// // Copyright (C) 2005-2025 Greg Landrum and other RDKit contributors // // @@ All Rights Reserved @@ // This file is part of the RDKit. // The contents are covered by the terms of the BSD license // which is included in the file license.txt, found at the root // of the RDKit source tree. // #pragma once #include #ifndef RD_SHAPE_UTILS_H_20050128 #define RD_SHAPE_UTILS_H_20050128 #include #include namespace RDGeom { class Point3D; class Transform3D; } // namespace RDGeom namespace RDKit { class ROMol; class Conformer; namespace MolShapes { //! Compute the size of the box that can fit the conformation, and offset of the /// box from the origin RDKIT_SHAPEHELPERS_EXPORT void computeConfDimsAndOffset( const Conformer &conf, RDGeom::Point3D &dims, RDGeom::Point3D &offSet, const RDGeom::Transform3D *trans = nullptr, double padding = 2.5); //! Compute the box that will fit the conformer /*! \param conf The conformer of interest \param leftBottom Storage for one extremity of the box \param rightTop Storage for other extremity of the box \param trans Optional transformation to be applied to the atom coordinates \param padding Padding added on the sides around the conformer */ RDKIT_SHAPEHELPERS_EXPORT void computeConfBox( const Conformer &conf, RDGeom::Point3D &leftBottom, RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans = nullptr, double padding = 2.5); //! Compute the union of two boxes RDKIT_SHAPEHELPERS_EXPORT void computeUnionBox( const RDGeom::Point3D &leftBottom1, const RDGeom::Point3D &rightTop1, const RDGeom::Point3D &leftBottom2, const RDGeom::Point3D &rightTop2, RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop); //! Compute dimensions of a conformer /*! \param conf Conformer of interest \param padding Padding added to the atom coordinates on all sides \param center Optionally specify the center \param ignoreHs if true, ignore the hydrogen atoms in computing the centroid */ RDKIT_SHAPEHELPERS_EXPORT std::vector getConfDimensions( const Conformer &conf, double padding = 2.5, const RDGeom::Point3D *center = nullptr, bool ignoreHs = true); //! Compute the shape tversky index between two molecule based on a /// predefined alignment /*! \param mol1 The first molecule of interest \param mol2 The second molecule of interest \param alpha \param beta \param confId1 Conformer in the first molecule (defaults to first conformer) \param confId2 Conformer in the second molecule (defaults to first conformer) \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point defaults to two bits per grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process */ RDKIT_SHAPEHELPERS_EXPORT double tverskyIndex( const ROMol &mol1, const ROMol &mol2, double alpha, double beta, int confId1 = -1, int confId2 = -1, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true); //! Compute the shape tversky index between two conformers based on a /// predefined alignment /*! \param conf1 The first conformer of interest \param conf2 The second conformer of interest \param alpha \param beta \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process */ RDKIT_SHAPEHELPERS_EXPORT double tverskyIndex( const Conformer &conf1, const Conformer &conf2, double alpha, double beta, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true); //! Compute the shape tanimoto distance between two molecule based on a /// predefined alignment /*! \param mol1 The first molecule of interest \param mol2 The second molecule of interest \param confId1 Conformer in the first molecule (defaults to first conformer) \param confId2 Conformer in the second molecule (defaults to first conformer) \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point defaults to two bits per grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process */ RDKIT_SHAPEHELPERS_EXPORT double tanimotoDistance( const ROMol &mol1, const ROMol &mol2, int confId1 = -1, int confId2 = -1, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true); //! Compute the shape tanimoto distance between two conformers based on a /// predefined alignment /*! \param conf1 The first conformer of interest \param conf2 The second conformer of interest \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process */ RDKIT_SHAPEHELPERS_EXPORT double tanimotoDistance( const Conformer &conf1, const Conformer &conf2, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true); //! Compute the shape protrusion distance between two molecule based on a /// predefined alignment /*! \param mol1 The first molecule of interest \param mol2 The second molecule of interest \param confId1 Conformer in the first molecule (defaults to first conformer) \param confId2 Conformer in the second molecule (defaults to first conformer) \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point defaults to two bits per grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process \param allowReordering if set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one. */ RDKIT_SHAPEHELPERS_EXPORT double protrudeDistance( const ROMol &mol1, const ROMol &mol2, int confId1 = -1, int confId2 = -1, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true, bool allowReordering = true); //! Compute the shape protrusion distance between two conformers based on a /// predefined alignment /*! \param conf1 The first conformer of interest \param conf2 The second conformer of interest \param gridSpacing resolution of the grid used to encode the molecular shapes \param bitsPerPoint number of bit used to encode the occupancy at each grid point \param vdwScale Scaling factor for the radius of the atoms to determine the base radius used in the encoding - grid points inside this sphere carry the maximum occupancy \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased from layer to layer from the maximum value \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits use per grid point - e.g. two bits per grid point will allow 3 layers \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process \param allowReordering if set the order will be automatically updated so that the value calculated is the protrusion of the smaller shape from the larger one. */ RDKIT_SHAPEHELPERS_EXPORT double protrudeDistance( const Conformer &conf1, const Conformer &conf2, double gridSpacing = 0.5, DiscreteValueVect::DiscreteValueType bitsPerPoint = DiscreteValueVect::TWOBITVALUE, double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true, bool allowReordering = true); } // namespace MolShapes } // namespace RDKit #endif