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
|
//
// Copyright (C) 2003-2006 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.
//
#include <RDGeneral/export.h>
#ifndef _RD_FRAGCATALOGENTRY_H_
#define _RD_FRAGCATALOGENTRY_H_
#include "FragCatParams.h"
#include <RDGeneral/utils.h>
#include <Catalogs/CatalogEntry.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <map>
#include <sstream>
namespace RDKit {
class RDKIT_FRAGCATALOG_EXPORT FragCatalogEntry : public RDCatalog::CatalogEntry {
public:
FragCatalogEntry() : dp_mol(0), d_descrip(""), d_order(0) {
dp_props = new Dict();
setBitId(-1);
}
FragCatalogEntry(const ROMol *omol, const PATH_TYPE &path,
const MatchVectType &aidToFid);
FragCatalogEntry(const std::string &pickle);
~FragCatalogEntry() {
delete dp_mol;
dp_mol = 0;
if (dp_props) {
delete dp_props;
dp_props = 0;
}
}
std::string getDescription() const { return d_descrip; }
void setDescription(const std::string &val) { d_descrip = val; }
void setDescription(const FragCatParams *params);
// check if this fragment macthes the one specified
//
bool match(const FragCatalogEntry *other, double tol) const;
Subgraphs::DiscrimTuple getDiscrims() const;
unsigned int getOrder() const { return dp_mol->getNumBonds(); }
const INT_INT_VECT_MAP &getFuncGroupMap() const { return d_aToFmap; }
// REVIEW: this should be removed?
std::string getSmarts() { return ""; }
// FUnctions on the property dictionary
template <typename T>
void setProp(const char *key, T &val) const {
dp_props->setVal(key, val);
}
template <typename T>
void setProp(const std::string &key, T &val) const {
setProp(key.c_str(), val);
}
void setProp(const char *key, int val) const { dp_props->setVal(key, val); }
void setProp(const std::string &key, int val) const {
setProp(key.c_str(), val);
}
void setProp(const char *key, float val) const { dp_props->setVal(key, val); }
void setProp(const std::string &key, float val) const {
setProp(key.c_str(), val);
}
void setProp(const std::string &key, std::string &val) const {
setProp(key.c_str(), val);
}
template <typename T>
void getProp(const char *key, T &res) const {
dp_props->getVal(key, res);
}
template <typename T>
void getProp(const std::string &key, T &res) const {
getProp(key.c_str(), res);
}
bool hasProp(const char *key) const {
if (!dp_props) return false;
return dp_props->hasVal(key);
}
bool hasProp(const std::string &key) const { return hasProp(key.c_str()); }
void clearProp(const char *key) const { dp_props->clearVal(key); }
void clearProp(const std::string &key) const { clearProp(key.c_str()); }
void toStream(std::ostream &ss) const;
std::string Serialize() const;
void initFromStream(std::istream &ss);
void initFromString(const std::string &text);
private:
ROMol *dp_mol;
Dict *dp_props;
std::string d_descrip;
unsigned int d_order;
// a map between the atom ids in mol that connect to
// a functional group and the corresponding functional
// group ID
INT_INT_VECT_MAP d_aToFmap;
};
}
#endif
|
