RDKit
Open-source cheminformatics and machine learning.
ShapeEncoder.h
Go to the documentation of this file.
1 //
2 // Copyright (C) 2005-2006 Rational Discovery LLC
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #include <RDGeneral/export.h>
11 #ifndef _RD_SHAPE_ENCODER_H_20050125_0800_
12 #define _RD_SHAPE_ENCODER_H_20050125_0800_
13 
14 namespace RDGeom {
15 class UniformGrid3D;
16 class Transform3D;
17 } // namespace RDGeom
18 
19 namespace RDKit {
20 class ROMol;
21 class Conformer;
22 namespace MolShapes {
23 //! Encode the shape of a molecule on to a grid
24 /*!
25  \param mol The molecule of interest
26  \param grid Grid onto which the molecule is encoded
27  \param confId Id of the conformation on the molecule to be encoded
28  \param trans Optional 3D transform to be applied to this conformation
29  \param vdwScale Scaling factor for the radius of the atoms to determine the
30  base radius
31  used in the encoding - grid points inside this sphere carry
32  the maximum occupany
33  \param stepSize thickness of the layers outside the base radius, the
34  occupancy value is decreased
35  from layer to layer from the maximum value
36  \param maxLayers the maximum number of layers - defaults to the number allowed
37  the number of bits
38  use per grid point - e.g. two bits per grid point will allow
39  3 layers
40  \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
41  process
42 */
44  const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId = -1,
45  const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
46  double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true);
47 
48 //! Emcode the shape of a conformer on to a grid
49 /*!
50  \param conf The conformer of interest
51  \param grid Grid onto which the molecule is encoded
52  \param trans Optional 3D transform to be applied to this conformation
53  \param vdwScale Scaling factor for the radius of the atoms to determine the
54  base radius
55  used in the encoding - grid points inside this sphere carry
56  the maximum occupany
57  \param stepSize thickness of the layers outside the base radius, the
58  occupancy value is decreased
59  from layer to layer from the maximum value
60  \param maxLayers the maximum number of layers - defaults to the number allowed
61  the number of bits
62  use per grid point - e.g. two bits per grid point will allow
63  3 layers
64  \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
65  process
66 */
68  const Conformer &conf, RDGeom::UniformGrid3D &grid,
69  const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
70  double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true);
71 } // namespace MolShapes
72 } // namespace RDKit
73 #endif
RDGeom
Definition: TorsionAngleM6.h:20
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:43
RDKit::MolShapes::EncodeShape
RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId=-1, const RDGeom::Transform3D *trans=0, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
Encode the shape of a molecule on to a grid.
RDKit
Std stuff.
Definition: Atom.h:30
RDGeom::Transform3D
Definition: Transform3D.h:22
RDKIT_SHAPEHELPERS_EXPORT
#define RDKIT_SHAPEHELPERS_EXPORT
Definition: export.h:606
RDGeom::UniformGrid3D
Definition: UniformGrid3D.h:20
export.h