RDKit: BoundsMatrix.h Source File

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BoundsMatrix.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 #ifndef __RD_BOUNDS_MATRIX_H__
11 #define __RD_BOUNDS_MATRIX_H__
12
13 #include <RDGeneral/Invariant.h>
14 #include <boost/smart_ptr.hpp>
15 #include <iostream>
16 #include <iomanip>
17 #include <Numerics/SquareMatrix.h>
18
19 namespace DistGeom {
20 //! Class to store the distance bound
21 /*!
22 Basically a N by N matrix
23 with lower distance bounds on the lower traingle and upper bounds in the upper
24 triangle
25 */
26 class BoundsMatrix : public RDNumeric::SquareMatrix<double> {
27 public:
28 typedef boost::shared_array<double> DATA_SPTR;
29
30 explicit BoundsMatrix(unsigned int N)
31 : RDNumeric::SquareMatrix<double>(N, 0.0){};
32 BoundsMatrix(unsigned int N, DATA_SPTR data)
33 : RDNumeric::SquareMatrix<double>(N, data){};
34
35 //! Get the upper bound between points i and j
36 inline double getUpperBound(unsigned int i, unsigned int j) const {
37 URANGE_CHECK(i, d_nRows - 1);
38 URANGE_CHECK(j, d_nCols - 1);
39
40 if (i < j) {
41 return getVal(i, j);
42 } else {
43 return getVal(j, i);
44 }
45 }
46
47 //! Set the lower bound between points i and j
48 inline void setUpperBound(unsigned int i, unsigned int j, double val) {
49 URANGE_CHECK(i, d_nRows - 1);
50 URANGE_CHECK(j, d_nCols - 1);
51 CHECK_INVARIANT(val >= 0.0, "Negative upper bound");
52 if (i < j) {
53 setVal(i, j, val);
54 } else {
55 setVal(j, i, val);
56 }
57 }
58
59 //! Set the upper bound between points i and j only if it is better than
60 //! previously existing value (i.e. the new value is smaller)
61 inline void setUpperBoundIfBetter(unsigned int i, unsigned int j,
62 double val) {
63 if ((val < getUpperBound(i, j)) && (val > getLowerBound(i, j))) {
64 setUpperBound(i, j, val);
65 }
66 }
67
68 //! Set the lower bound between points i and j
69 inline void setLowerBound(unsigned int i, unsigned int j, double val) {
70 URANGE_CHECK(i, d_nRows - 1);
71 URANGE_CHECK(j, d_nCols - 1);
72 CHECK_INVARIANT(val >= 0.0, "Negative lower bound");
73 if (i < j) {
74 setVal(j, i, val);
75 } else {
76 setVal(i, j, val);
77 }
78 }
79
80 //! Set the lower bound between points i and j only if it is better than
81 //! previously existing value (i.e. the new value is larger)
82 inline void setLowerBoundIfBetter(unsigned int i, unsigned int j,
83 double val) {
84 if ((val > getLowerBound(i, j)) && (val < getUpperBound(i, j))) {
85 setLowerBound(i, j, val);
86 }
87 }
88
89 //! Get the lower bound between points i and j
90 inline double getLowerBound(unsigned int i, unsigned int j) const {
91 URANGE_CHECK(i, d_nRows - 1);
92 URANGE_CHECK(j, d_nCols - 1);
93
94 if (i < j) {
95 return getVal(j, i);
96 } else {
97 return getVal(i, j);
98 }
99 }
100
101 //! Do a simple check of the current bounds - i.e. all lower bounds are
102 //! smaller than the existing upper bounds
103 inline bool checkValid() const {
104 unsigned int i, j;
105 for (i = 1; i < d_nRows; i++) {
106 for (j = 0; j < i; j++) {
107 if (getUpperBound(i, j) < getLowerBound(i, j)) {
108 return false;
109 }
110 }
111 }
112 return true;
113 }
114 };
115
116 typedef boost::shared_ptr<BoundsMatrix> BoundsMatPtr;
117 }
118
119 #endif
RDKit::Drawing::N
Definition: MolDrawing.h:41
SquareMatrix.h
RDNumeric
Definition: AlignPoints.h:17
DistGeom::BoundsMatrix::setLowerBoundIfBetter
void setLowerBoundIfBetter(unsigned int i, unsigned int j, double val)
Definition: BoundsMatrix.h:82
Invariant.h
CHECK_INVARIANT
#define CHECK_INVARIANT(expr, mess)
Definition: Invariant.h:95
DistGeom
Definition: BoundsMatrix.h:19
RDNumeric::Matrix< double >::setVal
virtual void setVal(unsigned int i, unsigned int j, doubleval)
sets a particular element of the matrix
Definition: Matrix.h:94
RDNumeric::SquareMatrix< double >::SquareMatrix
SquareMatrix()
brief Square matrix of size N
Definition: SquareMatrix.h:20
DistGeom::BoundsMatrix::checkValid
bool checkValid() const
Definition: BoundsMatrix.h:103
DistGeom::BoundsMatrix::getUpperBound
double getUpperBound(unsigned int i, unsigned int j) const
Get the upper bound between points i and j.
Definition: BoundsMatrix.h:36
DistGeom::BoundsMatPtr
boost::shared_ptr< BoundsMatrix > BoundsMatPtr
Definition: BoundsMatrix.h:116
DistGeom::BoundsMatrix::setUpperBound
void setUpperBound(unsigned int i, unsigned int j, double val)
Set the lower bound between points i and j.
Definition: BoundsMatrix.h:48
DistGeom::BoundsMatrix::setUpperBoundIfBetter
void setUpperBoundIfBetter(unsigned int i, unsigned int j, double val)
Definition: BoundsMatrix.h:61
RDNumeric::SquareMatrix
Definition: SquareMatrix.h:17
RDNumeric::Matrix< double >::d_nCols
unsigned int d_nCols
Definition: Matrix.h:233
DistGeom::BoundsMatrix::BoundsMatrix
BoundsMatrix(unsigned int N)
Definition: BoundsMatrix.h:30
URANGE_CHECK
#define URANGE_CHECK(x, hi)
Definition: Invariant.h:136
RDNumeric::Matrix< double >::d_nRows
unsigned int d_nRows
Definition: Matrix.h:231
DistGeom::BoundsMatrix::setLowerBound
void setLowerBound(unsigned int i, unsigned int j, double val)
Set the lower bound between points i and j.
Definition: BoundsMatrix.h:69
RDNumeric::Matrix< double >::getVal
virtual double getVal(unsigned int i, unsigned int j) const
returns a particular element of the matrix
Definition: Matrix.h:86
DistGeom::BoundsMatrix
Class to store the distance bound.
Definition: BoundsMatrix.h:26
DistGeom::BoundsMatrix::DATA_SPTR
boost::shared_array< double > DATA_SPTR
Definition: BoundsMatrix.h:28
DistGeom::BoundsMatrix::getLowerBound
double getLowerBound(unsigned int i, unsigned int j) const
Get the lower bound between points i and j.
Definition: BoundsMatrix.h:90
DistGeom::BoundsMatrix::BoundsMatrix
BoundsMatrix(unsigned int N, DATA_SPTR data)
Definition: BoundsMatrix.h:32