RDKit: ShapeEncoder.h Source File

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ShapeEncoder.h
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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 #ifndef _RD_SHAPE_ENCODER_H_20050125_0800_
11 #define _RD_SHAPE_ENCODER_H_20050125_0800_
12
13 namespace RDGeom {
14 class UniformGrid3D;
15 class Transform3D;
16 }
17
18 namespace RDKit {
19 class ROMol;
20 class Conformer;
21 namespace MolShapes {
22 //! Encode the shape of a molecule on to a grid
23 /*!
24 \param mol The molecule of interest
25 \param grid Grid onto which the molecule is encoded
26 \param confId Id of the conformation on the molecule to be encoded
27 \param trans Optional 3D transform to be applied to this conformation
28 \param vdwScale Scaling factor for the radius of the atoms to determine the
29 base radius
30 used in the encoding - grid points inside this sphere carry
31 the maximum occupany
32 \param stepSize thickness of the layers outside the base radius, the
33 occupancy value is decreased
34 from layer to layer from the maximum value
35 \param maxLayers the maximum number of layers - defaults to the number allowed
36 the number of bits
37 use per grid point - e.g. two bits per grid point will allow
38 3 layers
39 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
40 process
41 */
42 void EncodeShape(const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId = -1,
43 const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
44 double stepSize = 0.25, int maxLayers = -1,
45 bool ignoreHs = true);
46
47 //! Emcode the shape of a conformer on to a grid
48 /*!
49 \param conf The conformer of interest
50 \param grid Grid onto which the molecule is encoded
51 \param trans Optional 3D transform to be applied to this conformation
52 \param vdwScale Scaling factor for the radius of the atoms to determine the
53 base radius
54 used in the encoding - grid points inside this sphere carry
55 the maximum occupany
56 \param stepSize thickness of the layers outside the base radius, the
57 occupancy value is decreased
58 from layer to layer from the maximum value
59 \param maxLayers the maximum number of layers - defaults to the number allowed
60 the number of bits
61 use per grid point - e.g. two bits per grid point will allow
62 3 layers
63 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
64 process
65 */
66 void EncodeShape(const Conformer &conf, RDGeom::UniformGrid3D &grid,
67 const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
68 double stepSize = 0.25, int maxLayers = -1,
69 bool ignoreHs = true);
70 }
71 }
72 #endif
RDKit::MolShapes::EncodeShape
void EncodeShape(const Conformer &conf, RDGeom::UniformGrid3D &grid, const RDGeom::Transform3D *trans=0, double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true)
Emcode the shape of a conformer on to a grid.
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
RDKit
Std stuff.
Definition: Atom.h:29
RDGeom::UniformGrid3D
Definition: UniformGrid3D.h:19
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:41
RDGeom::Transform3D
Definition: Transform3D.h:21
RDGeom
Definition: TorsionAngleM6.h:19