RDCode: DepictUtils.h File Reference

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# DepictUtils.h File Reference

`#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 &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
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 &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.
## 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