages/autodocksuite/trunk/debian/patches/series
Log:
More.
Modified: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch 2010-08-01 13:58:53 UTC (rev 5085)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_35.patch 2010-08-01 19:41:41 UTC (rev 5086)
@@ -480,3 +480,213 @@
/*
SPOFA FACTORS A REAL SYMMETRIC POSITIVE DEFINITE MATRIX.
SPOFA IS USUALLY CALLED BY SPOCO, BUT IT CAN BE CALLED
+Index: autodocksuite-4.2.3/autodock/cluster_analysis.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/cluster_analysis.cc 2010-08-01 20:04:01.000000000 +0200
++++ autodocksuite-4.2.3/autodock/cluster_analysis.cc 2010-08-01 20:10:59.000000000 +0200
+@@ -32,21 +32,21 @@
+ #include "cluster_analysis.h"
+
+
+-int cluster_analysis( Real clus_rms_tol,
+- int cluster[MAX_RUNS][MAX_RUNS],
+- int num_in_clus[MAX_RUNS],
+- int isort[MAX_RUNS],
+- int nconf,
+- int natom,
+- int type[MAX_ATOMS],
+- Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
+- Real crdpdb[MAX_ATOMS][SPACE],
+- Real sml_center[SPACE],
+- Real clu_rms[MAX_RUNS][MAX_RUNS],
+- Boole B_symmetry_flag,
+- Real ref_crds[MAX_ATOMS][SPACE],
+- int ref_natoms,
+- Real ref_rms[MAX_RUNS])
++int cluster_analysis( const Real clus_rms_tol,
++ /* not const */ int cluster[MAX_RUNS][MAX_RUNS],
++ /* not const */ int num_in_clus[MAX_RUNS],
++ const int isort[MAX_RUNS],
++ const int nconf,
++ const int natom,
++ const int type[MAX_ATOMS],
++ const Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
++ const Real crdpdb[MAX_ATOMS][SPACE],
++ const Real sml_center[SPACE],
++ /* not const */ Real clu_rms[MAX_RUNS][MAX_RUNS],
++ const Boole B_symmetry_flag,
++ /* not const */ Real ref_crds[MAX_ATOMS][SPACE],
++ const int ref_natoms,
++ /* not const */ Real ref_rms[MAX_RUNS])
+ {
+ /* __________________________________________________________________________
+ | Cluster Analysis |
+Index: autodocksuite-4.2.3/autodock/cluster_analysis.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/cluster_analysis.h 2010-08-01 20:04:01.000000000 +0200
++++ autodocksuite-4.2.3/autodock/cluster_analysis.h 2010-08-01 20:11:26.000000000 +0200
+@@ -30,19 +30,19 @@
+ #include "getrms.h"
+
+
+-int cluster_analysis( Real clus_rms_tol,
+- int cluster[MAX_RUNS][MAX_RUNS],
+- int num_in_clus[MAX_RUNS],
+- int isort[MAX_RUNS],
+- int nconf,
+- int natom,
+- int type[MAX_ATOMS],
+- Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
+- Real crdpdb[MAX_ATOMS][SPACE],
+- Real sml_center[SPACE],
+- Real clu_rms[MAX_RUNS][MAX_RUNS],
+- Boole B_symmetry_flag,
+- Real ref_crds[MAX_ATOMS][SPACE],
+- int ref_natoms,
+- Real ref_rms[MAX_RUNS]);
++int cluster_analysis( const Real clus_rms_tol,
++ /* not const */ int cluster[MAX_RUNS][MAX_RUNS],
++ /* not const */ int num_in_clus[MAX_RUNS],
++ const int isort[MAX_RUNS],
++ const int nconf,
++ const int natom,
++ const int type[MAX_ATOMS],
++ const Real crd[MAX_RUNS][MAX_ATOMS][SPACE],
++ const Real crdpdb[MAX_ATOMS][SPACE],
++ const Real sml_center[SPACE],
++ /* not const */ Real clu_rms[MAX_RUNS][MAX_RUNS],
++ const Boole B_symmetry_flag,
++ /* not const */ Real ref_crds[MAX_ATOMS][SPACE],
++ const int ref_natoms,
++ /* not const */ Real ref_rms[MAX_RUNS]);
+ #endif
