IGMPlot 3.16 Optimized IGMplot version able to use wfn/wfx/xyz files

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Public Member Functions | Data Fields | Private Attributes
ProgData Class Reference

Class designed to store the program's main dataprovide some utilities concerning those. More...

`#include <ProgData.h>`

Collaboration diagram for ProgData:

## Public Member Functions
| ProgData (int nbAtomMolAParam, int nbAtomMolBParam, int nbTotalAtomParam, int numLigandParam, std::vector< std::pair< unsigned int, unsigned int > > &chosenBondsParam)
| Constructor.
| ~ProgData ()
| Destructor.
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.
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.
void | setCube (double *cubeParam)
| Sets the given cube has the reference cube to the problem.
void | setRadius (double *radiusParam)
| Sets the given radius has the reference cube to the problem.
unsigned int | getNbBond ()
| Gets the number of studied bonds.
int | getNbAtom ()
| Gets the number of atom.
int | getNbAtomMolA ()
| Gets the number of atom in molecule A.
int | getNbAtomMolB ()
| Gets the number of atom in molecule B.
double | getMaxCoord (int axis)
| Gets the max coordinate for the given axis.
double | getMinCoord (int axis)
| Gets the min coordinate for the given axis.
int | getNbSteps (int axis)
| Gets the number of steps for the given axis.
std::string | getGridBoxDefinition ()
| Gets the way the box was deinied by user.
void | setNbAtomMolA (int newValue)
| setter for nbAtomMolA variable
void | setNbAtomMolB (int newValue)
| setter for nbAtomMolB variable
void | setNbSteps (int nbStepsX, int nbStepsY, int nbStepsZ)
| Function to manually set the number of steps of each axis (IBSI case)
void | storeBondLength (unsigned int ibond, double length)
| Function to manually store the length of a studied bond (IBSI case)
void | storeBondVector (unsigned int ibond, double ABx, double ABy, double ABz)
| Function to manually store the vector components of the AB bond.
void | setIBSI (unsigned int ibond, double newValue)
| Function to manually set the IBSI score of a studied bond (IBSI case)
void | setBAF (unsigned int ibond, double newValue)
| Function to manually set the BDA score of a studied bond (IBSI case)
double | getIBSI (int ibond)
| Function to manually get the IBSI score of a studied bond (IBSI case)
double | getBAF (int ibond)
| Function to manually get the BDA score of a studied bond (IBSI case)

## Data Fields
int * | atomTypes
| arry of atom's type
positions_t | atomPositions
| Each atom's position.
bond_t * | bonds
| array of studied bonds (QM treatment)

## Private Attributes
int | nbAtomMolA
| Number of atoms in molecule A.
int | nbAtomMolB
| Number of atoms in molecule B.
int | numLigand
| Number of the ligand ; if none : -1.
int | nbAtom
| Number of atoms in both molecule (if two)
unsigned int | nbBond
| Number of bonds studied (QM treatment)
double | maxCoordinates [3]
| Max coordinates.
double | minCoordinates [3]
| Min coordinates.
int | nbSteps [3]
| Number of steps in loop for all three axis.
int | cursor
| Used to iterate through the arrays.
bool | boxSet
| Used to check whether CUBE option has been used.
bool | radiusSet
| Used to check whether RADIUS option has been used.
int | cnt
| TO DOCUMENT.

## Detailed Description

Class designed to store the program's main dataprovide some utilities concerning those.

Warning
  No copy constructor defined, careful when trying to pass this by value

## Constructor & Destructor Documentation

## ◆ ProgData()

ProgData::ProgData | ( | int | nbAtomMolAParam,
|  | int | nbAtomMolBParam,
|  | int | nbTotalAtomParam,
|  | int | numLigandParam,
|  | std::vector< std::pair< unsigned int, unsigned int > > & | chosenBondsParam )

Constructor.

Parameters

  nbAtomMolAParam | : the number of atoms in molecule A
  nbAtomMolBParam | : the number of atoms in molecule B
  nbTotalAtomParam, | the total number of atoms
  numLigandParam | : the molecule index corresponding to the ligand
  chosenBondsParam | : the studied bonds (only for QM treatment)

## Member Function Documentation

## ◆ addAtom()

void ProgData::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.

Parameters

  type | the type of the atom
  posx | the position of the atom on the x axis
  posy | the position of the atom on the y axis
  posz | the position of the atom on the z axis
  setLIGAND | : input --> says if the user has supplied or not the index of the ligand within the two fragments
  WFNmode | indicates if we are using WFN file (not by default)
  HirshMode | indicates if we are using the Hirshfeld partition (not by default)

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## ◆ getBAF()

double ProgData::getBAF | ( | int | ibond | ) |

Function to manually get the BDA score of a studied bond (IBSI case)

Parameters

  ibond | The bond index

## ◆ getGridBoxDefinition()

std::string ProgData::getGridBoxDefinition | ( |  | ) |

Gets the way the box was deinied by user.

