/usr/include/rdkit/Geometry/Utils.h is in librdkit-dev 201503-3.
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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.
//
#ifndef __RD_DIST_UTILS_H__
#define __RD_DIST_UTILS_H__
#include <math.h>
#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);
}
}
#endif
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