+Index: autodocksuite-4.2.3/autodock/getrms.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/getrms.cc 2010-08-01 20:12:04.000000000 +0200
++++ autodocksuite-4.2.3/autodock/getrms.cc 2010-08-01 20:13:46.000000000 +0200
+@@ -32,11 +32,11 @@
+ #include "getrms.h"
+
+
+-Real getrms ( Real Crd[MAX_ATOMS][SPACE],
+- Real CrdRef[MAX_ATOMS][SPACE],
+- Boole B_symmetry_flag,
+- int natom,
+- int type[MAX_ATOMS] )
++Real getrms ( const Real Crd[MAX_ATOMS][SPACE],
++ const Real CrdRef[MAX_ATOMS][SPACE],
++ const Boole B_symmetry_flag,
++ const int natom,
++ const int type[MAX_ATOMS] )
+
+ {
+ double sqrSum, sqrMin, dc[SPACE];
+Index: autodocksuite-4.2.3/autodock/getrms.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/getrms.h 2010-08-01 20:12:04.000000000 +0200
++++ autodocksuite-4.2.3/autodock/getrms.h 2010-08-01 20:13:30.000000000 +0200
+@@ -29,9 +29,9 @@
+
+ #include "constants.h"
+
+-Real getrms( Real Crd[MAX_ATOMS][SPACE],
+- Real CrdRef[MAX_ATOMS][SPACE],
+- Boole B_symmetry_flag,
+- int natom,
+- int type[MAX_ATOMS] );
++Real getrms( const Real Crd[MAX_ATOMS][SPACE],
++ const Real CrdRef[MAX_ATOMS][SPACE],
++ const Boole B_symmetry_flag,
++ const int natom,
++ const int type[MAX_ATOMS] );
+ #endif
+Index: autodocksuite-4.2.3/autodock/clmode.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/clmode.cc 2010-08-01 20:15:47.000000000 +0200
++++ autodocksuite-4.2.3/autodock/clmode.cc 2010-08-01 20:17:11.000000000 +0200
+@@ -41,17 +41,17 @@
+ extern FILE *logFile;
+ extern char *programname;
+
+-void clmode( int num_atm_maps,
+- Real clus_rms_tol,
+- char *hostnm,
+- Clock jobStart,
++void clmode( const int num_atm_maps,
++ const Real clus_rms_tol,
++ const char *const hostnm,
++ const Clock jobStart,
+ struct tms tms_jobStart,
+- Boole write_all_clusmem,
+- char *clusFN,
+- Real crdpdb[MAX_ATOMS][SPACE],
+- Real sml_center[SPACE],
+- Boole symmetry_flag,
+- char *rms_ref_crds )
++ const Boole write_all_clusmem,
++ const char *const clusFN,
++ const Real crdpdb[MAX_ATOMS][SPACE],
++ const Real sml_center[SPACE],
++ const Boole symmetry_flag,
++ const char *const rms_ref_crds )
+
+ {
+ FILE *clusFile;
+Index: autodocksuite-4.2.3/autodock/clmode.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/clmode.h 2010-08-01 20:15:47.000000000 +0200
++++ autodocksuite-4.2.3/autodock/clmode.h 2010-08-01 20:17:43.000000000 +0200
+@@ -39,15 +39,15 @@
+ #include "success.h"
+ #include "qmultiply.h"
+ #include "openfile.h"
+-void clmode( int num_atm_maps,
+- Real clus_rms_tol,
+- char hostnm[MAX_CHARS],
+- Clock jobStart,
++void clmode( const int num_atm_maps,
++ const Real clus_rms_tol,
++ const char hostnm[MAX_CHARS],
++ const Clock jobStart,
+ struct tms tms_jobStart,
+- Boole B_write_all_clusmem,
+- char *clusFN,
+- Real crdpdb[MAX_ATOMS][SPACE],
+- Real sml_center[SPACE],
+- Boole B_symmetry_flag,
+- char *rms_ref_crds );
++ const Boole B_write_all_clusmem,
++ const char *const clusFN,
++ const Real crdpdb[MAX_ATOMS][SPACE],
++ const Real sml_center[SPACE],
++ const Boole B_symmetry_flag,
++ const char *const rms_ref_crds );
+ #endif
+Index: autodocksuite-4.2.3/autodock/getpdbcrds.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/getpdbcrds.cc 2010-08-01 20:18:17.000000000 +0200
