#include <RDGeneral/types.h>#include <GraphMol/RDKitBase.h>#include <GraphMol/RWMol.h>#include <GraphMol/ROMol.h>#include <Geometry/Transform2D.h>#include <Geometry/point.h>#include <queue>Go to the source code of this file.
Namespaces | |
| namespace | RDDepict |
Classes | |
| struct | RDDepict::gtIIPair |
Typedefs | |
| typedef std::vector < const RDGeom::Point2D * > | RDDepict::VECT_C_POINT |
| typedef std::pair < int, int > | RDDepict::PAIR_I_I |
| typedef std::vector < PAIR_I_I > | RDDepict::VECT_PII |
| typedef std::priority_queue < PAIR_I_I, VECT_PII, gtIIPair > | RDDepict::PR_QUEUE |
| typedef std::pair < double, PAIR_I_I > | RDDepict::PAIR_D_I_I |
| typedef std::list < PAIR_D_I_I > | RDDepict::LIST_PAIR_DII |
| typedef std::pair < int, int > | RDDepict::INT_PAIR |
| typedef std::vector < INT_PAIR > | RDDepict::INT_PAIR_VECT |
| typedef INT_PAIR_VECT::const_iterator | RDDepict::INT_PAIR_VECT_CI |
| typedef std::pair < double, INT_PAIR > | RDDepict::DOUBLE_INT_PAIR |
Functions | |
| RDGeom::INT_POINT2D_MAP | RDDepict::embedRing (const RDKit::INT_VECT &ring) |
| Some utility functions used in generating 2D coordinates. | |
| void | RDDepict::transformPoints (RDGeom::INT_POINT2D_MAP &nringCor, const RDGeom::Transform2D &trans) |
| RDGeom::Point2D | RDDepict::computeBisectPoint (const RDGeom::Point2D &rcr, double ang, const RDGeom::Point2D &nb1, const RDGeom::Point2D &nb2) |
| Find a point that bisects the angle at rcr. | |
| void | RDDepict::reflectPoints (RDGeom::INT_POINT2D_MAP &coordMap, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2) |
| Reflect a set of point through a the line joining two point. | |
| RDGeom::Point2D | RDDepict::reflectPoint (const RDGeom::Point2D &point, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2) |
| RDKit::INT_VECT | RDDepict::setNbrOrder (unsigned int aid, const RDKit::INT_VECT &nbrs, const RDKit::ROMol &mol) |
| Set the neighbors yet to added to aid such that the atoms with the most subs fall on opposite sides. | |
| RDKit::INT_VECT | RDDepict::findNextRingToEmbed (const RDKit::INT_VECT &doneRings, const RDKit::VECT_INT_VECT &fusedRings, int &nextId) |
| template<class T> | |
| T | RDDepict::rankAtomsByRank (const RDKit::ROMol &mol, const T &commAtms, bool ascending=true) |
| Sort a list of atoms by their CIP rank. | |
| double | RDDepict::computeSubAngle (unsigned int degree, RDKit::Atom::HybridizationType htype) |
| computes a subangle for an atom of given hybridization and degree | |
| int | RDDepict::rotationDir (const RDGeom::Point2D ¢er, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2, double remAngle) |
| computes the rotation direction between two vectors | |
| RDGeom::Point2D | RDDepict::computeNormal (const RDGeom::Point2D ¢er, const RDGeom::Point2D &other) |
| computes and return the normal of a vector between two points | |
| double | RDDepict::computeAngle (const RDGeom::Point2D ¢er, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2) |
| computes the rotation angle between two vectors | |
| int | RDDepict::pickFirstRingToEmbed (const RDKit::ROMol &mol, const RDKit::VECT_INT_VECT &fusedRings) |
| RDKit::INT_VECT | RDDepict::getRotatableBonds (const RDKit::ROMol &mol, unsigned int aid1, unsigned int aid2) |
| find the rotatable bonds on the shortest path between two atoms we will ignore ring atoms, and double bonds which are marked cis/trans | |
| RDKit::INT_VECT | RDDepict::getAllRotatbleBonds (const RDKit::ROMol &mol) |
| find all the rotatable bonds in a molecule we will ignore ring atoms, and double bonds which are marked cis/trans | |
| void | RDDepict::getNbrAtomAndBondIds (unsigned int aid, const RDKit::ROMol *mol, RDKit::INT_VECT &aids, RDKit::INT_VECT &bids) |
| Get the ids of the atoms and bonds that are connected to aid. | |
| INT_PAIR_VECT | RDDepict::findBondsPairsToPermuteDeg4 (const RDGeom::Point2D ¢er, const RDKit::INT_VECT &nbrBids, const VECT_C_POINT &nbrLocs) |
| Find pairs of bonds that can be permuted at a non-ring degree 4 atom. | |
Variables | |
| const double | RDDepict::BOND_LEN = 1.5 |
| const double | RDDepict::COLLISION_THRES = 0.35 |
| const double | RDDepict::BOND_THRES = 0.50 |
| const double | RDDepict::ANGLE_OPEN = 0.1222 |
| const unsigned int | RDDepict::MAX_COLL_ITERS = 15 |
| const double | RDDepict::HETEROATOM_COLL_SCALE = 1.3 |
| const unsigned int | RDDepict::NUM_BONDS_FLIPS = 3 |
1.5.3