RDKit: Utils.h Source File

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Geometry/Utils.h
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1//
2// Copyright (C) 2004-2006 Rational Discovery LLC
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#ifndef __RD_DIST_UTILS_H__
12#define __RD_DIST_UTILS_H__
13
14#include <cmath>
15#include "point.h"
16#include "Transform3D.h"
17#include "Transform.h"
18
19namespace RDGeom {
20
21/*! \brief Compute the 13 distance between points give the 12 distances
22 * and the angle between the axes.
23 */
24 inline double compute13Dist(double d1, double d2, double angle) {
25 double res = d1 * d1 + d2 * d2 - 2 * d1 * d2 * cos(angle);
26 return sqrt(res);
27}
28
29/*! \brief Compute the 14 distances give the 12 distance and the angles
30 *
31 * This is computed by aligning the d2 axis with the x-axis (with atom 2 at
32 * the origin. Atom 1 is made to lie int he xy-plane with a +ve y-coordinate
33 * and finally the coordinates for atom 4 are computed.
34 *
35 * ARGUMENTS:
36 * d1 - distance between atoms 1 and 2
37 * d2 - distance between atoms 2 and 3
38 * d3 - distance between atoms 3 and 4
39 * ang12 - angle between the axes d1 and d2
40 * ang23 - angle between the axes d2 and d3
41 * torAng - torsional agnle of the axis d2
42 *
43 * NOTE:
44 * we are specifically calling this function compute14Dist3D because
45 * we assume the torsional angle can take any value including 0 and 180 deg.
46 * However, if using either 0 or 180 as the torsional angle (which is often
47 * the case) the user is recommended to use the specialized functions below
48 * instead of this function; they will be speedier.
49 */
50 inline double compute14Dist3D(double d1, double d2, double d3, double ang12,
51 double ang23, double torAng) {
52 // location of atom1
53 Point3D p1(d1 * cos(ang12), d1 * sin(ang12), 0.0);
54
55 // location of atom 4 if the rosion angle was 0
56 Point3D p4(d2 - d3 * cos(ang23), d3 * sin(ang23), 0.0);
57
58 // now we will rotate p4 about the x-axis by the desired torsion angle
59 Transform3D trans;
60 trans.SetRotation(torAng, X_Axis);
61 trans.TransformPoint(p4);
62
63 // find the distance
64 p4 -= p1;
65 return p4.length();
66}
67
68/*! \brief Compute the 14 distances give the 12 distance and bond angle
69 * for cis configuration
70 *
71 * This is simply a special case of the above function compute14Dist3D;
72 * with torsion angle set to 0. However, this function should be speedier
73 */
74 inline double compute14DistCis(double d1, double d2, double d3, double ang12,
75 double ang23) {
76 double dx = d2 - d3 * cos(ang23) - d1 * cos(ang12);
77 double dy = d3 * sin(ang23) - d1 * sin(ang12);
78 double res = dx * dx + dy * dy;
79 return sqrt(res);
80}
81
82/*! \brief Compute the 14 distances give the 12 distance and bond angle
83 * for trans configuration
84 *
85 * This is simply a special case of the above function compute14Dist3D;
86 * with torsion angle set to 180. However, this function should be speedier
87 */
88 inline double compute14DistTrans(double d1, double d2, double d3, double ang12,
89 double ang23) {
90 double dx = d2 - d3 * cos(ang23) - d1 * cos(ang12);
91 double dy = d3 * sin(ang23) + d1 * sin(ang12);
92 double res = dx * dx + dy * dy;
93 return sqrt(res);
94}
95} // namespace RDGeom
96
97#endif
Transform3D.h
Transform.h
RDGeom::Point3D
Definition point.h:53
RDGeom::Point3D::length
double length() const override
Definition point.h:158
RDGeom::Transform3D
Definition Transform3D.h:23
RDGeom::Transform3D::SetRotation
void SetRotation(double angle, AxisType axis)
set the rotation matrix
RDGeom::Transform3D::TransformPoint
void TransformPoint(Point3D &pt) const
export.h
RDGeom
Definition TorsionAngleContribs.h:17
RDGeom::compute14DistTrans
double compute14DistTrans(double d1, double d2, double d3, double ang12, double ang23)
Compute the 14 distances give the 12 distance and bond angle for trans configuration.
Definition Geometry/Utils.h:88
RDGeom::X_Axis
@ X_Axis
Definition Transform.h:16
RDGeom::compute14DistCis
double compute14DistCis(double d1, double d2, double d3, double ang12, double ang23)
Compute the 14 distances give the 12 distance and bond angle for cis configuration.
Definition Geometry/Utils.h:74
RDGeom::compute13Dist
double compute13Dist(double d1, double d2, double angle)
Compute the 13 distance between points give the 12 distances and the angle between the axes.
Definition Geometry/Utils.h:24
RDGeom::compute14Dist3D
double compute14Dist3D(double d1, double d2, double d3, double ang12, double ang23, double torAng)
Compute the 14 distances give the 12 distance and the angles.
Definition Geometry/Utils.h:50
point.h