RDKit: utils.h Source File

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utils.h
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1//
2// Copyright (C) 2002-2020 Greg Landrum and 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//
11#include <RDGeneral/export.h>
12#ifndef RD_UTILS_H
13#define RD_UTILS_H
14
15#include "types.h"
16#include <RDGeneral/Invariant.h>
17#include <RDGeneral/BoostStartInclude.h>
18#include <boost/random.hpp>
19#include <RDGeneral/BoostEndInclude.h>
20
21namespace RDKit {
22 const int NUM_PRIMES_AVAIL =
23 1000; //!< the number of primes available and stored
24 RDKIT_RDGENERAL_EXPORT extern int firstThousandPrimes[NUM_PRIMES_AVAIL];
25
26 const int FILE_MAXLINE =
27 256; //!< an assumed maximum length for lines read from files
28
29//! \brief compute the product of the set of primes corresponding to the
30//! values in an INT_VECT
31 RDKIT_RDGENERAL_EXPORT double computeIntVectPrimesProduct(const INT_VECT &ring);
32
33//! floating point comparison with a tolerance
34 RDKIT_RDGENERAL_EXPORT bool feq(double v1, double v2, double tol = 1e-4);
35
36 typedef boost::minstd_rand rng_type;
37 typedef boost::uniform_int<> uniform_int;
38 typedef boost::uniform_real<> uniform_double;
39 typedef boost::variate_generator<rng_type &, uniform_int> int_source_type;
40 typedef boost::variate_generator<rng_type &, uniform_double> double_source_type;
41
42//! Optionally seed and return a reference to the global (Boost) random
43/// generator
44 RDKIT_RDGENERAL_EXPORT rng_type &getRandomGenerator(int seed = -1);
45
46//! Return a random double value between 0.0 and 1.0
47//! Optionally seed the random number generator
48 RDKIT_RDGENERAL_EXPORT double getRandomVal(int seed = -1);
49
50//! return a reference to the global (Boost) random source
51 RDKIT_RDGENERAL_EXPORT double_source_type &getDoubleRandomSource();
52
53template <class T>
54 unsigned int countSwapsToInterconvert(const T &ref, T probe) {
55 PRECONDITION(ref.size() == probe.size(), "size mismatch");
56 typename T::const_iterator refIt = ref.begin();
57 typename T::iterator probeIt = probe.begin();
58 typename T::iterator probeIt2;
59
60 unsigned int nSwaps = 0;
61 while (refIt != ref.end()) {
62 if ((*probeIt) != (*refIt)) {
63 bool foundIt = false;
64 probeIt2 = probeIt;
65 while ((*probeIt2) != (*refIt) && probeIt2 != probe.end()) {
66 ++probeIt2;
67 }
68 if (probeIt2 != probe.end()) {
69 foundIt = true;
70 }
71 CHECK_INVARIANT(foundIt, "could not find probe element");
72
73 std::swap(*probeIt, *probeIt2);
74 nSwaps++;
75 }
76 ++probeIt;
77 ++refIt;
78 }
79 return nSwaps;
80}
81
82 RDKIT_RDGENERAL_EXPORT std::string augmentTagName(const std::string &tag);
83} // namespace RDKit
84
85// contribution from dkoes
86template <unsigned n>
87 inline double int_pow(double x) {
88 double half = int_pow<n / 2>(x);
89 if (n % 2 == 0) { // even
90 return half * half;
91 } else {
92 return half * half * x;
93 }
94}
95
96template <>
97 inline double int_pow<0>(double) {
98 return 1;
99}
100
101template <>
102 inline double int_pow<1>(double x) {
103 return x; // this does a series of muls
104}
105
106#endif
BoostEndInclude.h
BoostStartInclude.h
Invariant.h
CHECK_INVARIANT
#define CHECK_INVARIANT(expr, mess)
Definition Invariant.h:100
PRECONDITION
#define PRECONDITION(expr, mess)
Definition Invariant.h:108
export.h
RDKIT_RDGENERAL_EXPORT
#define RDKIT_RDGENERAL_EXPORT
Definition export.h:441
RDKit::v1
Definition ReactionParser.h:91
RDKit::v2
Definition ReactionParser.h:71
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition types.h:303
RDKit::uniform_int
boost::uniform_int uniform_int
Definition utils.h:37
RDKit::feq
RDKIT_RDGENERAL_EXPORT bool feq(double v1, double v2, double tol=1e-4)
floating point comparison with a tolerance
RDKit::rng_type
boost::minstd_rand rng_type
Definition utils.h:36
RDKit::double_source_type
boost::variate_generator< rng_type &, uniform_double > double_source_type
Definition utils.h:40
RDKit::computeIntVectPrimesProduct
RDKIT_RDGENERAL_EXPORT double computeIntVectPrimesProduct(const INT_VECT &ring)
compute the product of the set of primes corresponding to the values in an INT_VECT
RDKit::getDoubleRandomSource
RDKIT_RDGENERAL_EXPORT double_source_type & getDoubleRandomSource()
return a reference to the global (Boost) random source
RDKit::int_source_type
boost::variate_generator< rng_type &, uniform_int > int_source_type
Definition utils.h:39
RDKit::augmentTagName
RDKIT_RDGENERAL_EXPORT std::string augmentTagName(const std::string &tag)
RDKit::firstThousandPrimes
RDKIT_RDGENERAL_EXPORT int firstThousandPrimes[NUM_PRIMES_AVAIL]
RDKit::NUM_PRIMES_AVAIL
const int NUM_PRIMES_AVAIL
the number of primes available and stored
Definition utils.h:22
RDKit::getRandomGenerator
RDKIT_RDGENERAL_EXPORT rng_type & getRandomGenerator(int seed=-1)
RDKit::countSwapsToInterconvert
unsigned int countSwapsToInterconvert(const T &ref, T probe)
Definition utils.h:54
RDKit::uniform_double
boost::uniform_real uniform_double
Definition utils.h:38
RDKit::FILE_MAXLINE
const int FILE_MAXLINE
an assumed maximum length for lines read from files
Definition utils.h:26
RDKit::getRandomVal
RDKIT_RDGENERAL_EXPORT double getRandomVal(int seed=-1)
types.h
int_pow
double int_pow(double x)
Definition utils.h:87
int_pow< 0 >
double int_pow< 0 >(double)
Definition utils.h:97
int_pow< 1 >
double int_pow< 1 >(double x)
Definition utils.h:102