RDKit
Open-source cheminformatics and machine learning.
ChiralViolationContrib.h
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1 //
2 // Created by Santosh Putta, Nov 2006
3 //
4 #ifndef __RD_CHIRALVIOLATIONCONTRIB_H__
5 #define __RD_CHIRALVIOLATIONCONTRIB_H__
6 
7 #include <ForceField/Contrib.h>
8 #include <Geometry/point.h>
9 
10 namespace DistGeom {
11 class ChiralSet;
12 
13 //! A term to capture the violation of chirality at an atom center
14 //!
16  public:
18  : d_idx1(0),
19  d_idx2(0),
20  d_idx3(0),
21  d_idx4(0),
22  d_volLower(0.0),
23  d_volUpper(0.0),
24  d_weight(0.0){};
25 
26  //! Constructor
27  /*!
28  \param owner pointer to the owning forcefield
29  \param cset a chiral set containing the four chiral atom ids (in
30  sequence)
31  and the upper and lower limits on the signed chiral volume
32  \param weight (optional) the weight to be used for this contrib
33 
34  */
36  double weight = 1.0);
37 
38  //! return the contribution of this contrib to the energy of a given state
39  double getEnergy(double *pos) const;
40 
41  //! calculate the contribution of this contrib to the gradient at a given
42  //state
43  void getGrad(double *pos, double *grad) const;
44  virtual ChiralViolationContrib *copy() const {
45  return new ChiralViolationContrib(*this);
46  };
47 
48  static double calcChiralVolume(unsigned int idx1, unsigned int idx2,
49  unsigned int idx3, unsigned int idx4,
50  const double *pos, unsigned int dim) {
51  // even if we are minimizing in higher dimension the chiral volume is
52  // calculated using only the first 3 dimensions
53  RDGeom::Point3D v1(pos[idx1 * dim] - pos[idx4 * dim],
54  pos[idx1 * dim + 1] - pos[idx4 * dim + 1],
55  pos[idx1 * dim + 2] - pos[idx4 * dim + 2]);
56 
57  RDGeom::Point3D v2(pos[idx2 * dim] - pos[idx4 * dim],
58  pos[idx2 * dim + 1] - pos[idx4 * dim + 1],
59  pos[idx2 * dim + 2] - pos[idx4 * dim + 2]);
60 
61  RDGeom::Point3D v3(pos[idx3 * dim] - pos[idx4 * dim],
62  pos[idx3 * dim + 1] - pos[idx4 * dim + 1],
63  pos[idx3 * dim + 2] - pos[idx4 * dim + 2]);
64 
65  RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
66 
67  double vol = v1.dotProduct(v2xv3);
68  return vol;
69  }
70  static double calcChiralVolume(unsigned int idx1, unsigned int idx2,
71  unsigned int idx3, unsigned int idx4,
72  const RDGeom::PointPtrVect &pts) {
73  // even if we are minimizing in higher dimension the chiral volume is
74  // calculated using only the first 3 dimensions
75  RDGeom::Point3D v1((*pts[idx1])[0] - (*pts[idx4])[0],
76  (*pts[idx1])[1] - (*pts[idx4])[1],
77  (*pts[idx1])[2] - (*pts[idx4])[2]);
78 
79  RDGeom::Point3D v2((*pts[idx2])[0] - (*pts[idx4])[0],
80  (*pts[idx2])[1] - (*pts[idx4])[1],
81  (*pts[idx2])[2] - (*pts[idx4])[2]);
82 
83  RDGeom::Point3D v3((*pts[idx3])[0] - (*pts[idx4])[0],
84  (*pts[idx3])[1] - (*pts[idx4])[1],
85  (*pts[idx3])[2] - (*pts[idx4])[2]);
86 
87  RDGeom::Point3D v2xv3 = v2.crossProduct(v3);
88 
89  double vol = v1.dotProduct(v2xv3);
90  return vol;
91  }
92 
93  private:
94  unsigned int d_idx1, d_idx2, d_idx3, d_idx4;
95  double d_volLower;
96  double d_volUpper;
97  double d_weight;
98 };
99 }
100 
101 #endif
Point3D crossProduct(const Point3D &other) const
Cross product of this point with the another point.
Definition: point.h:200
static double calcChiralVolume(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const double *pos, unsigned int dim)
std::vector< RDGeom::Point * > PointPtrVect
Definition: point.h:492
double getEnergy(double *pos) const
return the contribution of this contrib to the energy of a given state
double dotProduct(const Point3D &other) const
Definition: point.h:144
abstract base class for contributions to ForceFields
Definition: Contrib.h:17
static double calcChiralVolume(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const RDGeom::PointPtrVect &pts)
void getGrad(double *pos, double *grad) const
calculate the contribution of this contrib to the gradient at a given
Class used to store a quartet of points and chiral volume bounds on them.
Definition: ChiralSet.h:23
A class to store forcefields and handle minimization.
Definition: ForceField.h:57
virtual ChiralViolationContrib * copy() const
return a copy