ShapeUtils.h

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//
//   Copyright (C) 2005-2006 Rational Discovery LLC
//
//   @@ 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.
//
#include <RDGeneral/export.h>
#ifndef _RD_SHAPE_UTILS_H_20050128_
#define _RD_SHAPE_UTILS_H_20050128_
#include <DataStructs/DiscreteValueVect.h>
#include <vector>
 
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<double> 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