rdkit.Chem.rdShapeAlign module

rdkit.Chem.rdShapeAlign.AlignMol((rdkit.Chem.rdchem.Mol)ref, (rdkit.Chem.rdchem.Mol)probe[, (int)refConfId=-1[, (int)probeConfId=-1[, (bool)useColors=True[, (float)opt_param=1.0[, (int)max_preiters=10[, (int)max_postiters=30]]]]]]) → tuple :

Aligns a probe molecule to a reference molecule. The probe is modified.

refRDKit.ROMol

Reference molecule

probeRDKit.ROMol

Probe molecule

refConfIdint, optional

Reference conformer ID (default is -1)

probeConfIdint, optional

Probe conformer ID (default is -1)

useColorsbool, optional

Whether or not to use colors in the scoring (default is True)

opt_paramfloat, optional

Balance of shape and color for optimization. 0 is only color, 0.5 is equal weight, and 1.0 is only shape. Default is 1.0.

max_preitersint, optional

In the two phase optimization, the maximum iterations done on all poses.

max_postitersint, optional

In the two phase optimization, the maximum iterations during the second phase on only the best poses from the first phase

2-tuple of doubles

The results are (shape_score, color_score) The color_score is zero if opt_param is 1.0.

C++ signature :

boost::python::tuple AlignMol(RDKit::ROMol,RDKit::ROMol {lvalue} [,int=-1 [,int=-1 [,bool=True [,double=1.0 [,unsigned int=10 [,unsigned int=30]]]]]])

AlignMol( (rdkit.Chem.rdchem.Mol)ref, (rdkit.Chem.rdchem.Mol)probe, (ShapeInputOptions)refShapeOpts, (ShapeInputOptions)probeShapeOpts [, (int)refConfId=-1 [, (int)probeConfId=-1 [, (float)opt_param=1.0 [, (int)max_preiters=10 [, (int)max_postiters=30]]]]]) -> tuple :

Aligns a probe molecule to a reference molecule. The probe is modified.

refRDKit.ROMol

Reference molecule

probeRDKit.ROMol

Probe molecule

refShapeOptsShapeInputOptions

Options for constructing the shape for the reference molecule

probeShapeOptsShapeInputOptions

Options for constructing the shape for the probe molecule

refConfIdint, optional

Reference conformer ID (default is -1)

probeConfIdint, optional

Probe conformer ID (default is -1)

opt_paramfloat, optional

Balance of shape and color for optimization. 0 is only color, 0.5 is equal weight, and 1.0 is only shape. Default is 1.0.

max_preitersint, optional

In the two phase optimization, the maximum iterations done on all poses.

max_postitersint, optional

In the two phase optimization, the maximum iterations during the second phase on only the best poses from the first phase

2-tuple of doubles

The results are (shape_score, color_score) The color_score is zero if opt_param is 1.0.

C++ signature :

boost::python::tuple AlignMol(RDKit::ROMol,RDKit::ROMol {lvalue},ShapeInputOptions,ShapeInputOptions [,int=-1 [,int=-1 [,double=1.0 [,unsigned int=10 [,unsigned int=30]]]]])

AlignMol( (ShapeInput)refShape, (rdkit.Chem.rdchem.Mol)probe [, (int)probeConfId=-1 [, (bool)useColors=True [, (float)opt_param=1.0 [, (int)max_preiters=10 [, (int)max_postiters=30 [, (bool)applyRefShift=False]]]]]]) -> tuple :

Aligns a probe molecule to a reference shape. The probe is modified. Assumes the shapes are both centred on the origin.

refShapeShapeInput

Reference shape

probeRDKit.ROMol

Probe molecule

probeConfIdint, optional

Probe conformer ID (default is -1)

useColorsbool, optional

Whether or not to use colors in the scoring (default is True)

opt_paramfloat, optional

Balance of shape and color for optimization. 0 is only color, 0.5 is equal weight, and 1.0 is only shape. Default is 1.0.

max_preitersint, optional

In the two phase optimization, the maximum iterations done on all poses.

max_postitersint, optional

In the two phase optimization, the maximum iterations during the second phase on only the best poses from the first phase

applyRefShiftbool, optional

If True, apply the reference shape’s shift translation to the final coordinates.

