RDDepict::EmbeddedAtom Class Reference

Class that contains the data for an atoms that has alredy been embedded. More...

#include <EmbeddedFrag.h>

List of all members.

Public Types
enum	EAtomType { UNSPECIFIED = 0, CISTRANS, RING }
Public Member Functions
	EmbeddedAtom ()
	EmbeddedAtom (unsigned int aid, const RDGeom::Point2D &pos)
EmbeddedAtom &	operator= (const EmbeddedAtom &other)
void	Transform (const RDGeom::Transform2D &trans)
void	Reflect (const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
Public Attributes
unsigned int	aid
double	angle
int	nbr1
	the first neighbor of this atom that form the 'angle'
int	nbr2
	the second neighbor of atom that from the 'angle'
int	CisTransNbr
bool	ccw
int	rotDir
RDGeom::Point2D	loc
RDGeom::Point2D	normal
RDKit::INT_VECT	neighs
	and these are the atom IDs of the neighbors that still need to be embedded
double	d_density

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Detailed Description

Class that contains the data for an atoms that has alredy been embedded.

Definition at line 29 of file EmbeddedFrag.h.

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Member Enumeration Documentation

enum RDDepict::EmbeddedAtom::EAtomType

Enumerator:

UNSPECIFIED
CISTRANS
RING

Definition at line 31 of file EmbeddedFrag.h.

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Constructor & Destructor Documentation

RDDepict::EmbeddedAtom::EmbeddedAtom

(

)

[inline]

Definition at line 36 of file EmbeddedFrag.h.

References neighs.

RDDepict::EmbeddedAtom::EmbeddedAtom	(	unsigned int	aid,
		const RDGeom::Point2D &	pos
	)			[inline]

Definition at line 41 of file EmbeddedFrag.h.

References loc.

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Member Function Documentation

EmbeddedAtom& RDDepict::EmbeddedAtom::operator=

(

const EmbeddedAtom &

other

)

[inline]

Definition at line 47 of file EmbeddedFrag.h.

References angle, ccw, CisTransNbr, d_density, loc, nbr1, nbr2, neighs, normal, and rotDir.

void RDDepict::EmbeddedAtom::Reflect	(	const RDGeom::Point2D &	loc1,
		const RDGeom::Point2D &	loc2
	)			[inline]

Definition at line 68 of file EmbeddedFrag.h.

References ccw, loc, normal, and RDDepict::reflectPoint().

void RDDepict::EmbeddedAtom::Transform

(

const RDGeom::Transform2D &

trans

)

[inline]

Definition at line 61 of file EmbeddedFrag.h.

References loc, normal, and RDGeom::Transform2D::TransformPoint().

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Member Data Documentation

unsigned int RDDepict::EmbeddedAtom::aid

Definition at line 77 of file EmbeddedFrag.h.

double RDDepict::EmbeddedAtom::angle

the angle that is already takes at this atom, so any new atom attaching to this atom with have to fall in the available part

Definition at line 81 of file EmbeddedFrag.h.

Referenced by operator=().

bool RDDepict::EmbeddedAtom::ccw

which direction do we rotate this normal to add the next bond if ccw is true we rotate counter cloack wise, otherwise rotate clock wise, by an angle that is <= PI/2

Definition at line 96 of file EmbeddedFrag.h.

Referenced by operator=(), and Reflect().

int RDDepict::EmbeddedAtom::CisTransNbr

is this is a cis/trans atom the neighbor of this atom that is involved in the cis/trans system - defaults to -1

Definition at line 91 of file EmbeddedFrag.h.

Referenced by operator=().

double RDDepict::EmbeddedAtom::d_density

Definition at line 116 of file EmbeddedFrag.h.

Referenced by operator=().

RDGeom::Point2D RDDepict::EmbeddedAtom::loc

Definition at line 103 of file EmbeddedFrag.h.

Referenced by EmbeddedAtom(), operator=(), Reflect(), and Transform().

int RDDepict::EmbeddedAtom::nbr1

the first neighbor of this atom that form the 'angle'

Definition at line 84 of file EmbeddedFrag.h.

Referenced by operator=().

int RDDepict::EmbeddedAtom::nbr2

the second neighbor of atom that from the 'angle'

Definition at line 87 of file EmbeddedFrag.h.

Referenced by operator=().

RDKit::INT_VECT RDDepict::EmbeddedAtom::neighs

and these are the atom IDs of the neighbors that still need to be embedded

Definition at line 111 of file EmbeddedFrag.h.

Referenced by EmbeddedAtom(), and operator=().

RDGeom::Point2D RDDepict::EmbeddedAtom::normal

this is a normal vector to one of the bonds that added this atom it provides the side on which we want to add a new bond to this atom, this is only relevant when we are dealing with non ring atoms. We would like to draw chains in a zig-zag manner

Definition at line 108 of file EmbeddedFrag.h.

Referenced by operator=(), Reflect(), and Transform().

int RDDepict::EmbeddedAtom::rotDir

rotation direction around this atom when adding new atoms, we determine this for the first neighbor and stick to this direction after that useful only on atoms that are degree >= 4

Definition at line 101 of file EmbeddedFrag.h.

Referenced by operator=().

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The documentation for this class was generated from the following file:

• EmbeddedFrag.h