[med-svn] r5087 - trunk/packages/autodocksuite/trunk/debian/patches
Steffen Möller
moeller at alioth.debian.org
Sun Aug 1 20:05:18 UTC 2010
Author: moeller
Date: 2010-08-01 20:05:12 +0000 (Sun, 01 Aug 2010)
New Revision: 5087
Modified:
trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
Log:
Update.
Modified: trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch 2010-08-01 19:41:41 UTC (rev 5086)
+++ trunk/packages/autodocksuite/trunk/debian/patches/const_manual_50.patch 2010-08-01 20:05:12 UTC (rev 5087)
@@ -1,7 +1,16 @@
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
++++ autodocksuite-4.2.3/autodock/ls.cc 2010-08-01 20:33:53.000000000 +0200
+@@ -85,7 +85,7 @@
+ // This has only one value of rho, for all genes.
+ // SW mapped individual
+ // SW returns TRUE if it modifies the individual
+-Boole Solis_Wets::SW(Phenotype &vector)
++Boole Solis_Wets::SW(/* not const */ Phenotype &vector)
+ {
+ register unsigned int i, j, num_successes = 0, num_failures = 0;
+ register Real temp_rho = rho;
@@ -106,10 +106,10 @@
#ifdef DEBUG
//convenience function for debugging
@@ -17,6 +26,15 @@
Real xyz[3];
Real prevxyz[3];
Real startxyz[3];
+@@ -245,7 +245,7 @@
+ // This has a different value of rho for each gene.
+ // PSW mapped individual
+ // PSW returns TRUE if it modifies the individual
+-Boole Pseudo_Solis_Wets::SW(Phenotype &vector)
++Boole Pseudo_Solis_Wets::SW(/* not const */ Phenotype &vector)
+ {
+ register unsigned int i, j, num_successes = 0, num_failures = 0, all_rho_stepsizes_too_small = 1;
+
@@ -523,10 +523,10 @@
return newPoint;
}
@@ -35,31 +53,35 @@
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 @@
++++ autodocksuite-4.2.3/autodock/ls.h 2010-08-01 20:34:27.000000000 +0200
+@@ -92,8 +92,8 @@
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 Boole SW(Phenotype &) = 0;
++ virtual double gen_deviates(const Real) const = 0;
++ virtual Boole SW(/* not const */ Phenotype &) = 0;
virtual void reset(void);
virtual int terminate(void) const;
-@@ -108,7 +108,7 @@
+ int search(Individual &);
+@@ -108,8 +108,8 @@
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 &);
+- Boole SW(Phenotype &);
++ virtual double gen_deviates(const Real) const = 0;
++ Boole SW(/* not const */ Phenotype &);
};
+ class Pseudo_Solis_Wets : public Solis_Wets_Base
@@ -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;
++ virtual double gen_deviates(const Real) const = 0;
Boole SW(Phenotype &);
};
@@ -68,7 +90,7 @@
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);
++ double gen_deviates(const Real) const;
};
class Solis_Wets2 : public Solis_Wets
@@ -77,7 +99,7 @@
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);
++ double gen_deviates(const Real) const;
};
class Pseudo_Solis_Wets1 : public Pseudo_Solis_Wets
@@ -86,7 +108,7 @@
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);
++ double gen_deviates(const Real) const;
};
class Pseudo_Solis_Wets2 : public Pseudo_Solis_Wets
@@ -95,7 +117,7 @@
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);
++ double gen_deviates(const Real) const;
};
// Inline Functions
@@ -104,7 +126,7 @@
}
-inline double Solis_Wets1::gen_deviates(Real rho)
-+inline double Solis_Wets1::gen_deviates(const Real rho)
++inline double Solis_Wets1::gen_deviates(const Real rho) const
{
return(gennor(0.0, rho));
}
@@ -113,7 +135,7 @@
}
-inline double Solis_Wets2::gen_deviates(Real rho)
-+inline double Solis_Wets2::gen_deviates(const Real rho)
++inline double Solis_Wets2::gen_deviates(const Real rho) const
{
return(genunf(-rho/2.0, rho/2.0));
}
@@ -122,7 +144,7 @@
}
-inline double Pseudo_Solis_Wets1::gen_deviates(Real rho)
