rdkit.Geometry.rdGeometry module

Module containing geometry objects like points, grids, etc.

class rdkit.Geometry.rdGeometry.Point2D(self)
class rdkit.Geometry.rdGeometry.Point2D(self, x: float, y: float)
class rdkit.Geometry.rdGeometry.Point2D(self, arg: rdkit.Geometry.rdGeometry.Point3D, /)

Bases: object

AngleTo(self, arg: rdkit.Geometry.rdGeometry.Point2D, /) → float

determines the angle between a vector to this point (between 0 and PI)

DirectionVector(self, arg: rdkit.Geometry.rdGeometry.Point2D, /) → rdkit.Geometry.rdGeometry.Point2D

return a normalized direction vector from this point to another

DotProduct(self, arg: rdkit.Geometry.rdGeometry.Point2D, /) → float

Dot product with another point

Length(self) → float

Length of the vector

LengthSq(self) → float

Square of the length

Normalize(self) → None

Normalize the vector (using L2 norm)

SignedAngleTo(self, arg: rdkit.Geometry.rdGeometry.Point2D, /) → float

determines the signed angle between a vector to this point (between 0 and 2*PI)

property x

(self) -> float

property y

(self) -> float

class rdkit.Geometry.rdGeometry.Point3D(self)
class rdkit.Geometry.rdGeometry.Point3D(self, x: float, y: float, z: float)
class rdkit.Geometry.rdGeometry.Point3D(self, arg: rdkit.Geometry.rdGeometry.Point3D)

Bases: object

AngleTo(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → float

determines the angle between a vector to this point (between 0 and PI)

CrossProduct(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → rdkit.Geometry.rdGeometry.Point3D

Get the cross product between two points

DirectionVector(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → rdkit.Geometry.rdGeometry.Point3D

return a normalized direction vector from this point to another

Distance(self, pt2: rdkit.Geometry.rdGeometry.Point3D) → float

Distance from this point to another point

DotProduct(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → float

Dot product with another point

Length(self) → float

Length of the vector

LengthSq(self) → float

Square of the length

Normalize(self) → None

Normalize the vector (using L2 norm)

SignedAngleTo(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → float

determines the signed angle between a vector to this point (between 0 and 2*PI)

property x

(self) -> float

property y

(self) -> float

property z

(self) -> float

class rdkit.Geometry.rdGeometry.PointND(self, dim: int)

Bases: object

AngleTo(self, arg: rdkit.Geometry.rdGeometry.PointND, /) → float

determines the angle between a vector to this point (between 0 and PI)

DirectionVector(self, arg: rdkit.Geometry.rdGeometry.PointND, /) → rdkit.Geometry.rdGeometry.PointND

return a normalized direction vector from this point to another

DotProduct(self, arg: rdkit.Geometry.rdGeometry.PointND, /) → float

Dot product with another point

Length(self) → float

Length of the vector

LengthSq(self) → float

Square of the length

Normalize(self) → None

Normalize the vector (using L2 norm)

class rdkit.Geometry.rdGeometry.UniformGrid3D(self, dimX: float, dimY: float, dimZ: float, spacing: float = 0.5, valType: rdkit.DataStructs.cDataStructs.DiscreteValueType = DiscreteValueType.TWOBITVALUE, offSet: rdkit.Geometry.rdGeometry.Point3D | None = None)
class rdkit.Geometry.rdGeometry.UniformGrid3D(self, pkl: str)
class rdkit.Geometry.rdGeometry.UniformGrid3D(self, arg: bytes, /)

Bases: object

Class to represent a uniform three-dimensional cubic grid. Each grid point can store a positive integer value. For the sake of efficiency these value can either be binary or fit in 2, 4, 8 or 16 bits

Overloaded function.

  1. __init__(self, dimX: float, dimY: float, dimZ: float, spacing: float = 0.5, valType: rdkit.DataStructs.cDataStructs.DiscreteValueType = DiscreteValueType.TWOBITVALUE, offSet: rdkit.Geometry.rdGeometry.Point3D | None = None) -> None

Constructor for a UniformGrid3D object

  1. __init__(self, pkl: str) -> None

pickle constructor

  1. __init__(self, arg: bytes, /) -> None

CompareParams(self, other: rdkit.Geometry.rdGeometry.UniformGrid3D) → bool

Compare the parameters between two grid object

GetGridIndex(self, xi: int, yi: int, zi: int) → int

Get the index to the grid point with the three integer indices provided

GetGridIndices(self, idx: int) → tuple[int, int, int]

Returns the integer indices of the grid index provided.