Returns
  the grid Box definition

## ◆ getIBSI()

double ProgData::getIBSI | ( | int | ibond | ) |

Function to manually get the IBSI score of a studied bond (IBSI case)

Parameters

  ibond | The bond index

## ◆ getMaxCoord()

double ProgData::getMaxCoord | ( | int | axis | ) |

Gets the max coordinate for the given axis.

Parameters

  axis | the given axis

Returns
  the max coordinate for the given axis

## ◆ getMinCoord()

double ProgData::getMinCoord | ( | int | axis | ) |

Gets the min coordinate for the given axis.

Parameters

  axis | : the given axis

Returns
  the min coordinate for the given axis

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## ◆ getNbAtom()

int ProgData::getNbAtom | ( |  | ) |

Gets the number of atom.

Returns
  the number of atom

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## ◆ getNbAtomMolA()

int ProgData::getNbAtomMolA | ( |  | ) |

Gets the number of atom in molecule A.

Returns
  the number of atom in molecule A

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## ◆ getNbAtomMolB()

int ProgData::getNbAtomMolB | ( |  | ) |

Gets the number of atom in molecule B.

Returns
  the number of atom in molecule B

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## ◆ getNbBond()

unsigned int ProgData::getNbBond | ( |  | ) |

Gets the number of studied bonds.

Returns
  the number of studied bonds

## ◆ getNbSteps()

int ProgData::getNbSteps | ( | int | axis | ) |

Gets the number of steps for the given axis.

Parameters

  axis | : the given axis

Returns
  the number of steps for the given axis

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## ◆ setBAF()

void ProgData::setBAF | ( | unsigned int | ibond,
|  | double | newValue )

Function to manually set the BDA score of a studied bond (IBSI case)

Parameters

  ibond | The bond index
  newValue | The BDA score

## ◆ setCube()

void ProgData::setCube | ( | double * | cubeParam | ) |

Sets the given cube has the reference cube to the problem.

Parameters

  cubeParam | the cube

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## ◆ setIBSI()

void ProgData::setIBSI | ( | unsigned int | ibond,
|  | double | newValue )

Function to manually set the IBSI score of a studied bond (IBSI case)

Parameters

  ibond | The bond index
  newValue | The IBSI score

## ◆ setNbAtomMolA()

void ProgData::setNbAtomMolA | ( | int | newValue | ) |

setter for nbAtomMolA variable

Parameters

  newValue | The new value for this variable

## ◆ setNbAtomMolB()

void ProgData::setNbAtomMolB | ( | int | newValue | ) |

setter for nbAtomMolB variable

Parameters

  newValue | The new value for this variable

## ◆ setNbSteps()

void ProgData::setNbSteps | ( | int | nbStepsX,
|  | int | nbStepsY,
|  | int | nbStepsZ )

Function to manually set the number of steps of each axis (IBSI case)

Parameters

  nbStepsX | The number of steps for X axis
  nbStepsY | The number of steps for Y axis
  nbStepsZ | The number of steps for Z axis

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## ◆ setRadius()

void ProgData::setRadius | ( | double * | radiusParam | ) |

Sets the given radius has the reference cube to the problem.

Parameters

  radiusParam | : the radius

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## ◆ storeBondLength()

void ProgData::storeBondLength | ( | unsigned int | ibond,
|  | double | length )

Function to manually store the length of a studied bond (IBSI case)

Parameters

  ibond | The bond index
  length | The bond length

## ◆ storeBondVector()

void ProgData::storeBondVector | ( | unsigned int | ibond,
|  | double | ABx,
|  | double | ABy,
|  | double | ABz )

Function to manually store the vector components of the AB bond.

Parameters

  ibond | index for storing the vector components
  ABx | the x component
  ABy | the y component
  ABz | the z component

## ◆ validate()

void ProgData::validate | ( | double * | increments,
|  | double | ligandRadius,
|  | bool | setLIGAND,
|  | bool | QMmode )

Ends the atom adding and update the coordinates before reporting whether the values are consistent.

Parameters

  increments | the increments values
  ligandRadius | the radius around the ligand that has been provided
  setLIGAND | : input --> to tell if the index of the ligand has been supplied or not by user
  QMmode | : input --> to tell if the QUANTUM mode is enabled or not

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The documentation for this class was generated from the following files:

- src/include/ProgData.h
- src/ProgData.cpp