rdkit.Chem.rdmolops module¶

Module containing RDKit functionality for manipulating molecules.

class rdkit.Chem.rdmolops.AddHsParameters(self)¶

Bases: object

Parameters controlling H addition.

property addCoords¶: add coordinates for the Hs

property addResidueInfo¶: add residue info to the Hs

property explicitOnly¶: only add explict Hs

property skipQueries¶: do not add Hs to query atoms or atoms with query bonds

class rdkit.Chem.rdmolops.AdjustQueryParameters(self)¶

Bases: object

Parameters controlling which components of the query atoms/bonds are adjusted.

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.

A note on the flags controlling which atoms/bonds are modified:

These generally limit the set of atoms/bonds to be modified. For example:

ADJUST_IGNORERINGS atoms/bonds in rings will not be modified.

ADJUST_IGNORENONE causes all atoms/bonds to be modified

ADJUST_IGNOREALL no atoms/bonds will be modified

Some of the options obviously make no sense for bonds

NoAdjustments = <nanobind.nb_func object>¶

property adjustConjugatedFiveRings¶: set bond queries in conjugated five-rings to SINGLE|DOUBLE|AROMATIC

property adjustDegree¶: add degree queries

property adjustDegreeFlags¶: controls which atoms have their degree queries changed

property adjustHeavyDegree¶: adjust the heavy-atom degree

property adjustHeavyDegreeFlags¶: controls which atoms have their heavy-atom degree queries changed

property adjustRingChain¶: add ring-chain queries to atoms

property adjustRingChainFlags¶: controls which atoms have ring-chain queries added

property adjustRingCount¶: add ring-count queries

property adjustRingCountFlags¶: controls which atoms have ring-count queries added

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

property adjustSingleBondsToDegreeOneNeighbors¶: set single bonds bewteen aromatic or conjugated atoms and degree-one neighbors to SINGLE|AROMATIC

property aromatizeIfPossible¶: perceive and set aromaticity

property makeAtomsGeneric¶: convert atoms to generic queries (any atoms)

property makeAtomsGenericFlags¶: controls which atoms are converted to generic queries

property makeBondsGeneric¶: converts bonds to generic queries (any bonds)

property makeBondsGenericFlags¶: controls which bonds are converted to generic queries

property makeDummiesQueries¶: convert dummy atoms without isotope labels to any-atom queries

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

property useStereoCareForBonds¶: if this is set sterochemistry information will be removed from double bonds that do not have the stereoCare property set

class rdkit.Chem.rdmolops.AdjustQueryWhichFlags(*values)¶

Bases: IntEnum

ADJUST_IGNOREALL = 268435455¶

ADJUST_IGNORECHAINS = 1¶

ADJUST_IGNOREDUMMIES = 2¶

ADJUST_IGNOREMAPPED = 16¶

ADJUST_IGNORENONDUMMIES = 8¶

ADJUST_IGNORENONE = 0¶

ADJUST_IGNORERINGS = 4¶

class rdkit.Chem.rdmolops.AromaticityModel(*values)¶

Bases: Enum

AROMATICITY_CUSTOM = 268435455¶

AROMATICITY_DEFAULT = 0¶

AROMATICITY_MDL = 4¶

AROMATICITY_MMFF94 = 8¶

AROMATICITY_RDKIT = 1¶

AROMATICITY_SIMPLE = 2¶

class rdkit.Chem.rdmolops.BondWedgingParameters¶

Bases: object

Parameters controlling how bond wedging is done.

property wedgeTwoBondsIfPossible¶

If this is enabled then two bonds will be wedged at chiral centers subject to the following constraints:

ring bonds will not be wedged

bonds to chiral centers will not be wedged

bonds separated by more than 120 degrees will not be
wedged

class rdkit.Chem.rdmolops.BoolVector(self)¶

class rdkit.Chem.rdmolops.BoolVector(self, arg: rdkit.Chem.rdmolops.BoolVector)

class rdkit.Chem.rdmolops.BoolVector(self, arg: collections.abc.Iterable[bool], /)

Bases: object

Overloaded function.

