00001 // 00002 // Copyright (C) 2005-2006 Rational Discovery LLC 00003 // 00004 // @@ All Rights Reserved @@ 00005 // 00006 #ifndef _RD_SHAPE_UTILS_H_20050128_ 00007 #define _RD_SHAPE_UTILS_H_20050128_ 00008 #include <DataStructs/DiscreteValueVect.h> 00009 #include <vector> 00010 00011 namespace RDGeom { 00012 class Point3D; 00013 class Transform3D; 00014 } 00015 00016 namespace RDKit { 00017 class ROMol; 00018 class Conformer; 00019 00020 namespace MolShapes { 00021 00022 //! Compute the size of the box that can fit the conformation, and offset of the box 00023 //! from the origin 00024 void computeConfDimsAndOffset(const Conformer &conf, RDGeom::Point3D &dims, 00025 RDGeom::Point3D &offSet, const RDGeom::Transform3D *trans=0, 00026 double padding=2.5); 00027 00028 //! Compute the a box that will fit the confomer 00029 /*! 00030 \param conf The conformer of interest 00031 \param leftBottom Storage for one extremity of the box 00032 \param rightTop Storage for other extremity of the box 00033 \param trans Optional transformation to be applied to the atom coordinates 00034 \param padding Padding added on the sides around the conformer 00035 */ 00036 void computeConfBox(const Conformer &conf, RDGeom::Point3D &leftBottom, 00037 RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans=0, 00038 double padding=2.5); 00039 00040 //! Compute the union of two boxes 00041 void computeUnionBox(const RDGeom::Point3D &leftBottom1, const RDGeom::Point3D &rightTop1, 00042 const RDGeom::Point3D &leftBottom2, const RDGeom::Point3D &rightTop2, 00043 RDGeom::Point3D &uLeftBottom, RDGeom::Point3D &uRightTop); 00044 00045 //! Compute dimensions of a conformer 00046 /*! 00047 \param conf Conformer of interest 00048 \param padding Padding added to the atom coordinates on all sides 00049 \param center Optionally specify the center 00050 \param ignoreHs if true, ignore the hydrogen atoms in computing the centroid 00051 */ 00052 std::vector<double> getConfDimensions(const Conformer &conf, double padding=2.5, 00053 const RDGeom::Point3D *center=0, bool ignoreHs=true); 00054 00055 //! Compute the shape tanimoto distance between two molecule based on a predefined alignment 00056 /*! 00057 \param mol1 The first molecule of interest 00058 \param mol2 The second molecule of interest 00059 \param confId1 Conformer in the first molecule (defaults to first conformer) 00060 \param confId2 Conformer in the second molecule (defaults to first conformer) 00061 \param gridSpacing resolution of the grid used to encode the molecular shapes 00062 \param bitsPerPoint number of bit used to encode the occupancy at each grid point 00063 defaults to two bits per grid point 00064 \param vdwScale Scaling factor for the radius of the atoms to determine the base radius 00065 used in the encoding - grid points inside this sphere carry the maximum occupany 00066 \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased 00067 from layer to layer from the maximum value 00068 \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits 00069 use per grid point - e.g. two bits per grid point will allow 3 layers 00070 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process 00071 */ 00072 00073 double tanimotoDistance(const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, 00074 double gridSpacing=0.5, 00075 DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, 00076 double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, 00077 bool ignoreHs=true); 00078 00079 00080 //! Compute the shape tanimoto distance between two conformers based on a predefined alignment 00081 /*! 00082 \param conf1 The first conformer of interest 00083 \param conf2 The second conformer of interest 00084 \param gridSpacing resolution of the grid used to encode the molecular shapes 00085 \param bitsPerPoint number of bit used to encode the occupancy at each grid point 00086 \param vdwScale Scaling factor for the radius of the atoms to determine the base radius 00087 used in the encoding - grid points inside this sphere carry the maximum occupany 00088 \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased 00089 from layer to layer from the maximum value 00090 \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits 00091 use per grid point - e.g. two bits per grid point will allow 3 layers 00092 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process 00093 */ 00094 00095 double tanimotoDistance(const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, 00096 DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, 00097 double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true); 00098 00099 00100 //! Compute the shape protrusion distance between two molecule based on a predefined alignment 00101 /*! 00102 \param mol1 The first molecule of interest 00103 \param mol2 The second molecule of interest 00104 \param confId1 Conformer in the first molecule (defaults to first conformer) 00105 \param confId2 Conformer in the second molecule (defaults to first conformer) 00106 \param gridSpacing resolution of the grid used to encode the molecular shapes 00107 \param bitsPerPoint number of bit used to encode the occupancy at each grid point 00108 defaults to two bits per grid point 00109 \param vdwScale Scaling factor for the radius of the atoms to determine the base radius 00110 used in the encoding - grid points inside this sphere carry the maximum occupany 00111 \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased 00112 from layer to layer from the maximum value 00113 \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits 00114 use per grid point - e.g. two bits per grid point will allow 3 layers 00115 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process 00116 \param allowReordering if set the order will be automatically updated so that the value calculated 00117 is the protrusion of the smaller shape from the larger one. 00118 */ 00119 00120 double protrudeDistance(const ROMol &mol1, const ROMol &mol2, int confId1=-1, int confId2=-1, 00121 double gridSpacing=0.5, 00122 DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, 00123 double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, 00124 bool ignoreHs=true, bool allowReordering=true); 00125 00126 00127 //! Compute the shape protrusion distance between two conformers based on a predefined alignment 00128 /*! 00129 \param conf1 The first conformer of interest 00130 \param conf2 The second conformer of interest 00131 \param gridSpacing resolution of the grid used to encode the molecular shapes 00132 \param bitsPerPoint number of bit used to encode the occupancy at each grid point 00133 \param vdwScale Scaling factor for the radius of the atoms to determine the base radius 00134 used in the encoding - grid points inside this sphere carry the maximum occupany 00135 \param stepSize thickness of the each layer outside the base radius, the occupancy value is decreased 00136 from layer to layer from the maximum value 00137 \param maxLayers the maximum number of layers - defaults to the number allowed the number of bits 00138 use per grid point - e.g. two bits per grid point will allow 3 layers 00139 \param ignoreHs if true, ignore the hydrogen atoms in the shape encoding process 00140 \param allowReordering if set the order will be automatically updated so that the value calculated 00141 is the protrusion of the smaller shape from the larger one. 00142 */ 00143 00144 double protrudeDistance(const Conformer &conf1, const Conformer &conf2, double gridSpacing=0.5, 00145 DiscreteValueVect::DiscreteValueType bitsPerPoint=DiscreteValueVect::TWOBITVALUE, 00146 double vdwScale=0.8, double stepSize=0.25, int maxLayers=-1, bool ignoreHs=true, 00147 bool allowReordering=true); 00148 00149 } 00150 00151 } 00152 00153 #endif
1.5.3