rdkit.Chem.rdDistGeom module

Module containing functions to compute atomic coordinates in 3D using distance geometry

rdkit.Chem.rdDistGeom.ETDG() → EmbedParameters :

Returns an EmbedParameters object for the ETDG method.

C++ signature :

(anonymous namespace)::PyEmbedParameters* ETDG()

rdkit.Chem.rdDistGeom.ETKDG() → EmbedParameters :

Returns an EmbedParameters object for the ETKDG method - version 1.

C++ signature :

(anonymous namespace)::PyEmbedParameters* ETKDG()

rdkit.Chem.rdDistGeom.ETKDGv2() → EmbedParameters :

Returns an EmbedParameters object for the ETKDG method - version 2.

C++ signature :

(anonymous namespace)::PyEmbedParameters* ETKDGv2()

rdkit.Chem.rdDistGeom.ETKDGv3() → EmbedParameters :

Returns an EmbedParameters object for the ETKDG method - version 3 (macrocycles).

C++ signature :

(anonymous namespace)::PyEmbedParameters* ETKDGv3()

class rdkit.Chem.rdDistGeom.EmbedFailureCauses

Bases: enum

BAD_DOUBLE_BOND_STEREO = rdkit.Chem.rdDistGeom.EmbedFailureCauses.BAD_DOUBLE_BOND_STEREO
CHECK_CHIRAL_CENTERS = rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS
CHECK_CHIRAL_CENTERS2 = rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS2
CHECK_TETRAHEDRAL_CENTERS = rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_TETRAHEDRAL_CENTERS
ETK_MINIMIZATION = rdkit.Chem.rdDistGeom.EmbedFailureCauses.ETK_MINIMIZATION
FINAL_CENTER_IN_VOLUME = rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CENTER_IN_VOLUME
FINAL_CHIRAL_BOUNDS = rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CHIRAL_BOUNDS
FIRST_MINIMIZATION = rdkit.Chem.rdDistGeom.EmbedFailureCauses.FIRST_MINIMIZATION
INITIAL_COORDS = rdkit.Chem.rdDistGeom.EmbedFailureCauses.INITIAL_COORDS
LINEAR_DOUBLE_BOND = rdkit.Chem.rdDistGeom.EmbedFailureCauses.LINEAR_DOUBLE_BOND
MINIMIZE_FOURTH_DIMENSION = rdkit.Chem.rdDistGeom.EmbedFailureCauses.MINIMIZE_FOURTH_DIMENSION
names = {'BAD_DOUBLE_BOND_STEREO': rdkit.Chem.rdDistGeom.EmbedFailureCauses.BAD_DOUBLE_BOND_STEREO, 'CHECK_CHIRAL_CENTERS': rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS, 'CHECK_CHIRAL_CENTERS2': rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS2, 'CHECK_TETRAHEDRAL_CENTERS': rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_TETRAHEDRAL_CENTERS, 'ETK_MINIMIZATION': rdkit.Chem.rdDistGeom.EmbedFailureCauses.ETK_MINIMIZATION, 'FINAL_CENTER_IN_VOLUME': rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CENTER_IN_VOLUME, 'FINAL_CHIRAL_BOUNDS': rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CHIRAL_BOUNDS, 'FIRST_MINIMIZATION': rdkit.Chem.rdDistGeom.EmbedFailureCauses.FIRST_MINIMIZATION, 'INITIAL_COORDS': rdkit.Chem.rdDistGeom.EmbedFailureCauses.INITIAL_COORDS, 'LINEAR_DOUBLE_BOND': rdkit.Chem.rdDistGeom.EmbedFailureCauses.LINEAR_DOUBLE_BOND, 'MINIMIZE_FOURTH_DIMENSION': rdkit.Chem.rdDistGeom.EmbedFailureCauses.MINIMIZE_FOURTH_DIMENSION}
values = {0: rdkit.Chem.rdDistGeom.EmbedFailureCauses.INITIAL_COORDS, 1: rdkit.Chem.rdDistGeom.EmbedFailureCauses.FIRST_MINIMIZATION, 2: rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_TETRAHEDRAL_CENTERS, 3: rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS, 4: rdkit.Chem.rdDistGeom.EmbedFailureCauses.MINIMIZE_FOURTH_DIMENSION, 5: rdkit.Chem.rdDistGeom.EmbedFailureCauses.ETK_MINIMIZATION, 6: rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CHIRAL_BOUNDS, 7: rdkit.Chem.rdDistGeom.EmbedFailureCauses.FINAL_CENTER_IN_VOLUME, 8: rdkit.Chem.rdDistGeom.EmbedFailureCauses.LINEAR_DOUBLE_BOND, 9: rdkit.Chem.rdDistGeom.EmbedFailureCauses.BAD_DOUBLE_BOND_STEREO, 10: rdkit.Chem.rdDistGeom.EmbedFailureCauses.CHECK_CHIRAL_CENTERS2}
rdkit.Chem.rdDistGeom.EmbedMolecule((Mol)mol[, (int)maxAttempts=0[, (int)randomSeed=-1[, (bool)clearConfs=True[, (bool)useRandomCoords=False[, (float)boxSizeMult=2.0[, (bool)randNegEig=True[, (int)numZeroFail=1[, (dict)coordMap={}[, (float)forceTol=0.001[, (bool)ignoreSmoothingFailures=False[, (bool)enforceChirality=True[, (bool)useExpTorsionAnglePrefs=True[, (bool)useBasicKnowledge=True[, (bool)printExpTorsionAngles=False[, (bool)useSmallRingTorsions=False[, (bool)useMacrocycleTorsions=True[, (int)ETversion=2[, (bool)useMacrocycle14config=True]]]]]]]]]]]]]]]]]]) → int :
Use distance geometry to obtain initial

