RDKit
Open-source cheminformatics and machine learning.
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#include <RDDepictor.h>
Public Attributes | |
const RDGeom::INT_POINT2D_MAP * | coordMap |
bool | canonOrient = false |
bool | clearConfs = true |
unsigned int | nFlipsPerSample = 0 |
unsigned int | nSamples = 0 |
the number of samples | |
int | sampleSeed = 0 |
seed for the random sampling process | |
bool | permuteDeg4Nodes = false |
bool | forceRDKit = false |
bool | useRingTemplates = false |
Definition at line 71 of file RDDepictor.h.
bool RDDepict::Compute2DCoordParameters::canonOrient = false |
canonicalize the orientation so that the long axes align with the x-axis etc.
Definition at line 77 of file RDDepictor.h.
bool RDDepict::Compute2DCoordParameters::clearConfs = true |
clear all existing conformations on the molecule before adding the 2D coordinates instead of simply adding to the list
Definition at line 79 of file RDDepictor.h.
const RDGeom::INT_POINT2D_MAP* RDDepict::Compute2DCoordParameters::coordMap |
a map of int to Point2D, between atom IDs and their locations. This is the container the user needs to fill if he/she wants to specify coordinates for a portion of the molecule, defaults to 0
Definition at line 72 of file RDDepictor.h.
bool RDDepict::Compute2DCoordParameters::forceRDKit = false |
use RDKit to generate coordinates even if preferCoordGen is set to true
Definition at line 89 of file RDDepictor.h.
unsigned int RDDepict::Compute2DCoordParameters::nFlipsPerSample = 0 |
the number of rotatable bonds that are flipped at random for each sample
Definition at line 82 of file RDDepictor.h.
unsigned int RDDepict::Compute2DCoordParameters::nSamples = 0 |
the number of samples
Definition at line 84 of file RDDepictor.h.
bool RDDepict::Compute2DCoordParameters::permuteDeg4Nodes = false |
try permuting the drawing order of bonds around atoms with four neighbors in order to improve the depiction
Definition at line 86 of file RDDepictor.h.
int RDDepict::Compute2DCoordParameters::sampleSeed = 0 |
seed for the random sampling process
Definition at line 85 of file RDDepictor.h.
bool RDDepict::Compute2DCoordParameters::useRingTemplates = false |
whether to use ring system templates for generating initial coordinates
Definition at line 91 of file RDDepictor.h.