++++ autodocksuite-4.2.3/autodock/getpdbcrds.cc 2010-08-01 20:19:02.000000000 +0200
+@@ -40,8 +40,8 @@
+ extern char *programname;
+
+
+-int getpdbcrds( char *rms_ref_crds_FN,
+- Real ref_crds[MAX_ATOMS][SPACE] )
++int getpdbcrds( const char *const rms_ref_crds_FN,
++ /* not const */ Real ref_crds[MAX_ATOMS][SPACE] )
+ {
+ int ii=0;
+ int natoms=0;
+Index: autodocksuite-4.2.3/autodock/getpdbcrds.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/getpdbcrds.h 2010-08-01 20:18:17.000000000 +0200
++++ autodocksuite-4.2.3/autodock/getpdbcrds.h 2010-08-01 20:19:17.000000000 +0200
+@@ -30,6 +30,6 @@
+ #include "constants.h"
+ #include "openfile.h"
+
+-int getpdbcrds( char *rms_ref_crds_FN,
+- Real ref_crds[MAX_ATOMS][SPACE] );
++int getpdbcrds( const char *const rms_ref_crds_FN,
++ /* not const */ Real ref_crds[MAX_ATOMS][SPACE] );
+ #endif
Added: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch 2010-08-01 19:41:41 UTC (rev 5086)
@@ -0,0 +1,137 @@
+Index: autodocksuite-4.2.3/autodock/ls.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/ls.cc 2010-08-01 20:21:56.000000000 +0200
++++ autodocksuite-4.2.3/autodock/ls.cc 2010-08-01 20:26:50.000000000 +0200
+@@ -106,10 +106,10 @@
+ #ifdef DEBUG
+ //convenience function for debugging
+ #define traceState(msg,vector) printDState(logFile,msg,vector,i,prevxyz,startxyz,prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates)
+-void printDState(FILE *const logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
+- Real startxyz[3], Quat prevQuat, Quat startQuat,
+- unsigned int num_successes, unsigned int num_failures,
+- Real temp_rho, Real * bias, Real * deviates);
++void printDState(FILE *const logFile, const char *const msg,Phenotype &newPh, const int i, const Real prevxyz[3],
++ const Real startxyz[3], const Quat prevQuat, const Quat startQuat,
++ const unsigned int num_successes, const unsigned int num_failures,
++ const Real temp_rho, Real *const bias, Real *const deviates);
+ Real xyz[3];
+ Real prevxyz[3];
+ Real startxyz[3];
+@@ -523,10 +523,10 @@
+ return newPoint;
+ }
+ //void printDState(logFile,msg,vector,i,prevxyz,startxyz, prevQuat,startQuat,num_successes,num_failures,temp_rho,bias,deviates);
+-void printDState(FILE *logFile, const char * msg,Phenotype &newPh, int i, Real prevxyz[3],
+- Real startxyz[3], const Quat prevQuat, const Quat startQuat,
+- unsigned int num_successes, unsigned int num_failures,
+- Real temp_rho, Real * bias, Real * deviates)
++void printDState(FILE *logFile, const char *const msg,Phenotype &newPh, const int i, const Real prevxyz[3],
++ const Real startxyz[3], const Quat prevQuat, const Quat startQuat,
++ const unsigned int num_successes, const unsigned int num_failures,
++ const Real temp_rho, const Real *const bias, const Real *const deviates)
+ {
+ #ifdef DEBUG
+ Real dt; // translation step scalar
+Index: autodocksuite-4.2.3/autodock/ls.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/ls.h 2010-08-01 20:21:56.000000000 +0200
++++ autodocksuite-4.2.3/autodock/ls.h 2010-08-01 20:28:54.000000000 +0200
+@@ -92,7 +92,7 @@
+ Solis_Wets_Base(void);
+ Solis_Wets_Base(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