coordinates for a molecule

ARGUMENTS:

  • mol : the molecule of interest

  • maxAttempts : the maximum number of attempts to try embedding

  • randomSeedprovide a seed for the random number generator

    so that the same coordinates can be obtained for a molecule on multiple runs. If -1, the RNG will not be seeded.

  • clearConfs : clear all existing conformations on the molecule

  • useRandomCoordsStart the embedding from random coordinates instead of

    using eigenvalues of the distance matrix.

  • boxSizeMultDetermines the size of the box that is used for

    random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times boxSizeMult. If this is a negative number, the side length will equal -boxSizeMult (i.e. independent of the elements of the distance matrix).

  • randNegEigIf the embedding yields a negative eigenvalue,

    pick coordinates that correspond to this component at random

  • numZeroFail : fail embedding if we have at least this many zero eigenvalues

  • coordMapa dictionary mapping atom IDs->coordinates. Use this to

    require some atoms to have fixed coordinates in the resulting conformation.

  • forceToltolerance to be used during the force-field minimization with

    the distance geometry force field.

  • ignoreSmoothingFailurestry to embed the molecule even if triangle smoothing

    of the bounds matrix fails.

  • enforceChirality : enforce the correct chirality if chiral centers are present.

  • useExpTorsionAnglePrefs : impose experimental torsion angle preferences

  • useBasicKnowledge : impose basic knowledge such as flat rings

  • printExpTorsionAngles : print the output from the experimental torsion angles

  • useMacrocycleTorsions : use additional torsion profiles for macrocycles

  • ETversionversion of the standard torsion definitions to use. NOTE for both

    ETKDGv2 and ETKDGv3 this should be 2 since ETKDGv3 uses the ETKDGv2 definitions for standard torsions

  • useMacrocycle14config : use the 1-4 distance bounds from ETKDGv3

RETURNS:

ID of the new conformation added to the molecule

C++ signature :

int EmbedMolecule(RDKit::ROMol {lvalue} [,unsigned int=0 [,int=-1 [,bool=True [,bool=False [,double=2.0 [,bool=True [,unsigned int=1 [,boost::python::dict {lvalue}={} [,double=0.001 [,bool=False [,bool=True [,bool=True [,bool=True [,bool=False [,bool=False [,bool=True [,unsigned int=2 [,bool=True]]]]]]]]]]]]]]]]]])

EmbedMolecule( (Mol)mol, (EmbedParameters)params) -> int :
Use distance geometry to obtain intial

coordinates for a molecule

ARGUMENTS:

  • mol : the molecule of interest

  • params : an EmbedParameters object

RETURNS:

ID of the new conformation added to the molecule

C++ signature :

int EmbedMolecule(RDKit::ROMol {lvalue},RDKit::DGeomHelpers::EmbedParameters {lvalue})

rdkit.Chem.rdDistGeom.EmbedMultipleConfs((Mol)mol[, (int)numConfs=10[, (int)maxAttempts=0[, (int)randomSeed=-1[, (bool)clearConfs=True[, (bool)useRandomCoords=False[, (float)boxSizeMult=2.0[, (bool)randNegEig=True[, (int)numZeroFail=1[, (float)pruneRmsThresh=-1.0[, (dict)coordMap={}[, (float)forceTol=0.001[, (bool)ignoreSmoothingFailures=False[, (bool)enforceChirality=True[, (int)numThreads=1[, (bool)useExpTorsionAnglePrefs=True[, (bool)useBasicKnowledge=True[, (bool)printExpTorsionAngles=False[, (bool)useSmallRingTorsions=False[, (bool)useMacrocycleTorsions=True[, (int)ETversion=2[, (bool)useMacrocycle14config=True]]]]]]]]]]]]]]]]]]]]]) → _vecti :
Use distance geometry to obtain multiple sets of

coordinates for a molecule

ARGUMENTS:

  • mol : the molecule of interest

  • numConfs : the number of conformers to generate

  • maxAttempts : the maximum number of attempts to try embedding

  • randomSeedprovide a seed for the random number generator

    so that the same coordinates can be obtained for a molecule on multiple runs. If -1, the RNG will not be seeded.

