| 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, bool useRingTemplates) | 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=nullptr, 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 | |
1.10.0