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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 () | |
Public Attributes | |
unsigned int | labels = AutoDetect |
unsigned int | matchingStrategy = GreedyChunks |
unsigned int | scoreMethod = Match |
unsigned int | rgroupLabelling = AtomMap | MDLRGroup |
unsigned int | alignment = MCS |
unsigned int | chunkSize = 5 |
bool | onlyMatchAtRGroups = false |
only allow rgroup decomposition at the specified rgroups | |
bool | removeAllHydrogenRGroups = true |
remove all user-defined rgroups that only have hydrogens | |
bool | removeAllHydrogenRGroupsAndLabels = true |
bool | removeHydrogensPostMatch = true |
remove all hydrogens from the output molecules | |
bool | allowNonTerminalRGroups = false |
allow labelled Rgroups of degree 2 or more | |
bool | allowMultipleRGroupsOnUnlabelled = false |
unlabelled core atoms can have multiple rgroups | |
bool | doTautomers = false |
bool | doEnumeration = false |
bool | includeTargetMolInResults = false |
double | timeout = -1.0 |
timeout in seconds. <=0 indicates no timeout | |
int | gaPopulationSize = -1 |
int | gaMaximumOperations = -1 |
int | gaNumberOperationsWithoutImprovement = -1 |
int | gaRandomSeed = -1 |
int | gaNumberRuns = 1 |
bool | gaParallelRuns = false |
SubstructMatchParameters | substructmatchParams |
Definition at line 64 of file RGroupDecompParams.h.
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inline |
Definition at line 129 of file RGroupDecompParams.h.
References RDKit::SubstructMatchParameters::useChirality.
void RDKit::RGroupDecompositionParameters::addDummyAtomsToUnlabelledCoreAtoms | ( | RWMol & | core | ) |
unsigned int RDKit::RGroupDecompositionParameters::autoGetLabels | ( | const RWMol & | ) |
unsigned int RDKit::RGroupDecompositionParameters::alignment = MCS |
Definition at line 69 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::allowMultipleRGroupsOnUnlabelled = false |
unlabelled core atoms can have multiple rgroups
Definition at line 84 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::allowNonTerminalRGroups = false |
allow labelled Rgroups of degree 2 or more
Definition at line 82 of file RGroupDecompParams.h.
unsigned int RDKit::RGroupDecompositionParameters::chunkSize = 5 |
Definition at line 71 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::doEnumeration = false |
Definition at line 87 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::doTautomers = false |
Definition at line 86 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaMaximumOperations = -1 |
Definition at line 112 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement = -1 |
Definition at line 115 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaNumberRuns = 1 |
Definition at line 119 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::gaParallelRuns = false |
Definition at line 124 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaPopulationSize = -1 |
Definition at line 110 of file RGroupDecompParams.h.
int RDKit::RGroupDecompositionParameters::gaRandomSeed = -1 |
Definition at line 117 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::includeTargetMolInResults = false |
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 94 of file RGroupDecompParams.h.
unsigned int RDKit::RGroupDecompositionParameters::labels = AutoDetect |
Definition at line 65 of file RGroupDecompParams.h.
unsigned int RDKit::RGroupDecompositionParameters::matchingStrategy = GreedyChunks |
Definition at line 66 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::onlyMatchAtRGroups = false |
only allow rgroup decomposition at the specified rgroups
Definition at line 73 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroups = true |
remove all user-defined rgroups that only have hydrogens
Definition at line 75 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroupsAndLabels = true |
remove all user-defined rgroups that only have hydrogens, and also remove the corresponding labels from the core
Definition at line 78 of file RGroupDecompParams.h.
bool RDKit::RGroupDecompositionParameters::removeHydrogensPostMatch = true |
remove all hydrogens from the output molecules
Definition at line 80 of file RGroupDecompParams.h.
unsigned int RDKit::RGroupDecompositionParameters::rgroupLabelling = AtomMap | MDLRGroup |
Definition at line 68 of file RGroupDecompParams.h.
unsigned int RDKit::RGroupDecompositionParameters::scoreMethod = Match |
Definition at line 67 of file RGroupDecompParams.h.
SubstructMatchParameters RDKit::RGroupDecompositionParameters::substructmatchParams |
Definition at line 127 of file RGroupDecompParams.h.
double RDKit::RGroupDecompositionParameters::timeout = -1.0 |
timeout in seconds. <=0 indicates no timeout
Definition at line 96 of file RGroupDecompParams.h.