  • clearConfs : clear all existing conformations on the molecule

  • useRandomCoordsStart the embedding from random coordinates instead of

    using eigenvalues of the distance matrix.

  • boxSizeMult Determines the size of the box that is used for

    random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times boxSizeMult. If this is a negative number, the side length will equal -boxSizeMult (i.e. independent of the elements of the distance matrix).

  • randNegEigIf the embedding yields a negative eigenvalue,

    pick coordinates that correspond to this component at random

  • numZeroFail : fail embedding if we have at least this many zero eigenvalues

  • pruneRmsThreshRetain only the conformations out of ‘numConfs’

    after embedding that are at least this far apart from each other. RMSD is computed on the heavy atoms. Pruning is greedy; i.e. the first embedded conformation is retained and from then on only those that are at least pruneRmsThresh away from all retained conformations are kept. The pruning is done after embedding and bounds violation minimization. No pruning by default.

  • coordMapa dictionary mapping atom IDs->coordinates. Use this to

    require some atoms to have fixed coordinates in the resulting conformation.

  • forceToltolerance to be used during the force-field minimization with

    the distance geometry force field.

  • ignoreSmoothingFailurestry to embed the molecule even if triangle smoothing

    of the bounds matrix fails.

  • enforceChirality : enforce the correct chirality if chiral centers are present.

  • numThreadsnumber of threads to use while embedding. This only has an effect if the RDKit

    was built with multi-thread support.

    If set to zero, the max supported by the system will be used.

  • useExpTorsionAnglePrefs : impose experimental torsion angle preferences

  • useBasicKnowledge : impose basic knowledge such as flat rings

  • printExpTorsionAngles : print the output from the experimental torsion angles

RETURNS:

List of new conformation IDs

C++ signature :

std::vector<int, std::allocator<int> > EmbedMultipleConfs(RDKit::ROMol {lvalue} [,unsigned int=10 [,unsigned int=0 [,int=-1 [,bool=True [,bool=False [,double=2.0 [,bool=True [,unsigned int=1 [,double=-1.0 [,boost::python::dict {lvalue}={} [,double=0.001 [,bool=False [,bool=True [,int=1 [,bool=True [,bool=True [,bool=False [,bool=False [,bool=True [,unsigned int=2 [,bool=True]]]]]]]]]]]]]]]]]]]]])

EmbedMultipleConfs( (Mol)mol, (int)numConfs, (EmbedParameters)params) -> _vecti :
Use distance geometry to obtain multiple sets of

coordinates for a molecule

ARGUMENTS:

  • mol : the molecule of interest

  • numConfs : the number of conformers to generate

  • params : an EmbedParameters object

RETURNS:

List of new conformation IDs

C++ signature :

std::vector<int, std::allocator<int> > EmbedMultipleConfs(RDKit::ROMol {lvalue},unsigned int,RDKit::DGeomHelpers::EmbedParameters {lvalue})

class rdkit.Chem.rdDistGeom.EmbedParameters((object)arg1)

Bases: instance

Parameters controlling embedding

C++ signature :

void __init__(_object*)

property ETversion

version of the experimental torsion-angle preferences

GetFailureCounts((EmbedParameters)self) → tuple :

returns the counts of each failure type

C++ signature :

boost::python::tuple GetFailureCounts((anonymous namespace)::PyEmbedParameters {lvalue})

SetBoundsMat((EmbedParameters)self, (AtomPairsParameters)boundsMatArg) → None :

set the distance-bounds matrix to be used (no triangle smoothing will be done on this) from a Numpy array

C++ signature :

void SetBoundsMat((anonymous namespace)::PyEmbedParameters {lvalue},boost::python::api::object)

SetCPCI((EmbedParameters)self, (dict)CPCIdict) → None :

set the customised pairwise Columb-like interaction to atom pairs.used during structural minimisation stage

C++ signature :

void SetCPCI((anonymous namespace)::PyEmbedParameters {lvalue},boost::python::dict)