-+inline double Pseudo_Solis_Wets1::gen_deviates(const Real rho)
++inline double Pseudo_Solis_Wets1::gen_deviates(const Real rho) const
{
return(gennor(0.0, rho));
}
@@ -131,7 +153,569 @@
}
-inline double Pseudo_Solis_Wets2::gen_deviates(Real rho)
-+inline double Pseudo_Solis_Wets2::gen_deviates(const Real rho)
++inline double Pseudo_Solis_Wets2::gen_deviates(const Real rho) const
{
return(genunf(-rho/2.0, rho/2.0));
}
+Index: autodocksuite-4.2.3/autodock/call_cpso.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/call_cpso.cc 2010-08-01 21:12:55.000000000 +0200
++++ autodocksuite-4.2.3/autodock/call_cpso.cc 2010-08-01 21:20:16.000000000 +0200
+@@ -48,7 +48,7 @@
+
+
+
+-Individual cnv_state_to_ind2(const State &original, int ntor)
++Individual cnv_state_to_ind2(const State &original, const int ntor)
+ {
+ // BEGIN ADDITION
+ // Added by gmm, 27-MAR-97, to solve these compiler warnings:
+@@ -71,13 +71,13 @@
+
+
+ State call_cpso(Local_Search * local_method,
+- State sInit,
+- int n_exec, int S, //swarm size
+- int D, //number of dimensions:7 + ntor
+- double *xmin, double *xmax,
+- unsigned int num_evals,
+- int K, double c1, double c2,
+- int outlev)
++ const State sInit,
++ const int n_exec, int S, //swarm size
++ const int D, //number of dimensions:7 + ntor
++ double *const xmin, double *const xmax,
++ const unsigned int num_evals,
++ const int K, const double c1, const double c2,
++ const int outlev)
+ {
+ int nb_eval = 0;
+ Position Xi[S_max]; //Max swarm size set to 1024 in constants.h
+Index: autodocksuite-4.2.3/autodock/support.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/support.cc 2010-08-01 20:43:23.000000000 +0200
++++ autodocksuite-4.2.3/autodock/support.cc 2010-08-01 21:39:19.000000000 +0200
+@@ -74,7 +74,7 @@
+ lhb to size-1 *in reverse order*.
+ */
+
+-void Population::swap(Individual &individual1, Individual &individual2)
++void Population::swap(Individual &individual1, Individual &individual2) const
+ {
+ Individual temp;
+
+@@ -92,7 +92,7 @@
+ between lhb and size-1 and that the new individual is in
+ position lhb-1.
+ */
+-void Population::SiftUp(void)
++void Population::SiftUp(void) /* not const */
+ {
+ int i, parent;
+
+@@ -112,7 +112,7 @@
+ /* This routine assumes that the heap condition is satisfied
+ between lhb & size-2 initially, and that the individual at size-1
+ needs to be accomodated.*/
+-void Population::SiftDown(void)
++void Population::SiftDown(void) /* not const */
+ {
+ int i, child;
+
+@@ -138,7 +138,7 @@
+ }
+ }
+
+-void Population::msort(int m)
++void Population::msort(const int m)
+ {
+ register int i;
+
+@@ -445,7 +445,7 @@
+ }
+
+ Genotype::Genotype(unsigned int init_number_of_vectors, Representation **
+-init_rep_vector)
++const init_rep_vector)
+ : number_of_vectors(init_number_of_vectors), rep_vector(init_rep_vector),
+ modified(0)
+ {
+@@ -475,6 +475,9 @@
+ }
+ }
+
++#if 0
++ # steffen thinks this is redundant with the const variant
++ # http://en.wikipedia.org/wiki/Copy_constructor
+ Genotype::Genotype(Genotype &original)
+ {
+ register unsigned int i;
+@@ -501,8 +504,9 @@
+ lookup[i] = original.lookup[i];
+ }
+ }
++#endif
+
+-Genotype::Genotype(Genotype const &original)
++Genotype::Genotype(const Genotype &original)
+ {
+ register unsigned int i;
+
+@@ -592,7 +596,7 @@
+ }
+
+
+-void Genotype::write(Element value, int gene_number)
++void Genotype::write(const Element value, const int gene_number) /* not const */
+ {
+
+ #ifdef DEBUG
+@@ -603,7 +607,7 @@
+ rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Genotype::write(unsigned char value, int gene_number)
