RDKit
Open-source cheminformatics and machine learning.
RDKit::MMFF::Tools Namespace Reference

Classes

class  DefaultTorsionBondSmarts
 

Enumerations

enum  { RELATION_1_2 = 0, RELATION_1_3 = 1, RELATION_1_4 = 2, RELATION_1_X = 3 }
 

Functions

unsigned int twoBitCellPos (unsigned int nAtoms, int i, int j)
 
void setTwoBitCell (boost::shared_array< boost::uint8_t > &res, unsigned int pos, boost::uint8_t value)
 
boost::uint8_t getTwoBitCell (boost::shared_array< boost::uint8_t > &res, unsigned int pos)
 
boost::shared_array< boost::uint8_t > buildNeighborMatrix (const ROMol &mol)
 
void addBonds (const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
 
void addAngles (const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
 
void addStretchBend (const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
 
void addOop (const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field)
 
void addTorsions (const ROMol &mol, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, const std::string &torsionBondSmarts=DefaultTorsionBondSmarts::string())
 
void addVdW (const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
 
void addEle (const ROMol &mol, int confId, MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double nonBondedThresh=100.0, bool ignoreInterfragInteractions=true)
 

Enumeration Type Documentation

anonymous enum
Enumerator
RELATION_1_2 
RELATION_1_3 
RELATION_1_4 
RELATION_1_X 

Definition at line 96 of file MMFF/Builder.h.

Function Documentation

void RDKit::MMFF::Tools::addAngles ( const ROMol mol,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field 
)
void RDKit::MMFF::Tools::addBonds ( const ROMol mol,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field 
)
void RDKit::MMFF::Tools::addEle ( const ROMol mol,
int  confId,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field,
boost::shared_array< boost::uint8_t >  neighborMatrix,
double  nonBondedThresh = 100.0,
bool  ignoreInterfragInteractions = true 
)
void RDKit::MMFF::Tools::addOop ( const ROMol mol,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field 
)
void RDKit::MMFF::Tools::addStretchBend ( const ROMol mol,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field 
)
void RDKit::MMFF::Tools::addTorsions ( const ROMol mol,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field,
const std::string &  torsionBondSmarts = DefaultTorsionBondSmarts::string() 
)
void RDKit::MMFF::Tools::addVdW ( const ROMol mol,
int  confId,
MMFFMolProperties mmffMolProperties,
ForceFields::ForceField field,
boost::shared_array< boost::uint8_t >  neighborMatrix,
double  nonBondedThresh = 100.0,
bool  ignoreInterfragInteractions = true 
)
boost::shared_array<boost::uint8_t> RDKit::MMFF::Tools::buildNeighborMatrix ( const ROMol mol)
boost::uint8_t RDKit::MMFF::Tools::getTwoBitCell ( boost::shared_array< boost::uint8_t > &  res,
unsigned int  pos 
)
void RDKit::MMFF::Tools::setTwoBitCell ( boost::shared_array< boost::uint8_t > &  res,
unsigned int  pos,
boost::uint8_t  value 
)
unsigned int RDKit::MMFF::Tools::twoBitCellPos ( unsigned int  nAtoms,
int  i,
int  j 
)