|
| int | conversionAtom (std::string &tmp) |
| | This function is used to convert an atom name in char into an integer. Note that the integer corresponds to the atomic number of the atom minus one to fit easily with the C indexes.
|
| |
| int | conversionParam (std::string ¶m) |
| | This function is used to convert a type of parameter from string to int so it may be used in a switch case.
|
| |
| bool | isANumber (const std::string &s) |
| | This function is used to check whether a string is a number or not.
|
| |
| void | readParam (const char *parameterFileName, param_t *params) |
| | Read the file param.nci.
|
| |
| ProgData * | readxyzMinMax (param_t *params) |
| | Reads files (.xyz) and find the Min (MinX,MinY,MinZ) and the Max (MinX,MinY,MinZ)
|
| |
| bool | isWFmodeActivated () |
| | Tool function which indicates if the current calculus is based on wfn/wfx/rkf files.
|
| |
| bool | isWFXmodeActivated () |
| | Tool function which indicates if the current calculus is based on wfx file.
|
| |
| bool | isWFNmodeActivated () |
| | Tool function which indicates if the current calculus is based on wfn file.
|
| |
| bool | isRKFmodeActivated () |
| | Tool function which indicates if the current calculus is based on rkf file.
|
| |
| bool | isIBSImodeActivated () |
| | Tool function which indicates if the current calculus uses IBSI mode.
|
| |
| bool | isELFmodeActivated () |
| | Tool function which indicates if ELF analysis is to be performed.
|
| |
| bool | isfullAOAccActivated () |
| | Indicates if full accuracy is used for AO calculations.
|
| |
| bool | isHirshmodeActivated () |
| | Tool function which indicates if the current calculus uses Hirsh mode.
|
| |
| bool | isCriticmodeActivated () |
| | Tool function which indicates if the current calculus uses Critic mode.
|
| |
| bool | isdgSCALED () |
| | Tool function which indicates if the dgSCALED mode is enabled.
|
| |
| bool | isParseRKF () |
| | Tool function which indicates if RKF has to be parsed without grid calculation.
|
| |
| bool | isPauli () |
| | Tool function which indicates if The Pauli exchange has to be estimated.
|
| |
| bool | isPauliAtomic () |
| | Tool function which indicates if The Pauli exchange has to be estimated with atomic contrib.
|
| |
| bool | isCriticMEDIUMmodeActivated () |
| | Tool function which indicates if the current calculus uses CriticMEDIUM mode.
|
| |
| bool | isCriticFINEmodeActivated () |
| | Tool function which indicates if the current calculus uses CriticFINE mode.
|
| |
| bool | isCriticULTRAFINEmodeActivated () |
| | Tool function which indicates if the current calculus uses CriticULTRAFINE mode.
|
| |
| bool | isCriticAddSeedsmodeActivated () |
| | Tool function which indicates if additional seeds are use for cp search.
|
| |
| bool | isPeakFocusIntraActivated () |
| | Tool function which indicates if a peakFocusIntra has been required by user.
|
| |
| bool | isPeakFocusInterActivated () |
| | Tool function which indicates if a peakFocusInter has been required by user.
|
| |
| void | setFrag (const std::string definition, const param_types_t FRAG, const int nbAtoms) |
| | This function is used to ascribe FRAG atom indexes from string definition given in param.igm input file.
|
| |
| bool | isInMoleculeA (unsigned int atomNaturalIndex) |
| | Function which indicated if the given atom (natural index coming from WFN file) belongs to molecule A.
|
| |
| bool | isInMoleculeB (unsigned int atomNaturalIndex) |
| | Function which indicated if the given atom (natural index coming from WFN file) belongs to molecule B.
|
| |
| std::string | getMoleculeAatomDefinition () |
| | Tool function which returns a string description of the FRAG1 atoms (given in param.igm)
|
| |
| std::string | getMoleculeBatomDefinition () |
| | Tool function which returns a string description of the FRAG2 atoms (given in param.igm)
|
| |
| unsigned int | wfn_getMoleculeAnbAtoms () |
| | Tool function which indicates the number of atoms in molecule A.
|
| |
| unsigned int | wfn_getMoleculeBnbAtoms () |
| | Tool function which indicates the number of atoms in molecule B.
|
| |
| std::string | getCondensedDescriptionOfMoleculeA () |
| | Function which returns the description of atoms included in molecule A.
|
| |
| std::string | getCondensedDescriptionOfMoleculeB () |
| | Function which returns the description of atoms included in molecule B.
|
| |
|
void | howUsingIGMplot () |
| | Tool function which prints how the application can be launched.
|
| |
| std::vector< std::pair< unsigned int, unsigned int > > & | getChosenBonds () |
| | Function to gain access to the chosen bonds.
|
| |
| bool | atomBondsHaveBeenRegistered () |
| | Tool function which indicates if atom bonds have been registered.
|
| |
| void | checkKeywords (param_t *params) |
| | Function to check the keywords compatibility.
|
| |
|
|
bool | wfMode =false |
| | Flag to indicate if we are using wfn/wfx files or not.
|
| |
|
bool | wfxMode =false |
| | Flag to indicate if we are using wfx files or not.
|
| |
|
bool | wfnMode =false |
| | Flag to indicate if we are using wfn files or not.
|
| |
|
bool | rkfMode =false |
| | Flag to indicate if we are using rkf files or not.
|
| |
|
bool | parseRKF =false |
| | Flag to indicate if we are parsing rkf without grid calculation.
|
| |
|
bool | pauli =false |
| | Flag to indicate if the Pauli exchange is to be estimated.
|
| |
|
bool | pauliatomic =false |
| | Flag to indicate if the Pauli exchange is to be estimated with atomic contributions.
|
| |
|
bool | ibsiMode =false |
| | Flag to indicate if we are using the IBSI mode.
|
| |
|
bool | elfMode =false |
| | Flag to indicate if we are using the ELF mode.
|
| |
|
bool | HirshMode =false |
| | Flag to indicate if we are using the HIRSH mode.
|
| |
|
bool | CriticMode =false |
| | Flag to indicate if we are searching for critical points.
|
| |
|
bool | dgSCALED =false |
| | Flag to indicate if the dgSCALED mode is enabled.
|
| |
|
bool | fullaoaccMode =false |
| | Flag to indicate if the full level of accuracy is enabled for AO calculation.
|
| |
| bool | CriticMEDIUMMode =true |
| |
| bool | CriticFINEMode =false |
| |
| bool | CriticULTRAFINEMode =false |
| |
| bool | CriticAddSeedsMode =false |
| |
|
bool | peakFocusIntra =false |
| | Flag to indicate if we the user has defined a peakfocus.
|
| |
|
bool | cubeIncrement = false |
| | Flag to indicate if increment have been set for a cube.
|
| |
|
bool | frag1Defined =false |
| | Flag to indicate if FRAG1/FRAG2 are defined.
|
| |
|
bool | setLIGAND =false |
| | Flag to indicate if the user has provided the index of the ligand within the set of two supplied fragments.
|
| |
| std::set< int > | moleculeAatoms |
| | The value associated to the keyword MOL2ID.
|
| |
| std::set< int > | moleculeBatoms |
| |
|
std::string | moleculeAatomDefinition |
| | The original user definition of the molecule A.
|
| |
|
std::vector< std::pair< unsigned int, unsigned int > > | chosenBonds |
| | The chosen bond i.e. pair of indexes.
|
| |
Implementation of methods declared in reader.h.