++void Genotype::write(const unsigned char value, const int gene_number) /* not const */
+ {
+
+ #ifdef DEBUG
+@@ -614,7 +618,7 @@
+ rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Genotype::write(FourByteLong value, int gene_number)
++void Genotype::write(const FourByteLong value, const int gene_number) /* not const */
+ {
+
+ #ifdef DEBUG
+@@ -625,7 +629,7 @@
+ rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Genotype::write(double value, int gene_number)
++void Genotype::write(const double value, const int gene_number) /* not const */
+ {
+
+ #ifdef DEBUG
+@@ -636,7 +640,7 @@
+ rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Genotype::write(const Representation &value, int gene_number)
++void Genotype::write(const Representation &value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -648,7 +652,7 @@
+ *(rep_vector[gene_number]) = value;
+ }
+
+-Quat Genotype::readQuat()
++Quat Genotype::readQuat() const
+ {
+ Quat q;
+ q.x = gread(3).real;
+@@ -659,7 +663,7 @@
+ return q;
+ }
+
+-void Genotype::writeQuat( Quat q )
++void Genotype::writeQuat( const Quat q )
+ {
+ write( q.x, 3 );
+ write( q.y, 4 );
+@@ -667,7 +671,7 @@
+ write( q.w, 6 );
+ }
+
+-Quat Phenotype::readQuat()
++Quat Phenotype::readQuat() const
+ {
+ Quat q;
+ q.x = gread(3).real;
+@@ -678,7 +682,7 @@
+ return q;
+ }
+
+-void Phenotype::writeQuat( Quat q )
++void Phenotype::writeQuat( const Quat q )
+ {
+ write( q.x, 3 );
+ write( q.y, 4 );
+@@ -687,7 +691,7 @@
+ }
+
+ // Maybe we should evaluate the Phenotype?
+-Phenotype::Phenotype(unsigned int init_number_of_dimensions, Representation **init_value_vector)
++Phenotype::Phenotype(const unsigned int init_number_of_dimensions, Representation **const init_value_vector)
+ : number_of_dimensions(init_number_of_dimensions), value_vector(init_value_vector),
+ value(0.0), evalflag(0)
+ {
+@@ -809,7 +813,7 @@
+ }
+ }
+
+-void Phenotype::write(Element value, int gene_number)
++void Phenotype::write(const Element value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -820,7 +824,7 @@
+ value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Phenotype::write(unsigned char value, int gene_number)
++void Phenotype::write(const unsigned char value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -831,7 +835,7 @@
+ value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Phenotype::write(FourByteLong value, int gene_number)
++void Phenotype::write(const FourByteLong value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -842,7 +846,7 @@
+ value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Phenotype::write(double value, int gene_number)
++void Phenotype::write(const double value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -853,7 +857,7 @@
+ value_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
+ }
+
+-void Phenotype::write(const Representation &value, int gene_number)
++void Phenotype::write(const Representation &value, const int gene_number)
+ {
+
+ #ifdef DEBUG
+@@ -865,7 +869,7 @@
+ *(value_vector[gene_number]) = value;
+ }
+
+-double Phenotype::evaluate(EvalMode mode)
++double Phenotype::evaluate(const EvalMode mode) /* not const */
+ {
+
+ #ifdef DEBUG
+@@ -932,7 +936,7 @@
+ }
+ }
+
+-State Individual::state(int ntor) const
++State Individual::state(const int ntor) const
+ {
+
+ #ifdef DEBUG
+@@ -942,7 +946,7 @@
+ return(phenotyp.make_state(ntor));
+ }
+
+-void Individual::getMol(Molecule *returnedMol)
++void Individual::getMol(Molecule * /* not const */ returnedMol) const // Steffen : bug candidate here
+ {
+ // Converts phenotype to mol's state and returns this individual's mol data.