__init__(self) -> None

Default constructor

__init__(self, arg: rdkit.Chem.rdmolops.BoolVector) -> None

Copy constructor

__init__(self, arg: collections.abc.Iterable[bool], /) -> None

Construct from an iterable object

append(self, arg: bool, /) → None¶: Append arg to the end of the list.

clear(self) → None¶: Remove all items from list.

count(self, arg: bool, /) → int¶: Return number of occurrences of arg.

extend(self, arg: rdkit.Chem.rdmolops.BoolVector, /) → None¶: Extend self by appending elements from arg.

insert(self, arg0: int, arg1: bool, /) → None¶: Insert object arg1 before index arg0.

pop(self, index: int = -1) → bool¶: Remove and return item at index (default last).

remove(self, arg: bool, /) → None¶: Remove first occurrence of arg.

class rdkit.Chem.rdmolops.MolzipLabel(*values)¶

Bases: Enum

AtomMapNumber = 0¶

AtomType = 3¶

FragmentOnBonds = 2¶

Isotope = 1¶

class rdkit.Chem.rdmolops.MolzipParams(self)¶

Bases: object

Parameters controlling how to zip molecules together

OPTIONS:: label : set the MolzipLabel option [default MolzipLabel.AtomMapNumber]
MolzipLabel.AtomMapNumber: atom maps are on dummy atoms, zip together the corresponding: attached atoms, i.e. zip ‘C[:1]’ ‘N[:1]’ results in ‘CN’
MolzipLabel.Isotope: isotope labels are on dummy atoms, zip together the corresponding: attached atoms, i.e. zip ‘C[1*]’ ‘N[1*]’ results in ‘CN’
MolzipLabel.FragmentOnBonds: zip together molecules generated by fragment on bonds.: Note the atom indices cannot change or be reordered from the output of fragmentOnBonds
MolzipLabel.AtomTypes: choose the atom types to act as matching dummy atoms.: i.e. ‘C[V]’ and ‘N[Xe]’ with atoms pairs [(‘V’, ‘Xe’)] results in ‘CN’

property alignCoordinates¶: if true and the input fragments have coordinates, the fragments will be aligned along connection vectors in the output molecule

property enforceValenceRules¶: If true (default) enforce valences after zipping Setting this to false allows assembling chemically incorrect fragments.

property generateCoordinates¶: If true will add depiction coordinates to input molecules and zipped molecule (for molzipFragments only)

property label¶: Set the atom labeling system to zip together

setAtomSymbols(self, symbols: object) → None¶: Set the atom symbols used to zip mols together when using AtomType labeling

class rdkit.Chem.rdmolops.RemoveHsParameters(self)¶

Bases: object

Parameters controlling which Hs are removed.

property removeAndTrackIsotopes¶: hydrogens with non-default isotopes and store them in the _isotopicHs atom property such that AddHs() can add the same isotope at a later stage

property removeDefiningBondStereo¶: hydrogens defining bond stereochemistry

property removeDegreeZero¶: hydrogens that have no bonds

property removeDummyNeighbors¶: hydrogens with at least one dummy-atom neighbor

property removeHigherDegrees¶: hydrogens with two (or more) bonds

property removeHydrides¶: hydrogens with formal charge -1

property removeInSGroups¶: hydrogens involved in SubstanceGroups

property removeIsotopes¶: hydrogens with non-default isotopes

property removeMapped¶: mapped hydrogens

property removeNonimplicit¶: DEPRECATED

property removeNontetrahedralNeighbors¶: hydrogens with neighbors that have non-tetrahedral stereochemistry

