RDKit
Open-source cheminformatics and machine learning.
ShapeEncoder.h
Go to the documentation of this file.
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//
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// Copyright (C) 2005-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#ifndef _RD_SHAPE_ENCODER_H_20050125_0800_
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#define _RD_SHAPE_ENCODER_H_20050125_0800_
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namespace
RDGeom
{
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class
UniformGrid3D;
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class
Transform3D;
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}
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namespace
RDKit
{
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class
ROMol;
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class
Conformer;
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namespace
MolShapes {
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//! Encode the shape of a molecule on to a grid
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/*!
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\param mol The molecule of interest
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\param grid Grid onto which the molecule is encoded
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\param confId Id of the conformation on the molecule to be encoded
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\param trans Optional 3D transform to be applied to this conformation
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\param vdwScale Scaling factor for the radius of the atoms to determine the
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base radius
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used in the encoding - grid points inside this sphere carry
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the maximum occupany
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\param stepSize thickness of the layers outside the base radius, the
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occupancy value is decreased
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from layer to layer from the maximum value
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\param maxLayers the maximum number of layers - defaults to the number allowed
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the number of bits
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use per grid point - e.g. two bits per grid point will allow
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3 layers
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\param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
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process
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*/
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void
EncodeShape
(
const
ROMol
&mol,
RDGeom::UniformGrid3D
&grid,
int
confId = -1,
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const
RDGeom::Transform3D
*trans = 0,
double
vdwScale = 0.8,
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double
stepSize = 0.25,
int
maxLayers = -1,
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bool
ignoreHs =
true
);
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//! Emcode the shape of a conformer on to a grid
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/*!
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\param conf The conformer of interest
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\param grid Grid onto which the molecule is encoded
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\param trans Optional 3D transform to be applied to this conformation
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\param vdwScale Scaling factor for the radius of the atoms to determine the
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base radius
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used in the encoding - grid points inside this sphere carry
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the maximum occupany
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\param stepSize thickness of the layers outside the base radius, the
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occupancy value is decreased
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from layer to layer from the maximum value
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\param maxLayers the maximum number of layers - defaults to the number allowed
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the number of bits
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use per grid point - e.g. two bits per grid point will allow
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3 layers
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\param ignoreHs if true, ignore the hydrogen atoms in the shape encoding
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process
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*/
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void
EncodeShape
(
const
Conformer
&conf,
RDGeom::UniformGrid3D
&grid,
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const
RDGeom::Transform3D
*trans = 0,
double
vdwScale = 0.8,
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double
stepSize = 0.25,
int
maxLayers = -1,
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bool
ignoreHs =
true
);
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}
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}
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#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:102
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition:
Atom.h:28
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
GraphMol
ShapeHelpers
ShapeEncoder.h
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