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75 lines
2.9 KiB
C++
75 lines
2.9 KiB
C++
//
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// Copyright (C) 2005-2025 Greg Landrum and other RDKit contributors
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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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#pragma once
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#include <RDGeneral/export.h>
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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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} // namespace RDGeom
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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 occupancy
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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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RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(
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const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId = -1,
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const RDGeom::Transform3D *trans = nullptr, double vdwScale = 0.8,
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double stepSize = 0.25, int maxLayers = -1, 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 occupancy
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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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RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(
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const Conformer &conf, RDGeom::UniformGrid3D &grid,
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const RDGeom::Transform3D *trans = nullptr, double vdwScale = 0.8,
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double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true);
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} // namespace MolShapes
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} // namespace RDKit
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#endif
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