2-tuple of doubles

The results are (shape_score, color_score) The color_score is zero if opt_param is 1.0.

C++ signature :

boost::python::tuple AlignMol(ShapeInput,RDKit::ROMol {lvalue} [,int=-1 [,bool=True [,double=1.0 [,unsigned int=10 [,unsigned int=30 [,bool=False]]]]]])

rdkit.Chem.rdShapeAlign.AlignShapes((ShapeInput)refShape, (ShapeInput)probeShape[, (float)opt_param=1.0[, (int)max_preiters=10[, (int)max_postiters=30]]]) → tuple :

Aligns a probe shape to a reference shape. The probe is modified.

Parameters:

• refShape (ShapeInput) – Reference shape

• probeShape (ShapeInput) – Probe shape

• opt_param (float, optional) – Balance of shape and color for optimization. 0 is only color, 0.5 is equal weight, and 1.0 is only shape

• max_preiters (int, optional) – In the two phase optimization, the maximum iterations done on all poses.

• max_postiters (int, optional) – In the two phase optimization, the maximum iterations during the second phase on only the best poses from the first phase

Returns:

The results are (shape_score, color_score, matrix) The matrix is a 12-float list giving the transformation matrix that overlays the probe onto the reference.

Return type:

3-tuple of double, double, list of doubles

C++ signature :

boost::python::tuple AlignShapes(ShapeInput,ShapeInput {lvalue} [,double=1.0 [,unsigned int=10 [,unsigned int=30]]])

class rdkit.Chem.rdShapeAlign.FloatVector((object)arg1) → None :

Bases: instance

C++ signature :

void __init__(_object*)

append((FloatVector)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :

C++ signature :

void append(std::vector<float, std::allocator<float> > {lvalue},boost::python::api::object)

extend((FloatVector)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :

C++ signature :

void extend(std::vector<float, std::allocator<float> > {lvalue},boost::python::api::object)

rdkit.Chem.rdShapeAlign.PrepareConformer((rdkit.Chem.rdchem.Mol)mol[, (int)confId=-1[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)opts=None]]) → ShapeInput :

Generates a ShapeInput object for a molecule

Parameters:

• mol (RDKit.ROMol) – Reference molecule

• confId (int, optional) – Conformer ID to use (default is -1)

• opts (ShapeInputOptions, optional) – Options for Shapeinput

Return type:

a ShapeInput for the molecule

C++ signature :

ShapeInput* PrepareConformer(RDKit::ROMol [,int=-1 [,boost::python::api::object=None]])

rdkit.Chem.rdShapeAlign.ScoreMol((rdkit.Chem.rdchem.Mol)mol1, (rdkit.Chem.rdchem.Mol)mol2, (ShapeInputOptions)mol1ShapeOpts, (ShapeInputOptions)mol2ShapeOpts[, (int)mol1ConfId=-1[, (int)mol2ConfId=-1]]) → tuple :

Calculate the scores between a shape and a molecule without moving them.

mol1RDKit.ROMol

First molecule

mol2RDKit.ROMol

Second molecule

mol1ShapeOptions:

Options for constructing the shape for molecule 1

mol2ShapeOptions:

Options for constructing the shape for molecule 2

mol1ConfIdint, optional

First molecule conformer ID (default is -1)

mol2ConfIdint, optional

Second conformer ID (default is -1)

2-tuple of doubles

The results are (shape_score, color_score) The color_score is zero if useColors is False for either of the

shape options

C++ signature :

boost::python::tuple ScoreMol(RDKit::ROMol,RDKit::ROMol {lvalue},ShapeInputOptions,ShapeInputOptions [,int=-1 [,int=-1]])

ScoreMol( (ShapeInput)shape, (rdkit.Chem.rdchem.Mol)mol, (ShapeInputOptions)molShapeOpts [, (int)molConfId=-1]) -> tuple :

