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RDKit
Open-source cheminformatics and machine learning.
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#include <RGroupDecompParams.h>
Public Member Functions | |
unsigned int | autoGetLabels (const RWMol &) |
bool | prepareCore (RWMol &, const RWMol *alignCore) |
void | addDummyAtomsToUnlabelledCoreAtoms (RWMol &core) |
RGroupDecompositionParameters () | |
Definition at line 56 of file RGroupDecompParams.h.
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inline |
Definition at line 122 of file RGroupDecompParams.h.
References RDKit::SubstructMatchParameters::useChirality.
Definition at line 62 of file RGroupDecompParams.h.
unlabelled core atoms can have multiple rgroups
Definition at line 77 of file RGroupDecompParams.h.
allow labelled Rgroups of degree 2 or more
Definition at line 75 of file RGroupDecompParams.h.
Definition at line 64 of file RGroupDecompParams.h.
Definition at line 80 of file RGroupDecompParams.h.
Definition at line 79 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaMaximumOperations = -1 |
Definition at line 105 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement = -1 |
Definition at line 108 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaNumberRuns = 1 |
Definition at line 112 of file RGroupDecompParams.h.
Definition at line 117 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaPopulationSize = -1 |
Definition at line 103 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaRandomSeed = -1 |
Definition at line 110 of file RGroupDecompParams.h.
include target molecule (featuring explicit hydrogens where they coincide with R groups in the core) into RGD results, and set _rgroupTargetAtoms and _rgroupTargetBonds properties on R groups and core as vectors of target atom and bond indices to enable highlighting for SAR analysis (see https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html)
Definition at line 87 of file RGroupDecompParams.h.
Definition at line 57 of file RGroupDecompParams.h.
Definition at line 58 of file RGroupDecompParams.h.
only allow rgroup decomposition at the specified rgroups
Definition at line 66 of file RGroupDecompParams.h.
remove all user-defined rgroups that only have hydrogens
Definition at line 68 of file RGroupDecompParams.h.
remove all user-defined rgroups that only have hydrogens, and also remove the corresponding labels from the core
Definition at line 71 of file RGroupDecompParams.h.
remove all hydrogens from the output molecules
Definition at line 73 of file RGroupDecompParams.h.
Definition at line 60 of file RGroupDecompParams.h.
Definition at line 59 of file RGroupDecompParams.h.
SubstructMatchParameters RDKit::RGroupDecompositionParameters::substructmatchParams |
Definition at line 120 of file RGroupDecompParams.h.
double RDKit::RGroupDecompositionParameters::timeout = -1.0 |
timeout in seconds. <=0 indicates no timeout
Definition at line 89 of file RGroupDecompParams.h.