Loading...
Searching...
No Matches
DepictUtils.h File Reference
`#include <RDGeneral/export.h>`
`#include <RDGeneral/types.h>`
`#include <GraphMol/RDKitBase.h>`
`#include <GraphMol/RWMol.h>`
`#include <GraphMol/ROMol.h>`
`#include <GraphMol/Substruct/SubstructUtils.h>`
`#include <Geometry/Transform2D.h>`
`#include <Geometry/Transform3D.h>`
`#include <Geometry/point.h>`
`#include <queue>`

Go to the source code of this file.

## Classes

struct | RDDepict::gtIIPair

## Namespaces

namespace | RDDepict

## 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

RDKIT_DEPICTOR_EXPORT RDGeom::INT_POINT2D_MAP | RDDepict::embedRing (const RDKit::INT_VECT &ring)
| Some utility functions used in generating 2D coordinates.
RDKIT_DEPICTOR_EXPORT void | RDDepict::transformPoints (RDGeom::INT_POINT2D_MAP &nringCor, const RDGeom::Transform2D &trans)
RDKIT_DEPICTOR_EXPORT 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.
RDKIT_DEPICTOR_EXPORT void | RDDepict::reflectPoints (RDGeom::INT_POINT2D_MAP &coordMap, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
| Reflect a set of point through the line joining two point.
RDKIT_DEPICTOR_EXPORT RDGeom::Point2D | RDDepict::reflectPoint (const RDGeom::Point2D &point, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT | RDDepict::setNbrOrder (unsigned int aid, const RDKit::INT_VECT &nbrs, const RDKit::ROMol &mol)
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT | RDDepict::findNextRingToEmbed (const RDKit::INT_VECT &doneRings, const RDKit::VECT_INT_VECT &fusedRings, int &nextId)
| From a given set of rings find the ring the largest common elements with other rings.
template<class T >
RDKIT_DEPICTOR_EXPORT 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 &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2, double remAngle)
| computes the rotation direction between two vectors
RDGeom::Point2D | RDDepict::computeNormal (const RDGeom::Point2D &center, const RDGeom::Point2D &other)
| computes and return the normal of a vector between two points
double | RDDepict::computeAngle (const RDGeom::Point2D &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
| computes the rotation angle between two vectors
RDKIT_DEPICTOR_EXPORT int | RDDepict::pickFirstRingToEmbed (const RDKit::ROMol &mol, const RDKit::VECT_INT_VECT &fusedRings)
| pick the ring to embed first in a fused system
RDKIT_DEPICTOR_EXPORT 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_DEPICTOR_EXPORT RDKit::INT_VECT | RDDepict::getAllRotatableBonds (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
RDKIT_DEPICTOR_EXPORT 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.
RDKIT_DEPICTOR_EXPORT INT_PAIR_VECT | RDDepict::findBondsPairsToPermuteDeg4 (const RDGeom::Point2D &center, 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.
int | RDDepict::getAtomDepictRank (const RDKit::Atom *at)
| returns the rank of the atom for determining draw order
RDKIT_DEPICTOR_EXPORT bool | RDDepict::hasTerminalRGroupOrQueryHydrogen (const RDKit::ROMol &query)
RDKIT_DEPICTOR_EXPORT std::unique_ptr< RDKit::RWMol > | RDDepict::prepareTemplateForRGroups (RDKit::RWMol &templateMol)
RDKIT_DEPICTOR_EXPORT void | RDDepict::reducedToFullMatches (const RDKit::RWMol &reducedQuery, const RDKit::RWMol &molHs, std::vector< RDKit::MatchVectType > &matches)
RDKIT_DEPICTOR_EXPORT bool | RDDepict::invertWedgingIfMolHasFlipped (RDKit::ROMol &mol, const RDGeom::Transform3D &trans)

## Variables

RDKIT_DEPICTOR_EXPORT double | RDDepict::BOND_LEN
RDKIT_DEPICTOR_EXPORT double | RDDepict::COLLISION_THRES
RDKIT_DEPICTOR_EXPORT double | RDDepict::BOND_THRES
RDKIT_DEPICTOR_EXPORT double | RDDepict::ANGLE_OPEN
RDKIT_DEPICTOR_EXPORT unsigned int | RDDepict::MAX_COLL_ITERS
RDKIT_DEPICTOR_EXPORT double | RDDepict::HETEROATOM_COLL_SCALE
RDKIT_DEPICTOR_EXPORT unsigned int | RDDepict::NUM_BONDS_FLIPS