RDDepict::EmbeddedFrag Member List

This is the complete list of members for RDDepict::EmbeddedFrag, including all inherited members.

addNonRingAtom(unsigned int aid, unsigned int toAid) | RDDepict::EmbeddedFrag |
canonicalizeOrientation() | RDDepict::EmbeddedFrag |
computeBox() | RDDepict::EmbeddedFrag |
computeDistMat(DOUBLE_SMART_PTR &dmat) | RDDepict::EmbeddedFrag |
EmbeddedFrag() | RDDepict::EmbeddedFrag | inline
EmbeddedFrag(unsigned int aid, const RDKit::ROMol *mol) | RDDepict::EmbeddedFrag |
EmbeddedFrag(const RDKit::ROMol *mol, const RDGeom::INT_POINT2D_MAP &coordMap) | RDDepict::EmbeddedFrag |
EmbeddedFrag(const RDKit::ROMol *mol, const RDKit::VECT_INT_VECT &fusedRings) | RDDepict::EmbeddedFrag |
EmbeddedFrag(const RDKit::Bond *dblBond) | RDDepict::EmbeddedFrag | explicit
expandEfrag(RDKit::INT_LIST &nratms, std::list< EmbeddedFrag > &efrags) | RDDepict::EmbeddedFrag |
findCollisions(const double *dmat, bool includeBonds=1) | RDDepict::EmbeddedFrag |
findCommonAtoms(const EmbeddedFrag &efrag2) | RDDepict::EmbeddedFrag |
findNeighbor(unsigned int aid) | RDDepict::EmbeddedFrag |
findNumNeigh(const RDGeom::Point2D &pt, double radius) | RDDepict::EmbeddedFrag |
flipAboutBond(unsigned int bondId, bool flipEnd=true) | RDDepict::EmbeddedFrag |
getBoxNx() | RDDepict::EmbeddedFrag | inline
getBoxNy() | RDDepict::EmbeddedFrag | inline
getBoxPx() | RDDepict::EmbeddedFrag | inline
getBoxPy() | RDDepict::EmbeddedFrag | inline
GetEmbeddedAtom(unsigned int aid) const | RDDepict::EmbeddedFrag | inline
GetEmbeddedAtoms() const | RDDepict::EmbeddedFrag | inline
getMol() const | RDDepict::EmbeddedFrag | inline
isDone() | RDDepict::EmbeddedFrag | inline
markDone() | RDDepict::EmbeddedFrag | inline
mergeFragsWithComm(std::list< EmbeddedFrag > &efrags) | RDDepict::EmbeddedFrag |
mergeNoCommon(EmbeddedFrag &embObj, unsigned int toAid, unsigned int nbrAid) | RDDepict::EmbeddedFrag |
mergeWithCommon(EmbeddedFrag &embObj, RDKit::INT_VECT &commAtms) | RDDepict::EmbeddedFrag |
mimicDistMatAndDensityCostFunc(const DOUBLE_SMART_PTR *dmat, double mimicDmatWt) | RDDepict::EmbeddedFrag |
openAngles(const double *dmat, unsigned int aid1, unsigned int aid2) | RDDepict::EmbeddedFrag |
permuteBonds(unsigned int aid, unsigned int aid1, unsigned int aid2) | RDDepict::EmbeddedFrag |
randomSampleFlipsAndPermutations(unsigned int nBondsPerSample=3, unsigned int nSamples=100, int seed=100, const DOUBLE_SMART_PTR *dmat=0, double mimicDmatWt=0.0, bool permuteDeg4Nodes=false) | RDDepict::EmbeddedFrag |
Reflect(const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2) | RDDepict::EmbeddedFrag |
removeCollisionsBondFlip() | RDDepict::EmbeddedFrag |
removeCollisionsOpenAngles() | RDDepict::EmbeddedFrag |
removeCollisionsShortenBonds() | RDDepict::EmbeddedFrag |
setupNewNeighs() | RDDepict::EmbeddedFrag |
Size() const | RDDepict::EmbeddedFrag | inline
Transform(const RDGeom::Transform2D &trans) | RDDepict::EmbeddedFrag |
Translate(const RDGeom::Point2D &shift) | RDDepict::EmbeddedFrag | inline
updateNewNeighs(unsigned int aid) | RDDepict::EmbeddedFrag |