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RDKit
Open-source cheminformatics and machine learning.
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Class that contains the data for an atoms that has already been embedded. More...
#include <EmbeddedFrag.h>
Public Types | |
enum | EAtomType { UNSPECIFIED = 0 , CISTRANS , RING } |
Public Member Functions | |
EmbeddedAtom () | |
EmbeddedAtom (const EmbeddedAtom &other)=default | |
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 {0} |
double | angle {-1.0} |
the angle that is already takes at this atom, so any new atom attaching to More... | |
int | nbr1 {-1} |
the first neighbor of this atom that form the 'angle' More... | |
int | nbr2 {-1} |
the second neighbor of atom that from the 'angle' More... | |
int | CisTransNbr {-1} |
is this is a cis/trans atom the neighbor of this atom that is involved in More... | |
bool | ccw {true} |
<= PI/2 More... | |
int | rotDir {0} |
useful only on atoms that are degree >= 4 More... | |
RDGeom::Point2D | loc |
RDGeom::Point2D | normal |
a zig-zag manner More... | |
RDKit::INT_VECT | neighs |
and these are the atom IDs of the neighbors that still need to be embedded More... | |
double | d_density {-1.0} |
bool | df_fixed {false} |
Class that contains the data for an atoms that has already been embedded.
Definition at line 29 of file EmbeddedFrag.h.
Enumerator | |
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UNSPECIFIED | |
CISTRANS | |
RING |
Definition at line 31 of file EmbeddedFrag.h.
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inline |
Definition at line 33 of file EmbeddedFrag.h.
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default |
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inline |
Definition at line 41 of file EmbeddedFrag.h.
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inline |
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inline |
Definition at line 80 of file EmbeddedFrag.h.
References RDDepict::reflectPoint().
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inline |
Definition at line 73 of file EmbeddedFrag.h.
References RDGeom::Transform2D::TransformPoint().
unsigned int RDDepict::EmbeddedAtom::aid {0} |
Definition at line 88 of file EmbeddedFrag.h.
double RDDepict::EmbeddedAtom::angle {-1.0} |
the angle that is already takes at this atom, so any new atom attaching to
atom with have to fall in the available part
Definition at line 93 of file EmbeddedFrag.h.
Referenced by operator=().
bool RDDepict::EmbeddedAtom::ccw {true} |
<= PI/2
which direction do we rotate this normal to add the next bond if ccw is true we rotate counter clockwise, otherwise rotate clock wise,
Definition at line 110 of file EmbeddedFrag.h.
Referenced by operator=().
int RDDepict::EmbeddedAtom::CisTransNbr {-1} |
is this is a cis/trans atom the neighbor of this atom that is involved in
cis/trans system - defaults to -1
Definition at line 104 of file EmbeddedFrag.h.
Referenced by operator=().
double RDDepict::EmbeddedAtom::d_density {-1.0} |
Definition at line 133 of file EmbeddedFrag.h.
Referenced by operator=().
bool RDDepict::EmbeddedAtom::df_fixed {false} |
if set this atom is fixed: further operations on the fragment may not move it.
Definition at line 137 of file EmbeddedFrag.h.
Referenced by operator=().
RDGeom::Point2D RDDepict::EmbeddedAtom::loc |
Definition at line 118 of file EmbeddedFrag.h.
Referenced by operator=().
int RDDepict::EmbeddedAtom::nbr1 {-1} |
the first neighbor of this atom that form the 'angle'
Definition at line 96 of file EmbeddedFrag.h.
Referenced by operator=().
int RDDepict::EmbeddedAtom::nbr2 {-1} |
the second neighbor of atom that from the 'angle'
Definition at line 99 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 127 of file EmbeddedFrag.h.
Referenced by operator=().
RDGeom::Point2D RDDepict::EmbeddedAtom::normal |
a zig-zag manner
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
Definition at line 124 of file EmbeddedFrag.h.
Referenced by operator=().
int RDDepict::EmbeddedAtom::rotDir {0} |
useful only on atoms that are degree >= 4
rotation direction around this atom when adding new atoms, we determine this for the first neighbor and stick to this direction after
Definition at line 116 of file EmbeddedFrag.h.
Referenced by operator=().