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Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
RDKit::MolOps::AdjustQueryParameters Struct Reference

Parameters controlling the behavior of MolOps::adjustQueryProperties. More...

#include <MolOps.h>

Public Member Functions

 AdjustQueryParameters ()
 

Static Public Member Functions

static AdjustQueryParameters noAdjustments ()
 returns an AdjustQueryParameters object with all adjustments disabled
 

Public Attributes

bool adjustDegree = true
 
std::uint32_t adjustDegreeFlags = ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS
 
bool adjustRingCount = false
 
std::uint32_t adjustRingCountFlags
 
bool makeDummiesQueries = true
 
bool aromatizeIfPossible = true
 
bool makeBondsGeneric
 
std::uint32_t makeBondsGenericFlags = ADJUST_IGNORENONE
 
bool makeAtomsGeneric
 
std::uint32_t makeAtomsGenericFlags = ADJUST_IGNORENONE
 
bool adjustHeavyDegree = false
 
std::uint32_t adjustHeavyDegreeFlags
 
bool adjustRingChain = false
 
std::uint32_t adjustRingChainFlags = ADJUST_IGNORENONE
 
bool useStereoCareForBonds
 
bool adjustConjugatedFiveRings
 
bool setMDLFiveRingAromaticity
 
bool adjustSingleBondsToDegreeOneNeighbors
 
bool adjustSingleBondsBetweenAromaticAtoms
 

Detailed Description

Parameters controlling the behavior of MolOps::adjustQueryProperties.

Note that some of the options here are either directly contradictory or make no sense when combined with each other. We generally assume that client code is doing something sensible and don't attempt to detect possible conflicts or problems.

Definition at line 417 of file MolOps.h.

Constructor & Destructor Documentation

◆ AdjustQueryParameters()

RDKit::MolOps::AdjustQueryParameters::AdjustQueryParameters ( )
inline

Definition at line 475 of file MolOps.h.

Referenced by noAdjustments().

Member Function Documentation

◆ noAdjustments()

static AdjustQueryParameters RDKit::MolOps::AdjustQueryParameters::noAdjustments ( )
inlinestatic

returns an AdjustQueryParameters object with all adjustments disabled

Definition at line 468 of file MolOps.h.

References adjustDegree, AdjustQueryParameters(), aromatizeIfPossible, and makeDummiesQueries.

Member Data Documentation

◆ adjustConjugatedFiveRings

bool RDKit::MolOps::AdjustQueryParameters::adjustConjugatedFiveRings
Initial value:
=
false

sets bond queries in conjugated five-rings to SINGLE|DOUBLE|AROMATIC

Definition at line 450 of file MolOps.h.

◆ adjustDegree

bool RDKit::MolOps::AdjustQueryParameters::adjustDegree = true

add degree queries

Definition at line 418 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams(), and noAdjustments().

◆ adjustDegreeFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags = ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS

Definition at line 419 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), and RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams().

◆ adjustHeavyDegree

bool RDKit::MolOps::AdjustQueryParameters::adjustHeavyDegree = false

adjust the heavy-atom degree instead of overall degree

Definition at line 438 of file MolOps.h.

◆ adjustHeavyDegreeFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::adjustHeavyDegreeFlags
Initial value:
=
ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS
RDKit::MolOps::ADJUST_IGNOREDUMMIES
@ ADJUST_IGNOREDUMMIES
Definition MolOps.h:402
RDKit::MolOps::ADJUST_IGNORECHAINS
@ ADJUST_IGNORECHAINS
Definition MolOps.h:400

Definition at line 440 of file MolOps.h.

◆ adjustRingChain

bool RDKit::MolOps::AdjustQueryParameters::adjustRingChain = false

add ring-chain queries

Definition at line 443 of file MolOps.h.

◆ adjustRingChainFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::adjustRingChainFlags = ADJUST_IGNORENONE

Definition at line 444 of file MolOps.h.

◆ adjustRingCount

bool RDKit::MolOps::AdjustQueryParameters::adjustRingCount = false

add ring-count queries

Definition at line 421 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), and RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams().

◆ adjustRingCountFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags
Initial value:
=
ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS

Definition at line 422 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), and RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams().

◆ adjustSingleBondsBetweenAromaticAtoms

bool RDKit::MolOps::AdjustQueryParameters::adjustSingleBondsBetweenAromaticAtoms
Initial value:
=
false

sets non-ring single bonds between two aromatic or conjugated atoms to SINGLE|AROMATIC

Definition at line 462 of file MolOps.h.

◆ adjustSingleBondsToDegreeOneNeighbors

bool RDKit::MolOps::AdjustQueryParameters::adjustSingleBondsToDegreeOneNeighbors
Initial value:
=
false

sets single bonds between aromatic or conjugated atoms and degree one neighbors to SINGLE|AROMATIC

Definition at line 458 of file MolOps.h.

◆ aromatizeIfPossible

bool RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible = true

perceive and set aromaticity

Definition at line 428 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams(), and noAdjustments().

◆ makeAtomsGeneric

bool RDKit::MolOps::AdjustQueryParameters::makeAtomsGeneric
Initial value:
=
false

convert atoms to generic queries (any atoms)

Definition at line 434 of file MolOps.h.

◆ makeAtomsGenericFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::makeAtomsGenericFlags = ADJUST_IGNORENONE

Definition at line 436 of file MolOps.h.

◆ makeBondsGeneric

bool RDKit::MolOps::AdjustQueryParameters::makeBondsGeneric
Initial value:
=
false

convert bonds to generic queries (any bonds)

Definition at line 430 of file MolOps.h.

◆ makeBondsGenericFlags

std::uint32_t RDKit::MolOps::AdjustQueryParameters::makeBondsGenericFlags = ADJUST_IGNORENONE

Definition at line 432 of file MolOps.h.

◆ makeDummiesQueries

bool RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries = true

convert dummy atoms without isotope labels to any-atom queries

Definition at line 425 of file MolOps.h.

Referenced by RDKit::RxnOps::ChemDrawRxnAdjustParams(), RDKit::RxnOps::DefaultRxnAdjustParams(), RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams(), and noAdjustments().

◆ setMDLFiveRingAromaticity

bool RDKit::MolOps::AdjustQueryParameters::setMDLFiveRingAromaticity
Initial value:
=
false

uses the 5-ring aromaticity behavior of the (former) MDL software as documented in the Chemical Representation Guide

Definition at line 454 of file MolOps.h.

◆ useStereoCareForBonds

bool RDKit::MolOps::AdjustQueryParameters::useStereoCareForBonds
Initial value:
=
false

remove stereochemistry info from double bonds that do not have the stereoCare property set

Definition at line 446 of file MolOps.h.

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