RDKit
Open-source cheminformatics and machine learning.
RDKit::UFF::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

void addAtomChargeFlags (const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true)
 
std::string getAtomLabel (const Atom *atom)
 
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, const AtomicParamVect &params, ForceFields::ForceField *field)
 
void addAngles (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
 
void addNonbonded (const ROMol &mol, int confId, const AtomicParamVect &params, ForceFields::ForceField *field, boost::shared_array< boost::uint8_t > neighborMatrix, double vdwThresh=100.0, bool ignoreInterfragInteractions=true)
 
void addTorsions (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field, const std::string &torsionBondSmarts=DefaultTorsionBondSmarts::string())
 
void addInversions (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
 

Enumeration Type Documentation

anonymous enum
Enumerator
RELATION_1_2 
RELATION_1_3 
RELATION_1_4 
RELATION_1_X 

Definition at line 92 of file UFF/Builder.h.

Function Documentation

void RDKit::UFF::Tools::addAngles ( const ROMol mol,
const AtomicParamVect params,
ForceFields::ForceField field 
)
void RDKit::UFF::Tools::addAtomChargeFlags ( const Atom atom,
std::string &  atomKey,
bool  tolerateChargeMismatch = true 
)
void RDKit::UFF::Tools::addBonds ( const ROMol mol,
const AtomicParamVect params,
ForceFields::ForceField field 
)
void RDKit::UFF::Tools::addInversions ( const ROMol mol,
const AtomicParamVect params,
ForceFields::ForceField field 
)
void RDKit::UFF::Tools::addNonbonded ( const ROMol mol,
int  confId,
const AtomicParamVect params,
ForceFields::ForceField field,
boost::shared_array< boost::uint8_t >  neighborMatrix,
double  vdwThresh = 100.0,
bool  ignoreInterfragInteractions = true 
)
void RDKit::UFF::Tools::addTorsions ( const ROMol mol,
const AtomicParamVect params,
ForceFields::ForceField field,
const std::string &  torsionBondSmarts = DefaultTorsionBondSmarts::string() 
)
boost::shared_array<boost::uint8_t> RDKit::UFF::Tools::buildNeighborMatrix ( const ROMol mol)
std::string RDKit::UFF::Tools::getAtomLabel ( const Atom atom)
boost::uint8_t RDKit::UFF::Tools::getTwoBitCell ( boost::shared_array< boost::uint8_t > &  res,
unsigned int  pos 
)
void RDKit::UFF::Tools::setTwoBitCell ( boost::shared_array< boost::uint8_t > &  res,
unsigned int  pos,
boost::uint8_t  value 
)
unsigned int RDKit::UFF::Tools::twoBitCellPos ( unsigned int  nAtoms,
int  i,
int  j 
)