SetCoordMap((EmbedParameters)arg1, (dict)self) → None :

sets the coordmap to be used

C++ signature :

void SetCoordMap((anonymous namespace)::PyEmbedParameters {lvalue},boost::python::dict)

property boundsMatForceScaling

scale the weights of the atom pair distance restraints relative to the other types of restraints

property boxSizeMult

determines the size of the box used for random coordinates

property clearConfs

clear all existing conformations on the molecule

property embedFragmentsSeparately

split the molecule into fragments and embed them separately

property enableSequentialRandomSeeds

handle random number seeds so that conformer generation can be restarted

property enforceChirality

enforce correct chirilaty if chiral centers are present

property forceTransAmides

constrain amide bonds to be trans

property ignoreSmoothingFailures

try and embed the molecule if if triangle smoothing of the bounds matrix fails

property maxIterations

maximum number of embedding attempts to use for a single conformation

property numThreads

number of threads to use when embedding multiple conformations

property numZeroFail

fail embedding if we have at least this many zero eigenvalues

property onlyHeavyAtomsForRMS

Only consider heavy atoms when doing RMS filtering

property optimizerForceTol

the tolerance to be used during the distance-geometry force field minimization

property pruneRmsThresh

used to filter multiple conformations: keep only conformations that are at least this far apart from each other

property randNegEig

if the embedding yields a negative eigenvalue, pick coordinates that correspond to this component at random

property randomSeed

seed for the random number generator

property symmetrizeConjugatedTerminalGroupsForPruning

symmetrize terminal conjugated groups for RMSD pruning

property trackFailures

keep track of which checks during the embedding process fail

property useBasicKnowledge

impose basic-knowledge constraints such as flat rings

property useExpTorsionAnglePrefs

impose experimental torsion angle preferences

property useMacrocycle14config

use the 1-4 distance bounds from ETKDGv3

property useMacrocycleTorsions

impose macrocycle torsion angle preferences

property useRandomCoords

start the embedding from random coordinates instead of using eigenvalues of the distance matrix

property useSmallRingTorsions

impose small ring torsion angle preferences

property useSymmetryForPruning

use molecule symmetry when doing the RMSD pruning. Note that this option automatically also sets onlyHeavyAtomsForRMS to true.

property verbose

be verbose about configuration

rdkit.Chem.rdDistGeom.GetExperimentalTorsions((Mol)mol[, (bool)useExpTorsionAnglePrefs=True[, (bool)useSmallRingTorsions=False[, (bool)useMacrocycleTorsions=True[, (bool)useBasicKnowledge=True[, (int)ETversion=2[, (bool)printExpTorsionAngles=False]]]]]]) → tuple :

returns information about the bonds corresponding to experimental torsions

C++ signature :

boost::python::tuple GetExperimentalTorsions(RDKit::ROMol [,bool=True [,bool=False [,bool=True [,bool=True [,unsigned int=2 [,bool=False]]]]]])

GetExperimentalTorsions( (Mol)mol, (EmbedParameters)embedParams) -> tuple :

returns information about the bonds corresponding to experimental torsions

C++ signature :

boost::python::tuple GetExperimentalTorsions(RDKit::ROMol,RDKit::DGeomHelpers::EmbedParameters)

rdkit.Chem.rdDistGeom.GetMoleculeBoundsMatrix((Mol)mol[, (bool)set15bounds=True[, (bool)scaleVDW=False[, (bool)doTriangleSmoothing=True[, (bool)useMacrocycle14config=False]]]]) → object :

Returns the distance bounds matrix for a molecule

ARGUMENTS:

  • mol : the molecule of interest

  • set15boundsset bounds for 1-5 atom distances based on

    topology (otherwise stop at 1-4s)

  • scaleVDWscale down the sum of VDW radii when setting the

    lower bounds for atoms less than 5 bonds apart

  • doTriangleSmoothingrun triangle smoothing on the bounds

    matrix before returning it

RETURNS:

the bounds matrix as a Numeric array with lower bounds in the lower triangle and upper bounds in the upper triangle

C++ signature :

_object* GetMoleculeBoundsMatrix(RDKit::ROMol {lvalue} [,bool=True [,bool=False [,bool=True [,bool=False]]]])

rdkit.Chem.rdDistGeom.KDG() → EmbedParameters :

Returns an EmbedParameters object for the KDG method.

C++ signature :

(anonymous namespace)::PyEmbedParameters* KDG()

rdkit.Chem.rdDistGeom.srETKDGv3() → EmbedParameters :

Returns an EmbedParameters object for the ETKDG method - version 3 (small rings).

C++ signature :

(anonymous namespace)::PyEmbedParameters* srETKDGv3()