Calculate the scores between 2 molecules without moving them.

shapeShapeInput

Shape

molRDKit.ROMol

Molecule

molShapeOptions:

Options for constructing the shape for molecule

molConfIdint, optional

Molecule conformer ID (default is -1)

2-tuple of doubles

The results are (shape_score, color_score) The color_score is zero if shape.useColors is False

C++ signature :

boost::python::tuple ScoreMol(ShapeInput,RDKit::ROMol {lvalue},ShapeInputOptions [,int=-1])

rdkit.Chem.rdShapeAlign.ScoreShape((ShapeInput)shape1, (ShapeInput)shape2[, (bool)useColors=False]) → tuple :

Calculate the scores between 2 shapes without moving them.

Parameters:

• shape1 (ShapeInput) – Shape

• shape2 (ShapeInput) – Shape

• useColors (bool) – Whether to use colors for the score or not.

Returns:

The results are (shape_score, color_score) The color_score is zero if useColors is False

Return type:

2-tuple of doubles

C++ signature :

boost::python::tuple ScoreShape(ShapeInput,ShapeInput {lvalue} [,bool=False])

class rdkit.Chem.rdShapeAlign.ShapeInput

Bases: instance

Raises an exception This class cannot be instantiated from Python

property alpha_vector

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> rdkit.rdBase._vectd:

C++ signature :

std::vector<double, std::allocator<double> > {lvalue} None(ShapeInput {lvalue})

property atom_type_vector

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> rdkit.rdBase._vectj:

C++ signature :

std::vector<unsigned int, std::allocator<unsigned int> > {lvalue} None(ShapeInput {lvalue})

property coord

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> rdkit.Chem.rdShapeAlign.FloatVector:

C++ signature :

std::vector<float, std::allocator<float> > {lvalue} None(ShapeInput {lvalue})

property inertialRot

Rotation applied to put the shape into its principal axes frame of reference.

property shift

Translation of centre of shape coordinates to origin.

property sof

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> float:

C++ signature :

double {lvalue} None(ShapeInput {lvalue})

property sov

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> float:

C++ signature :

double {lvalue} None(ShapeInput {lvalue})

property volumeAtomIndexVector

None( (rdkit.Chem.rdShapeAlign.ShapeInput)arg1) -> rdkit.rdBase._vectj:

C++ signature :

std::vector<unsigned int, std::allocator<unsigned int> > {lvalue} None(ShapeInput {lvalue})

class rdkit.Chem.rdShapeAlign.ShapeInputOptions((object)arg1) → None :

Bases: instance

Shape Input Options

C++ signature :

void __init__(_object*)

property atomRadii

Non-standard radii to use for the atoms specified by their indices in the molecule. A list of tuples of [int, float].

property atomSubset

If not empty, use just these atoms in the molecule to form the ShapeInput object.

property customFeatures

Custom features for the shape.

property dummyRadius

If using dummy atoms in the alignment, what radius to use for them. Default=2.16 (the radius of Xe).

property includeDummies

Whether to use dummy atoms in the alignment. Default=False.

property normalize

Whether to normalise the shape by putting intoits inertial frame. Default=True.

property notColorAtoms

Any atoms mentioned here by index should not be used in a color feature.

property useColors

Whether to use colors (pharmacophore features) in the score. Default=True.

rdkit.Chem.rdShapeAlign.TransformConformer((list)arg1, (list)finalTrans, (list)matrix, (ShapeInput)probeShape, (rdkit.Chem.rdchem.Conformer)probeConformer) → None :

Assuming that probeShape has been overlaid onto refShape to give the supplied transformation matrix, applies that transformation to the

given conformer.

Parameters:

• finalTrans (list[float * 3]) – The final translation to apply to conformer.

• matrix (list[float * 12]) – The transformation matrix

• probeShape (ShapeInput) – Probe shape

• probeConformer (Conformer) – Probe conformer

C++ signature :

void TransformConformer(boost::python::list,boost::python::list,boost::python::list,ShapeInput,RDKit::Conformer {lvalue})