property removeOnlyHNeighbors¶: hydrogens with bonds only to other hydrogens

property removeWithQuery¶: hydrogens with queries defined

property removeWithWedgedBond¶: hydrogens with wedged bonds to them

property showWarnings¶: display warning messages for some classes of removed Hs

property updateExplicitCount¶: DEPRECATED

class rdkit.Chem.rdmolops.SanitizeFlags(*values)¶

Bases: IntEnum

SANITIZE_ADJUSTHS = 512¶

SANITIZE_ALL = 268435455¶

SANITIZE_CLEANUP = 1¶

SANITIZE_CLEANUPATROPISOMERS = 2048¶

SANITIZE_CLEANUPCHIRALITY = 256¶

SANITIZE_CLEANUP_ORGANOMETALLICS = 1024¶

SANITIZE_FINDRADICALS = 16¶

SANITIZE_KEKULIZE = 8¶

SANITIZE_NONE = 0¶

SANITIZE_PROPERTIES = 2¶

SANITIZE_SETAROMATICITY = 32¶

SANITIZE_SETCONJUGATION = 64¶

SANITIZE_SETHYBRIDIZATION = 128¶

SANITIZE_SYMMRINGS = 4¶

class rdkit.Chem.rdmolops.StereoBondThresholds¶

Bases: object

Constants used to set the thresholds for which single bonds can be made wavy.

CHIRAL_ATOM = 100000¶

DBL_BOND_NO_STEREO = 1000¶

DBL_BOND_SPECIFIED_STEREO = 10000¶

DIRECTION_SET = 1000000¶

class rdkit.Chem.rdmolops.StereoGroupAbsOptions(*values)¶

Bases: Enum

AlwaysInclude = 2¶

NeverInclude = 1¶

OnlyIncludeWhenOtherGroupsExist = 0¶

class rdkit.Chem.rdmolops.SubsetInfo(self)¶

Bases: object

property atomMapping¶: mapping from the original atom index to the subset atom index

property bondMapping¶: mapping from the original bond index to the subset bond index

class rdkit.Chem.rdmolops.SubsetMethod(*values)¶

Bases: Enum

BONDS = 1¶

BONDS_BETWEEN_ATOMS = 0¶

class rdkit.Chem.rdmolops.SubsetOptions(self)¶

Bases: object

property clearComputedProps¶: clear all computed props on the subsetted molecule

property conformerIdx¶: What conformer idx to use for the coordinates default is -1

property copyAsQuery¶: Return the subset as a query

property copyCoordinates¶: Copy the active coordinates from the molecule

property method¶: Subsetting method to use

property sanitize¶: Sanitize the resulting subset

class rdkit.Chem.rdmolops.SymmetrizeSSSRAlgorithm(*values)¶

Bases: Enum

DEFAULT = 0¶

LEGACY = 1¶

RDL = 2¶

class rdkit.Chem.rdmolops.UIntUIntMap(self)¶

class rdkit.Chem.rdmolops.UIntUIntMap(self, arg: rdkit.Chem.rdmolops.UIntUIntMap)

class rdkit.Chem.rdmolops.UIntUIntMap(self, arg: dict[int, int], /)

Bases: object

Overloaded function.

__init__(self) -> None

Default constructor

__init__(self, arg: rdkit.Chem.rdmolops.UIntUIntMap) -> None

Copy constructor

__init__(self, arg: dict[int, int], /) -> None

Construct from a dictionary

class ItemView¶: Bases: object

class KeyView¶: Bases: object

class ValueView¶: Bases: object

clear(self) → None¶: Remove all items

items(self) → rdkit.Chem.rdmolops.UIntUIntMap.ItemView¶: Returns an iterable view of the map’s items.

keys(self) → rdkit.Chem.rdmolops.UIntUIntMap.KeyView¶: Returns an iterable view of the map’s keys.

update(self, arg: rdkit.Chem.rdmolops.UIntUIntMap, /) → None¶: Update the map with element from arg

values(self) → rdkit.Chem.rdmolops.UIntUIntMap.ValueView¶: Returns an iterable view of the map’s values.

rdkit.Chem.rdmolops module¶

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