Geometry/Utils.h

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//
//  Copyright (C) 2004-2006 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_DIST_UTILS_H__
#define __RD_DIST_UTILS_H__
 
#include <cmath>
#include "point.h"
#include "Transform3D.h"
#include "Transform.h"
 
namespace RDGeom {
 
/*! \brief Compute the 13 distance between points give the 12 distances
 *  and the angle between the axes.
 */
inline double compute13Dist(double d1, double d2, double angle) {
  double res = d1 * d1 + d2 * d2 - 2 * d1 * d2 * cos(angle);
  return sqrt(res);
}
 
/*! \brief Compute the 14 distances give the 12 distance and the angles
 *
 *   This is computed by aligning the d2 axis with the x-axis (with atom 2 at
 *   the origin. Atom 1 is made to lie int he xy-plane with a +ve y-coordinate
 *   and finally the coordinates for atom 4 are computed.
 *
 * ARGUMENTS:
 *   d1 - distance between atoms 1 and 2
 *   d2 - distance between atoms 2 and 3
 *   d3 - distance between atoms 3 and 4
 *   ang12 - angle between the axes d1 and d2
 *   ang23 - angle between the axes d2 and d3
 *   torAng - torsional agnle of the axis d2
 *
 * NOTE:
 *   we are specifically calling this function compute14Dist3D because
 *   we assume the torsional angle can take any value including 0 and 180 deg.
 *   However, if using either 0 or 180 as the torsional angle (which is often
 *   the case) the user is recommended to use the specialized functions below
 *   instead of this function; they will be speedier.
 */
inline double compute14Dist3D(double d1, double d2, double d3, double ang12,
                              double ang23, double torAng) {
  // location of atom1
  Point3D p1(d1 * cos(ang12), d1 * sin(ang12), 0.0);
 
  // location of atom 4 if the rosion angle was 0
  Point3D p4(d2 - d3 * cos(ang23), d3 * sin(ang23), 0.0);
 
  // now we will rotate p4 about the x-axis by the desired torsion angle
  Transform3D trans;
  trans.SetRotation(torAng, X_Axis);
  trans.TransformPoint(p4);
 
  // find the distance
  p4 -= p1;
  return p4.length();
}
 
/*! \brief Compute the 14 distances give the 12 distance and bond angle
 *  for cis configuration
 *
 *  This is simply a special case of the above function compute14Dist3D;
 *  with torsion angle set to 0. However, this function should be speedier
 */
inline double compute14DistCis(double d1, double d2, double d3, double ang12,
                               double ang23) {
  double dx = d2 - d3 * cos(ang23) - d1 * cos(ang12);
  double dy = d3 * sin(ang23) - d1 * sin(ang12);
  double res = dx * dx + dy * dy;
  return sqrt(res);
}
 
/*! \brief Compute the 14 distances give the 12 distance and bond angle
 *  for trans configuration
 *
 *  This is simply a special case of the above function compute14Dist3D;
 *  with torsion angle set to 180. However, this function should be speedier
 */
inline double compute14DistTrans(double d1, double d2, double d3, double ang12,
                                 double ang23) {
  double dx = d2 - d3 * cos(ang23) - d1 * cos(ang12);
  double dy = d3 * sin(ang23) + d1 * sin(ang12);
  double res = dx * dx + dy * dy;
  return sqrt(res);
}
}  // namespace RDGeom
 
#endif