RDKit
Open-source cheminformatics and machine learning.
RDKit::MMFF::MMFFMolProperties Class Reference

#include <AtomTyper.h>

Public Member Functions

 MMFFMolProperties (ROMol &mol, const std::string &mmffVariant="MMFF94", boost::uint8_t verbosity=MMFF_VERBOSITY_NONE, std::ostream &oStream=std::cout)
 
 ~MMFFMolProperties ()
 
unsigned int getMMFFBondType (const Bond *bond)
 
unsigned int getMMFFAngleType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)
 
const std::pair< unsigned int, unsigned int > getMMFFTorsionType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4)
 
void computeMMFFCharges (const ROMol &mol)
 
const ForceFields::MMFF::MMFFTorgetMMFFTorsionEmpiricalRuleParams (const ROMol &mol, unsigned int idx2, unsigned int idx3)
 
const ForceFields::MMFF::MMFFBondgetMMFFBondStretchEmpiricalRuleParams (const ROMol &mol, const Bond *bond)
 
boost::uint8_t getMMFFAtomType (const unsigned int idx)
 
double getMMFFFormalCharge (const unsigned int idx)
 
double getMMFFPartialCharge (const unsigned int idx)
 
void setMMFFBondTerm (const bool state)
 
bool getMMFFBondTerm ()
 
void setMMFFAngleTerm (const bool state)
 
bool getMMFFAngleTerm ()
 
void setMMFFStretchBendTerm (const bool state)
 
bool getMMFFStretchBendTerm ()
 
void setMMFFOopTerm (const bool state)
 
bool getMMFFOopTerm ()
 
void setMMFFTorsionTerm (const bool state)
 
bool getMMFFTorsionTerm ()
 
void setMMFFVdWTerm (const bool state)
 
bool getMMFFVdWTerm ()
 
void setMMFFEleTerm (const bool state)
 
bool getMMFFEleTerm ()
 
void setMMFFVariant (const std::string &mmffVariant)
 
const std::string getMMFFVariant ()
 
void setMMFFDielectricConstant (const double dielConst)
 
double getMMFFDielectricConstant ()
 
void setMMFFDielectricModel (boost::uint8_t dielModel)
 
boost::uint8_t getMMFFDielectricModel ()
 
void setMMFFVerbosity (boost::uint8_t verbosity)
 
boost::uint8_t getMMFFVerbosity ()
 
void setMMFFOStream (std::ostream *oStream)
 
std::ostream & getMMFFOStream ()
 
bool isValid ()
 
bool getMMFFBondStretchParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, unsigned int &bondType, MMFFBond &mmffBondStretchParams)
 
bool getMMFFAngleBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &angleType, MMFFAngle &mmffAngleBendParams)
 
bool getMMFFStretchBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &stretchBendType, MMFFStbn &mmffStretchBendParams, MMFFBond mmffBondStretchParams[2], MMFFAngle &mmffAngleBendParams)
 
bool getMMFFTorsionParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, unsigned int &torsionType, MMFFTor &mmffTorsionParams)
 
bool getMMFFOopBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, MMFFOop &mmffOopBendParams)
 
bool getMMFFVdWParams (const unsigned int idx1, const unsigned int idx2, MMFFVdWRijstarEps &mmffVdWParams)
 

Detailed Description

Definition at line 46 of file MMFF/AtomTyper.h.

Constructor & Destructor Documentation

RDKit::MMFF::MMFFMolProperties::MMFFMolProperties ( ROMol mol,
const std::string &  mmffVariant = "MMFF94",
boost::uint8_t  verbosity = MMFF_VERBOSITY_NONE,
std::ostream &  oStream = std::cout 
)
RDKit::MMFF::MMFFMolProperties::~MMFFMolProperties ( )
inline

Definition at line 51 of file MMFF/AtomTyper.h.