+
+@@ -951,7 +955,7 @@
+
+ molState = phenotyp.make_state(mol->S.ntor);
+ molcopy = copyStateToMolecule(&molState, mol);
+- returnedMol = &molcopy;
++ returnedMol = &molcopy; // Steffen : or here, molcopy is not returned
+ }
+
+ void Individual::printIndividualsState(FILE *const filePtr, const int ntor, const int detail) const
+@@ -964,7 +968,7 @@
+ fprintf( filePtr, "\n" );
+ }
+
+-void Individual::incrementAge(void)
++void Individual::incrementAge(void) /* not const */
+ {
+ ++age;
+ }
+Index: autodocksuite-4.2.3/autodock/support.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/support.h 2010-08-01 20:43:23.000000000 +0200
++++ autodocksuite-4.2.3/autodock/support.h 2010-08-01 21:40:15.000000000 +0200
+@@ -171,25 +171,30 @@
+
+ public:
+ Genotype(void);
++#if 0
++ # Steffen thinks this is redundant with the const variant
++ # http://en.wikipedia.org/wiki/Copy_constructor
+ Genotype(Genotype &); /* copy constructor */
+- Genotype(Genotype const &);
+- Genotype(unsigned int, Representation **); /* creates a genotype from the
++#endif
++ Genotype(const Genotype &);
++ Genotype(unsigned int, Representation **const); /* creates a genotype from the
+ representation & total # vectors */
++ /* Steffen's comment - representation is apparently unused */
+ ~Genotype(void); /* destructor */
+ Genotype &operator=(const Genotype &);
+ unsigned int num_vectors(void); /* e.g. "real,bit,bit,int" would = 4 */
+ unsigned int num_genes(void); /* returns number_of_genes (see above) */
+ RepType gtype(int); /* returns the type (real,bit,int) for
+ a particular gene */
+- const Element gread(int);
+- const Representation *vread(int);
+- void write(Element, int);
+- void write(unsigned char, int);
+- void write(FourByteLong, int);
+- void write(double, int);
+- void write(const Representation &, int);
+- Quat readQuat();
+- void writeQuat( Quat q );
++ const Element gread(const int) const;
++ const Representation *vread(int) const;
++ void write(const Element, const int); /* not const */
++ void write(const unsigned char, const int); /* not const */
++ void write(const FourByteLong, const int); /* not const */
++ void write(const double, const int); /* not const */
++ void write(const Representation &, const int); /* not const */
++ Quat readQuat() const;
++ void writeQuat( const Quat q );
+ };
+
+ // Should Phenotype automatically evaluate itself upon construction?
+@@ -208,23 +213,23 @@
+ Phenotype(void);
+ Phenotype(const Phenotype &);
+ //Phenotype(const Genotype &);//to do
+- Phenotype(unsigned int, Representation **);
++ Phenotype(const unsigned int, Representation **const);
+ ~Phenotype(void);
+ Phenotype &operator=(const Phenotype &);
+ RepType gtype(int);
+- const Element gread(int);
+- const Representation *vread(int);
+- void write(Element, int);
+- void write(unsigned char, int);
+- void write(FourByteLong, int);
+- void write(double, int);
+- void write(const Representation &, int);
+- double evaluate(EvalMode); // This should return evaluation if that's the right answer, and it should evaluate otherwise.
++ const Element gread(const int) const;
++ const Representation *vread(int) const;
++ void write(const Element, const int);
++ void write(const unsigned char, const int);
++ void write(const FourByteLong, const int);
++ void write(const double, const int);
++ void write(const Representation &, const int);
++ double evaluate(const EvalMode) /* not const */ ; // This should return evaluation if that's the right answer, and it should evaluate otherwise.