GetGridPointIndex(self, point: rdkit.Geometry.rdGeometry.Point3D) → int

Get the index to the grid point closest to the specified point

GetGridPointLoc(self, pointId: int) → rdkit.Geometry.rdGeometry.Point3D

Get the location of the specified grid point

GetNumX(self) → int

Get the number of grid points along x-axis

GetNumY(self) → int

Get the number of grid points along y-axis

GetNumZ(self) → int

Get the number of grid points along z-axis

GetOccupancyVect(self) → rdkit.DataStructs.cDataStructs.DiscreteValueVect

Get the occupancy vector for the grid

GetOffset(self) → rdkit.Geometry.rdGeometry.Point3D

Get the location of the center of the grid

GetSize(self) → int

Get the size of the grid (number of grid points)

GetSpacing(self) → float

Get the grid spacing

GetVal(self, id: int) → int

Get the value at the specified grid index

GetValPoint(self, pt: rdkit.Geometry.rdGeometry.Point3D) → int

Get the value at the closest grid point

SetSphereOccupancy(self, center: rdkit.Geometry.rdGeometry.Point3D, radius: float, stepSize: float, maxLayers: int = -1, ignoreOutOfBound: bool = True) → None
Set the occupancy on the grid for a sphere or specified radius

and multiple layers around this sphere, with decreasing values of

occupancy

SetVal(self, id: int, val: int) → None

Set the value at the specified grid index

SetValPoint(self, pt: rdkit.Geometry.rdGeometry.Point3D, val: int) → None

Set the value at grid point closest to the specified point

class rdkit.Geometry.rdGeometry.UniformRealValueGrid3D(self)
class rdkit.Geometry.rdGeometry.UniformRealValueGrid3D(self, arg: rdkit.Geometry.rdGeometry.UniformRealValueGrid3D)
class rdkit.Geometry.rdGeometry.UniformRealValueGrid3D(self, dimX: float, dimY: float, dimZ: float, spacing: float = 0.5, offSet: rdkit.Geometry.rdGeometry.Point3D | None = None)
class rdkit.Geometry.rdGeometry.UniformRealValueGrid3D(self, arg: bytes, /)

Bases: object

Class to represent a uniform three-dimensional cubic grid. Each grid point can store a floating point value.

Overloaded function.

  1. __init__(self) -> None

Default constructor

  1. __init__(self, arg: rdkit.Geometry.rdGeometry.UniformRealValueGrid3D) -> None

Copy constructor

  1. __init__(self, dimX: float, dimY: float, dimZ: float, spacing: float = 0.5, offSet: rdkit.Geometry.rdGeometry.Point3D | None = None) -> None

Constructor

  1. __init__(self, arg: bytes, /) -> None

CompareGrids(self, arg: rdkit.Geometry.rdGeometry.UniformRealValueGrid3D, /) → bool

Compare the parameters and values between two grid objects.

CompareParams(self, arg: rdkit.Geometry.rdGeometry.UniformRealValueGrid3D, /) → bool

Compare the parameters between two grid object.

CompareVectors(self, arg: rdkit.Geometry.rdGeometry.UniformRealValueGrid3D, /) → bool

Compare the vector values between two grid objects.

GetGridIndex(self, arg0: int, arg1: int, arg2: int, /) → int

Get the index to the grid point with the three integer indices provided

GetGridIndices(self, idx: int) → tuple[int, int, int]

Returns the integer indices of the grid index provided.

GetGridPointIndex(self, arg: rdkit.Geometry.rdGeometry.Point3D, /) → int

Get the index to the grid point closest to the specified point

GetGridPointLoc(self, pointId: int) → rdkit.Geometry.rdGeometry.Point3D

Get the location of the specified grid point

GetNumX(self) → int

Get the number of grid points along x-axis

GetNumY(self) → int

Get the number of grid points along y-axis

GetNumZ(self) → int

Get the number of grid points along z-axis

GetOccupancyVect(self) → rdkit.DataStructs.cDataStructs.RealValueVect

Get the occupancy vector for the grid

GetOffset(self) → rdkit.Geometry.rdGeometry.Point3D

Get the location of the center of the grid

GetSize(self) → int

Get the size of the grid (number of grid points)

GetSpacing(self) → float

Get the grid spacing

GetVal(self, id: int) → float

Get the value at the specified grid index

GetValPoint(self, pt: rdkit.Geometry.rdGeometry.Point3D) → float

Get the value at the closest grid point

SetVal(self, id: int, val: float) → None

Set the value at the specified grid index

SetValPoint(self, pt: rdkit.Geometry.rdGeometry.Point3D, val: float) → None

Set the value at grid point closest to the specified point