1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
|
// $Id$
//
// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API
#include <RDBoost/python.h>
#include <RDBoost/Wrap.h>
#include <boost/python/numeric.hpp>
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <map>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
#include <SimDivPickers/DistPicker.h>
#include <SimDivPickers/MaxMinPicker.h>
#include <SimDivPickers/HierarchicalClusterPicker.h>
#include <iostream>
namespace python = boost::python;
namespace RDPickers {
// REVIEW: the poolSize can be pulled from the numeric array
RDKit::INT_VECT MaxMinPicks(MaxMinPicker *picker, python::object distMat,
int poolSize, int pickSize,
python::object firstPicks, int seed) {
if (pickSize >= poolSize) {
throw ValueErrorException("pickSize must be less than poolSize");
}
if (!PyArray_Check(distMat.ptr())) {
throw ValueErrorException("distance mat argument must be a numpy matrix");
}
PyArrayObject *copy;
copy = (PyArrayObject *)PyArray_ContiguousFromObject(distMat.ptr(),
NPY_DOUBLE, 1, 1);
double *dMat = (double *)PyArray_DATA(copy);
RDKit::INT_VECT firstPickVect;
for (unsigned int i = 0;
i < python::extract<unsigned int>(firstPicks.attr("__len__")()); ++i) {
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res =
picker->pick(dMat, poolSize, pickSize, firstPickVect, seed);
Py_DECREF(copy);
return res;
}
class pyobjFunctor {
public:
pyobjFunctor(python::object obj, bool useCache)
: dp_obj(obj), dp_cache(NULL) {
if (useCache)
dp_cache = new std::map<std::pair<unsigned int, unsigned int>, double>();
}
~pyobjFunctor() { delete dp_cache; }
double operator()(unsigned int i, unsigned int j) {
double res;
std::pair<unsigned int, unsigned int> idxPair(i, j);
if (dp_cache && dp_cache->count(idxPair) > 0) {
res = (*dp_cache)[idxPair];
} else {
res = python::extract<double>(dp_obj(i, j));
if (dp_cache) (*dp_cache)[idxPair] = res;
}
return res;
}
private:
python::object dp_obj;
std::map<std::pair<unsigned int, unsigned int>, double> *dp_cache;
};
RDKit::INT_VECT LazyMaxMinPicks(MaxMinPicker *picker, python::object distFunc,
int poolSize, int pickSize,
python::object firstPicks, int seed,
bool useCache) {
RDKit::INT_VECT firstPickVect;
for (unsigned int i = 0;
i < python::extract<unsigned int>(firstPicks.attr("__len__")()); ++i) {
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res;
pyobjFunctor functor(distFunc, useCache);
res = picker->lazyPick(functor, poolSize, pickSize, firstPickVect, seed);
return res;
}
// NOTE: TANIMOTO and DICE provably return the same results for the diversity
// picking
// this is still here just in case we ever later want to support other
// methods.
typedef enum { TANIMOTO = 1, DICE } DistanceMethod;
template <typename BV>
class pyBVFunctor {
public:
pyBVFunctor(const std::vector<const BV *> &obj, DistanceMethod method,
bool useCache)
: d_obj(obj), d_method(method), dp_cache(NULL) {
if (useCache)
dp_cache = new std::map<std::pair<unsigned int, unsigned int>, double>();
}
~pyBVFunctor() { delete dp_cache; }
double operator()(unsigned int i, unsigned int j) {
double res = 0.0;
std::pair<unsigned int, unsigned int> idxPair(i, j);
if (dp_cache && dp_cache->count(idxPair) > 0) {
res = (*dp_cache)[idxPair];
} else {
switch (d_method) {
case TANIMOTO:
res = 1. - TanimotoSimilarity(*d_obj[i], *d_obj[j]);
break;
case DICE:
res = 1. - DiceSimilarity(*d_obj[i], *d_obj[j]);
break;
default:
throw_value_error("unsupported similarity value");
}
if (dp_cache) {
(*dp_cache)[idxPair] = res;
}
}
return res;
}
private:
const std::vector<const BV *> &d_obj;
DistanceMethod d_method;
std::map<std::pair<unsigned int, unsigned int>, double> *dp_cache;
};
RDKit::INT_VECT LazyVectorMaxMinPicks(MaxMinPicker *picker, python::object objs,
int poolSize, int pickSize,
python::object firstPicks, int seed,
bool useCache) {
std::vector<const ExplicitBitVect *> bvs(poolSize);
for (int i = 0; i < poolSize; ++i) {
bvs[i] = python::extract<const ExplicitBitVect *>(objs[i]);
}
pyBVFunctor<ExplicitBitVect> functor(bvs, TANIMOTO, useCache);
RDKit::INT_VECT firstPickVect;
for (unsigned int i = 0;
i < python::extract<unsigned int>(firstPicks.attr("__len__")()); ++i) {
firstPickVect.push_back(python::extract<int>(firstPicks[i]));
}
RDKit::INT_VECT res =
picker->lazyPick(functor, poolSize, pickSize, firstPickVect, seed);
return res;
}
} // end of namespace RDPickers
struct MaxMin_wrap {
static void wrap() {
python::class_<RDPickers::MaxMinPicker>(
"MaxMinPicker",
"A class for diversity picking of items using the MaxMin Algorithm\n")
.def("Pick", RDPickers::MaxMinPicks,
(python::arg("self"), python::arg("distMat"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1),
"Pick a subset of items from a pool of items using the MaxMin "
"Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n\n"
"ARGUMENTS:\n"
" - distMat: 1D distance matrix (only the lower triangle "
"elements)\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n")
.def("LazyPick", RDPickers::LazyMaxMinPicks,
(python::arg("self"), python::arg("distFunc"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1, python::arg("useCache") = true),
"Pick a subset of items from a pool of items using the MaxMin "
"Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - distFunc: a function that should take two indices and return "
"the\n"
" distance between those two points.\n"
" NOTE: the implementation caches distance values, "
"so the\n"
" client code does not need to do so; indeed, it "
"should not.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n"
" - useCache: (optional) toggles use of a cache for the distance "
"calculation\n"
" This trades memory usage for speed.\n")
.def("LazyBitVectorPick", RDPickers::LazyVectorMaxMinPicks,
(python::arg("self"), python::arg("objects"),
python::arg("poolSize"), python::arg("pickSize"),
python::arg("firstPicks") = python::tuple(),
python::arg("seed") = -1, python::arg("useCache") = true),
"Pick a subset of items from a pool of bit vectors using the "
"MaxMin Algorithm\n"
"Ashton, M. et. al., Quant. Struct.-Act. Relat., 21 (2002), "
"598-604 \n"
"ARGUMENTS:\n\n"
" - vectors: a sequence of the bit vectors that should be picked "
"from.\n"
" - poolSize: number of items in the pool\n"
" - pickSize: number of items to pick from the pool\n"
" - firstPicks: (optional) the first items to be picked (seeds "
"the list)\n"
" - seed: (optional) seed for the random number generator\n"
" - useCache: (optional) toggles use of a cache for the distance "
"calculation\n"
" This trades memory usage for speed.\n"
);
};
};
void wrap_maxminpick() { MaxMin_wrap::wrap(); }
|
