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