+ virtual ~Solis_Wets_Base(void);
+- virtual double gen_deviates(Real) = 0;
++ virtual double gen_deviates(const Real) = 0;
+ virtual Boole SW(Phenotype &) = 0;
+ virtual void reset(void);
+ virtual int terminate(void) const;
+@@ -108,7 +108,7 @@
+ Solis_Wets(void);
+ Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
+ virtual ~Solis_Wets(void);
+- virtual double gen_deviates(Real) = 0;
++ virtual double gen_deviates(const Real) = 0;
+ Boole SW(Phenotype &);
+ };
+
+@@ -123,7 +123,7 @@
+ Pseudo_Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
+ Pseudo_Solis_Wets(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
+ virtual ~Pseudo_Solis_Wets(void);
+- virtual double gen_deviates(Real) = 0;
++ virtual double gen_deviates(const Real) = 0;
+ Boole SW(Phenotype &);
+ };
+
+@@ -133,7 +133,7 @@
+ Solis_Wets1(void);
+ Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
+ ~Solis_Wets1(void);
+- double gen_deviates(Real);
++ double gen_deviates(const Real);
+ };
+
+ class Solis_Wets2 : public Solis_Wets
+@@ -142,7 +142,7 @@
+ Solis_Wets2(void);
+ Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real, Real);
+ ~Solis_Wets2(void);
+- double gen_deviates(Real);
++ double gen_deviates(const Real);
+ };
+
+ class Pseudo_Solis_Wets1 : public Pseudo_Solis_Wets
+@@ -152,7 +152,7 @@
+ Pseudo_Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
+ Pseudo_Solis_Wets1(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
+ ~Pseudo_Solis_Wets1(void);
+- double gen_deviates(Real);
++ double gen_deviates(const Real);
+ };
+
+ class Pseudo_Solis_Wets2 : public Pseudo_Solis_Wets
+@@ -162,7 +162,7 @@
+ Pseudo_Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real);
+ Pseudo_Solis_Wets2(unsigned int, unsigned int, unsigned int, unsigned int, Real, Real, Real, Real *, Real *);
+ ~Pseudo_Solis_Wets2(void);
+- double gen_deviates(Real);
++ double gen_deviates(const Real);
+ };
+
+ // Inline Functions
+@@ -288,7 +288,7 @@
+ {
+ }
+
+-inline double Solis_Wets1::gen_deviates(Real rho)
++inline double Solis_Wets1::gen_deviates(const Real rho)
+ {
+ return(gennor(0.0, rho));
+ }
+@@ -310,7 +310,7 @@
+ {
+ }
+
+-inline double Solis_Wets2::gen_deviates(Real rho)
++inline double Solis_Wets2::gen_deviates(const Real rho)
+ {
+ return(genunf(-rho/2.0, rho/2.0));
+ }
+@@ -343,7 +343,7 @@
+ {
+ }
+
+-inline double Pseudo_Solis_Wets1::gen_deviates(Real rho)
++inline double Pseudo_Solis_Wets1::gen_deviates(const Real rho)
+ {
+ return(gennor(0.0, rho));
+ }
+@@ -376,7 +376,7 @@
+ {
+ }
+
+-inline double Pseudo_Solis_Wets2::gen_deviates(Real rho)
++inline double Pseudo_Solis_Wets2::gen_deviates(const Real rho)
+ {
+ return(genunf(-rho/2.0, rho/2.0));
+ }
Modified: trunk/packages/autodocksuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/series 2010-08-01 13:58:53 UTC (rev 5085)
+++ trunk/packages/autodocksuite/trunk/debian/patches/series 2010-08-01 19:41:41 UTC (rev 5086)
@@ -1,3 +1,4 @@
+const_manual_40.patch
const_suggetsions_gcc4.6_1st_iteration.patch
manual_const_1.patch
const_manual_2nd.patch
@@ -7,3 +8,4 @@
const_manual_25.patch
const_manual_30.patch
const_manual_35.patch
+const_manual_50.patch
More information about the debian-med-commit
mailing list