+ State make_state(int) const;
+- unsigned int num_dimensions(void);
+- unsigned int num_pts(void);
+- Quat readQuat();
+- void writeQuat( Quat q );
++ unsigned int num_dimensions(void) const; // Steffen : implementation not found
++ unsigned int num_pts(void) const;
++ Quat readQuat() const;
++ void writeQuat( const Quat q );
+ };
+
+ // This should be an encapsulated class within Population
+@@ -248,11 +253,11 @@
+ Individual &inverse_mapping(void); //updates genotype from current phenotype values
+ //Phenotype mapping(void); /* takes the genotype and converts it into a phenotype. */
+ //Genotype inverse_mapping(void); // Scott should do: Also copy Phenotype's value
+- double value(EvalMode); /* evaluation of the individual gives its value */
+- State state(int) const; /* state variables in AutoDock */
+- void getMol(Molecule *); /* converts phenotype to mol's state and returns this individual's mol data */
++ double value(EvalMode); /* not const */ /* evaluation of the individual gives its value */ /* not const */
++ State state(const int) const; /* state variables in AutoDock */
++ void getMol(Molecule * /* not const */) const; /* converts phenotype to mol's state and returns this individual's mol data */
+ void printIndividualsState(FILE *const, const int, const int) const; /* print out the state of this individual */
+- void incrementAge(); /* make individual grow 1 generation older */
++ void incrementAge(); /* not const */ /* make individual grow 1 generation older */
+ int serial; // serial number of this individual
+ };
+
+@@ -263,9 +268,9 @@
+ int lhb; // These keep track of the lower & upper heap bounds
+ int size; /* the number of individuals in the population */
+ Individual *heap; /* a heap of individuals -- special binary tree */
+- void swap(Individual &, Individual &); /* for maintaining the heap order*/
+- void SiftUp(void); /* for maintaining the heap order*/
+- void SiftDown(void); /* for maintaining the heap order*/
++ void swap(Individual &, Individual &) const; /* for maintaining the heap order*/
++ void SiftUp(void); /* not const */ /* for maintaining the heap order*/
++ void SiftDown(void); /* not const */ /* for maintaining the heap order*/
+ int end_of_branch[MAX_TORS]; // For Branch Crossover Mode
+
+ public:
+@@ -277,7 +282,7 @@
+ Individual &operator[](const int) const; /* for accessing a particular indiv.in pop*/
+ Population &operator=(const Population &);
+ unsigned int num_individuals(void) const; /* returns the size of the pop. */
+- void msort(int); /* sorts the first m individuals using heap properties */
++ void msort(const int); /* sorts the first m individuals using heap properties */
+ // void print(ostream &, int); /* prints top int energies */
+ void print(FILE *const, const int) const; /* like above */
+ int printPopulationStatistics(FILE *const, const int, const Boole) const; /* prints best, worse, mean, etc energies */
+@@ -317,12 +322,12 @@
+ return(rep_vector[lookup[gene_number].vector]->type());
+ }
+
+-inline const Element Genotype::gread(int gene_number)
++inline const Element Genotype::gread(const int gene_number) const
+ {
+ return(rep_vector[lookup[gene_number].vector]->gene(lookup[gene_number].index));
+ }
+
+-inline const Representation *Genotype::vread(int vector_number)
++inline const Representation *Genotype::vread(int vector_number) const
+ {
+ return(rep_vector[vector_number]);
+ }
+@@ -343,17 +348,17 @@
+ return(value_vector[lookup[gene_number].vector]->type());
+ }
+
+-inline const Element Phenotype::gread(int gene_number)
++inline const Element Phenotype::gread(const int gene_number) const
+ {
+ return(value_vector[lookup[gene_number].vector]->gene(lookup[gene_number].index));
+ }
+
+-inline const Representation *Phenotype::vread(int vector_number)
++inline const Representation *Phenotype::vread(int vector_number) const
+ {
+ return(value_vector[vector_number]);
+ }
+
+-inline unsigned int Phenotype::num_pts(void)
++inline unsigned int Phenotype::num_pts(void) const
+ {
+ return(number_of_points);
+ }
+@@ -392,7 +397,7 @@
+ return(*this);
+ }
+
+-inline double Individual::value(EvalMode mode)
