rdkit.Chem.rdShapeAlign module

rdkit.Chem.rdShapeAlign.AlignMol((Mol)ref, (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_param : float, optional max_preiters : int, optional max_postiters : int, optional

2-tuple of doubles

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

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( (ShapeInput)refShape, (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)

optParam : float, optional max_preiters : int, optional max_postiters : int, optional applyRefShift : bool, 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 useColors is False

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) –

  • max_preiters (int, optional) –

  • max_postiters (int, optional) –

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)

Bases: instance

C++ signature :

void __init__(_object*)

append((FloatVector)arg1, (AtomPairsParameters)arg2) → None :
C++ signature :

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

extend((FloatVector)arg1, (AtomPairsParameters)arg2) → None :
C++ signature :

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

rdkit.Chem.rdShapeAlign.PrepareConformer((Mol)mol[, (int)confId=-1[, (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)

  • useColors (bool, optional) – Whether or not to assign chemical features (colors) (default is True)

Return type:

a ShapeInput for the molecule

C++ signature :

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

class rdkit.Chem.rdShapeAlign.ShapeInput

Bases: instance

Raises an exception This class cannot be instantiated from Python

property alpha_vector
property atom_type_vector
property coord
property shift

Translation of centre of shape coordinates to origin.

property sof
property sov
property volumeAtomIndexVector
class rdkit.Chem.rdShapeAlign.ShapeInputOptions((object)arg1)

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 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 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)finalTrans, (list)matrix, (ShapeInput)probeShape, (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:

  • refShape (ShapeInput) – Reference shape

  • 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,ShapeInput,RDKit::Conformer {lvalue})