Member Function Documentation

void RDKit::MMFF::MMFFMolProperties::computeMMFFCharges ( const ROMol mol)
bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleBendParams ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3,
unsigned int &  angleType,
MMFFAngle mmffAngleBendParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleTerm ( )
inline

Definition at line 82 of file MMFF/AtomTyper.h.

unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFAngleType ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3 
)
boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFAtomType ( const unsigned int  idx)
inline

Definition at line 64 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

const ForceFields::MMFF::MMFFBond* RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams ( const ROMol mol,
const Bond bond 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchParams ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
unsigned int &  bondType,
MMFFBond mmffBondStretchParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFBondTerm ( )
inline

Definition at line 80 of file MMFF/AtomTyper.h.

unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFBondType ( const Bond bond)
double RDKit::MMFF::MMFFMolProperties::getMMFFDielectricConstant ( )
inline

Definition at line 109 of file MMFF/AtomTyper.h.

boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFDielectricModel ( )
inline

Definition at line 113 of file MMFF/AtomTyper.h.

bool RDKit::MMFF::MMFFMolProperties::getMMFFEleTerm ( )
inline

Definition at line 94 of file MMFF/AtomTyper.h.

double RDKit::MMFF::MMFFMolProperties::getMMFFFormalCharge ( const unsigned int  idx)
inline

Definition at line 69 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

bool RDKit::MMFF::MMFFMolProperties::getMMFFOopBendParams ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3,
const unsigned int  idx4,
MMFFOop mmffOopBendParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFOopTerm ( )
inline

Definition at line 88 of file MMFF/AtomTyper.h.

std::ostream& RDKit::MMFF::MMFFMolProperties::getMMFFOStream ( )
inline

Definition at line 119 of file MMFF/AtomTyper.h.

double RDKit::MMFF::MMFFMolProperties::getMMFFPartialCharge ( const unsigned int  idx)
inline

Definition at line 74 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendParams ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3,
unsigned int &  stretchBendType,
MMFFStbn mmffStretchBendParams,
MMFFBond  mmffBondStretchParams[2],
MMFFAngle mmffAngleBendParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendTerm ( )
inline

Definition at line 86 of file MMFF/AtomTyper.h.

const ForceFields::MMFF::MMFFTor* RDKit::MMFF::MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams ( const ROMol mol,
unsigned int  idx2,
unsigned int  idx3 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionParams ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3,
const unsigned int  idx4,
unsigned int &  torsionType,
MMFFTor mmffTorsionParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionTerm ( )
inline

Definition at line 90 of file MMFF/AtomTyper.h.

const std::pair<unsigned int, unsigned int> RDKit::MMFF::MMFFMolProperties::getMMFFTorsionType ( const ROMol mol,
const unsigned int  idx1,
const unsigned int  idx2,
const unsigned int  idx3,
const unsigned int  idx4 
)
const std::string RDKit::MMFF::MMFFMolProperties::getMMFFVariant ( )
inline

Definition at line 101 of file MMFF/AtomTyper.h.

bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWParams ( const unsigned int  idx1,
const unsigned int  idx2,
MMFFVdWRijstarEps mmffVdWParams 
)
bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWTerm ( )
inline

Definition at line 92 of file MMFF/AtomTyper.h.

boost::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFVerbosity ( )
inline

Definition at line 117 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFAngleTerm ( const bool  state)
inline

Definition at line 81 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFBondTerm ( const bool  state)
inline

Definition at line 79 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricConstant ( const double  dielConst)
inline

Definition at line 104 of file MMFF/AtomTyper.h.

References PRECONDITION.

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricModel ( boost::uint8_t  dielModel)
inline

Definition at line 110 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFEleTerm ( const bool  state)
inline

Definition at line 93 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFOopTerm ( const bool  state)
inline

Definition at line 87 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFOStream ( std::ostream *  oStream)
inline

Definition at line 118 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFStretchBendTerm ( const bool  state)
inline

Definition at line 83 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFTorsionTerm ( const bool  state)
inline

Definition at line 89 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFVariant ( const std::string &  mmffVariant)
inline

Definition at line 95 of file MMFF/AtomTyper.h.

References PRECONDITION.

void RDKit::MMFF::MMFFMolProperties::setMMFFVdWTerm ( const bool  state)
inline

Definition at line 91 of file MMFF/AtomTyper.h.

void RDKit::MMFF::MMFFMolProperties::setMMFFVerbosity ( boost::uint8_t  verbosity)
inline

Definition at line 114 of file MMFF/AtomTyper.h.


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