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
|
#include "RDMolImpl.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/Fileparsers.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <string>
#include <vector>
#include <nsMemory.h>
NS_IMPL_ISUPPORTS1(RDMolecule, IRDMolecule)
RDMolecule::~RDMolecule()
{
if(this->dp_mol){
delete dp_mol;
dp_mol=0;
}
}
/* double GetMW (); */
NS_IMETHODIMP RDMolecule::GetMW(double *_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
RDKit::PeriodicTable *pt=RDKit::PeriodicTable::getTable();
*_retval=0.0;
for(RDKit::ROMol::AtomIterator atIt=dp_mol->beginAtoms();
atIt!=dp_mol->endAtoms();atIt++){
*_retval += (*atIt)->getMass()+(*atIt)->getNumImplicitHs()*pt->getAtomicWeight(1);
}
return NS_OK;
}
/* string GetSmiles (); */
NS_IMETHODIMP RDMolecule::GetSmiles(char **_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
std::string smi=RDKit::MolToSmiles(*dp_mol);
*_retval=(char *)nsMemory::Clone(smi.c_str(),sizeof(char)*(smi.size()+1));
return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
}
/* unsigned long GetSmartsMatchCount (in string smarts); */
NS_IMETHODIMP RDMolecule::GetSmartsMatchCount(const char *smarts, PRUint32 *_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
RDKit::ROMol *patt=RDKit::SmartsToMol(std::string(smarts));
if(!patt) return NS_ERROR_FAILURE;
std::vector<RDKit::MatchVectType> matches;
int res=RDKit::SubstructMatch(dp_mol,patt,matches);
*_retval = res;
return NS_OK;
}
/* double LogP (); */
NS_IMETHODIMP RDMolecule::LogP(double *_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
double logp;
if(dp_mol->hasProp("_CrippenLogP")) {
dp_mol->getProp("_CrippenLogP",logp);
} else {
double mr;
RDKit::Descriptors::CalcCrippenDescriptors(dp_mol,logp,mr);
dp_mol->setProp("_CrippenLogP",logp,true);
dp_mol->setProp("_CrippenMR",mr,true);
}
*_retval=logp;
return NS_OK;
}
/* double MR (); */
NS_IMETHODIMP RDMolecule::MR(double *_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
double mr;
if(dp_mol->hasProp("_CrippenMR")) {
dp_mol->getProp("_CrippenMR",mr);
} else {
double logp;
RDKit::Descriptors::CalcCrippenDescriptors(dp_mol,logp,mr);
dp_mol->setProp("_CrippenLogP",logp,true);
dp_mol->setProp("_CrippenMR",mr,true);
}
*_retval=mr;
return NS_OK;
}
/* string GetMolBlock (); */
NS_IMETHODIMP RDMolecule::GetMolBlock(char **_retval)
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
std::string molB=RDKit::MolToMolBlock(dp_mol);
*_retval=(char *)nsMemory::Clone(molB.c_str(),sizeof(char)*(molB.size()+1));
return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
}
/* void Generate3DCoords (); */
NS_IMETHODIMP RDMolecule::Generate3DCoords()
{
if(!dp_mol) return NS_ERROR_NOT_INITIALIZED;
bool embedded=RDKit::DGeomHelpers::EmbedMolecule(*dp_mol);
if(!embedded) return NS_ERROR_FAILURE;
ForceFields::ForceField *ff=RDKit::UFF::constructForceField(dp_mol);
if(!ff) return NS_ERROR_FAILURE;
ff->initialize();
int needsMore=ff->minimize();
delete ff;
if(needsMore) return NS_ERROR_FAILURE;
return NS_OK;
}
|
