88 double maxCoordinatesA[3];
89 double maxCoordinatesB[3];
93 double minCoordinatesA[3];
94 double minCoordinatesB[3];
137 ProgData(
int nbAtomMolAParam,
int nbAtomMolBParam,
int nbTotalAtomParam,
int numLigandParam, std::vector<std::pair< unsigned int, unsigned int> > &chosenBondsParam);
154 void addAtom(
int type,
double posx,
double posy,
double posz,
bool setLIGAND=
false,
bool WFNmode=
false,
bool HirshMode=
false);
164 void validate(
double * increments,
double ligandRadius,
bool setLIGAND,
bool QMmode);
170 void setCube(
double * cubeParam );
247 void setNbSteps(
int nbStepsX,
int nbStepsY,
int nbStepsZ);
263 void storeBondVector(
unsigned int ibond,
double ABx,
double ABy,
double ABz);
270 void setIBSI(
unsigned int ibond,
double newValue);
277 void setBAF(
unsigned int ibond,
double newValue);
Class designed to store Gradient related values and provide some utilities concerning those.
int nbAtomMolA
Number of atoms in molecule A.
Definition ProgData.h:72
void storeBondLength(unsigned int ibond, double length)
Function to manually store the length of a studied bond (IBSI case)
Definition ProgData.cpp:631
unsigned int nbBond
Number of bonds studied (QM treatment)
Definition ProgData.h:84
void setCube(double *cubeParam)
Sets the given cube has the reference cube to the problem.
Definition ProgData.cpp:511
int * atomTypes
arry of atom's type
Definition ProgData.h:118
int getNbSteps(int axis)
Gets the number of steps for the given axis.
Definition ProgData.cpp:595
int cursor
Used to iterate through the arrays.
Definition ProgData.h:102
void storeBondVector(unsigned int ibond, double ABx, double ABy, double ABz)
Function to manually store the vector components of the AB bond.
Definition ProgData.cpp:655
bond_t * bonds
array of studied bonds (QM treatment)
Definition ProgData.h:124
double getBAF(int ibond)
Function to manually get the BDA score of a studied bond (IBSI case)
Definition ProgData.cpp:728
void addAtom(int type, double posx, double posy, double posz, bool setLIGAND=false, bool WFNmode=false, bool HirshMode=false)
Adds an atom with the given properties to the atom's array.
Definition ProgData.cpp:118
void validate(double *increments, double ligandRadius, bool setLIGAND, bool QMmode)
Ends the atom adding and update the coordinates before reporting whether the values are consistent.
Definition ProgData.cpp:386
int numLigand
Number of the ligand ; if none : -1.
Definition ProgData.h:78
double minCoordinates[3]
Min coordinates.
Definition ProgData.h:92
double getMaxCoord(int axis)
Gets the max coordinate for the given axis.
Definition ProgData.cpp:583
void setRadius(double *radiusParam)
Sets the given radius has the reference cube to the problem.
Definition ProgData.cpp:537
~ProgData()
Destructor.
Definition ProgData.cpp:101
unsigned int getNbBond()
Gets the number of studied bonds.
Definition ProgData.cpp:559
double maxCoordinates[3]
Max coordinates.
Definition ProgData.h:87
double getMinCoord(int axis)
Gets the min coordinate for the given axis.
Definition ProgData.cpp:589
void setIBSI(unsigned int ibond, double newValue)
Function to manually set the IBSI score of a studied bond (IBSI case)
Definition ProgData.cpp:679
void setNbAtomMolB(int newValue)
setter for nbAtomMolB variable
Definition ProgData.cpp:623
int getNbAtomMolA()
Gets the number of atom in molecule A.
Definition ProgData.cpp:571
void setNbSteps(int nbStepsX, int nbStepsY, int nbStepsZ)
Function to manually set the number of steps of each axis (IBSI case)
Definition ProgData.cpp:503
bool radiusSet
Used to check whether RADIUS option has been used.
Definition ProgData.h:108
int getNbAtom()
Gets the number of atom.
Definition ProgData.cpp:565
void setNbAtomMolA(int newValue)
setter for nbAtomMolA variable
Definition ProgData.cpp:617
int nbSteps[3]
Number of steps in loop for all three axis.
Definition ProgData.h:97
void setBAF(unsigned int ibond, double newValue)
Function to manually set the BDA score of a studied bond (IBSI case)
Definition ProgData.cpp:705
double getIBSI(int ibond)
Function to manually get the IBSI score of a studied bond (IBSI case)
Definition ProgData.cpp:722
int cnt
TO DOCUMENT.
Definition ProgData.h:111
bool boxSet
Used to check whether CUBE option has been used.
Definition ProgData.h:105
ProgData(int nbAtomMolAParam, int nbAtomMolBParam, int nbTotalAtomParam, int numLigandParam, std::vector< std::pair< unsigned int, unsigned int > > &chosenBondsParam)
Constructor.
Definition ProgData.cpp:58
int getNbAtomMolB()
Gets the number of atom in molecule B.
Definition ProgData.cpp:577
int nbAtomMolB
Number of atoms in molecule B.
Definition ProgData.h:75
int nbAtom
Number of atoms in both molecule (if two)
Definition ProgData.h:81
std::string getGridBoxDefinition()
Gets the way the box was deinied by user.
Definition ProgData.cpp:601
positions_t atomPositions
Each atom's position.
Definition ProgData.h:121
bool HirshMode
Flag to indicate if we are using the HIRSH mode.
Definition reader.cpp:85
bool setLIGAND
Flag to indicate if the user has provided the index of the ligand within the set of two supplied frag...
Definition reader.cpp:128
Structure describing studied bond (QM treatment)
Definition general.h:658
Structure containing a serie of 3D position.
Definition general.h:705