++inline double Individual::value(EvalMode mode) /* not const */
+ { // TO DO: check if mapping from genotyp to phenotyp is up-to-date
+ // note that phenotyp.evaluate only does evaluation if evalflag is false
+ return(phenotyp.evaluate(mode));
+Index: autodocksuite-4.2.3/autodock/swap.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/swap.cc 2010-08-01 20:40:54.000000000 +0200
++++ autodocksuite-4.2.3/autodock/swap.cc 2010-08-01 20:43:03.000000000 +0200
+@@ -39,8 +39,8 @@
+ #endif /* DEBUG */
+
+ void swap ( int v[],
+- int i,
+- int j )
++ const int i,
++ const int j )
+
+ {
+ int temp;
+Index: autodocksuite-4.2.3/autodock/swap.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/swap.h 2010-08-01 20:40:54.000000000 +0200
++++ autodocksuite-4.2.3/autodock/swap.h 2010-08-01 20:43:12.000000000 +0200
+@@ -26,5 +26,5 @@
+
+ #ifndef SWAP
+ #define SWAP
+-void swap( int v[], int i, int j );
++void swap( int v[], const int i, const int j );
+ #endif
+Index: autodocksuite-4.2.3/autodock/timesys.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/timesys.cc 2010-08-01 20:38:40.000000000 +0200
++++ autodocksuite-4.2.3/autodock/timesys.cc 2010-08-01 20:39:58.000000000 +0200
+@@ -43,9 +43,9 @@
+
+ /*----------------------------------------------------------------------------*/
+
+-void timesys( Clock duration,
+- struct tms *start,
+- struct tms *end)
++void timesys( const Clock duration,
++ const struct tms *const start,
++ const struct tms *const end)
+
+ /*----------------------------------------------------------------------------*/
+
+Index: autodocksuite-4.2.3/autodock/timesys.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/timesys.h 2010-08-01 20:38:40.000000000 +0200
++++ autodocksuite-4.2.3/autodock/timesys.h 2010-08-01 20:40:13.000000000 +0200
+@@ -33,7 +33,7 @@
+ #include <time.h>
+ #include "autocomm.h"
+
+-void timesys( Clock duration,
+- struct tms *start,
+- struct tms *end );
++void timesys( const Clock duration,
++ const struct tms *const start,
++ const struct tms *const end );
+ #endif
+Index: autodocksuite-4.2.3/autodock/torsion.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/torsion.cc 2010-08-01 20:37:35.000000000 +0200
++++ autodocksuite-4.2.3/autodock/torsion.cc 2010-08-01 20:38:11.000000000 +0200
+@@ -35,7 +35,7 @@
+
+
+ void torsion( const State now,
+- Real crd[MAX_ATOMS][SPACE],
++ /* not const */ Real crd[MAX_ATOMS][SPACE],
+ const Real v[MAX_TORS][SPACE],
+ const int tlist[MAX_TORS][MAX_ATOMS],
+ const int ntor )
+Index: autodocksuite-4.2.3/autodock/torsion.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/torsion.h 2010-08-01 20:37:35.000000000 +0200
++++ autodocksuite-4.2.3/autodock/torsion.h 2010-08-01 20:38:28.000000000 +0200
+@@ -28,7 +28,7 @@
+ #define TORSION
+
+ void torsion( const State now,
+- Real crd[MAX_ATOMS][SPACE],
++ /* not const */ Real crd[MAX_ATOMS][SPACE],
+ const Real vt[MAX_TORS][SPACE],
+ const int tlist[MAX_TORS][MAX_ATOMS],
+ const int ntor );
+Index: autodocksuite-4.2.3/autodock/warn_bad_file.cc
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/warn_bad_file.cc 2010-08-01 20:35:09.000000000 +0200
++++ autodocksuite-4.2.3/autodock/warn_bad_file.cc 2010-08-01 20:35:23.000000000 +0200
+@@ -37,8 +37,8 @@
+
+ /*----------------------------------------------------------------------------*/
+
+-void warn_bad_file( char *filename,
+- char message[LINE_LEN] )
++void warn_bad_file( const char *const filename,
++ const char message[LINE_LEN] )
+
+ /*----------------------------------------------------------------------------*/
+ {
+Index: autodocksuite-4.2.3/autodock/warn_bad_file.h
+===================================================================
+--- autodocksuite-4.2.3.orig/autodock/warn_bad_file.h 2010-08-01 20:35:09.000000000 +0200
++++ autodocksuite-4.2.3/autodock/warn_bad_file.h 2010-08-01 20:35:33.000000000 +0200
+@@ -29,6 +29,6 @@
+ #include "constants.h"
+ #include "print_2x.h"
+
+-void warn_bad_file( char *filename,
+- char *message );
++void warn_bad_file( const char *const filename,
++ const char *const message );
+ #endif
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