1 #include "RDMolImpl.h"
2 #include <GraphMol/RDKitBase.h>
3 #include <GraphMol/SmilesParse/SmilesParse.h>
4 #include <GraphMol/SmilesParse/SmilesWrite.h>
5 #include <GraphMol/FileParsers/Fileparsers.h>
6 #include <GraphMol/Substruct/SubstructMatch.h>
7 #include <GraphMol/Descriptors/MolDescriptors.h>
8 #include <GraphMol/DistGeomHelpers/Embedder.h>
9 #include <ForceField/ForceField.h>
10 #include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
11 #include <string>
12 #include <vector>
13 #include <nsMemory.h>
14
NS_IMPL_ISUPPORTS1(RDMolecule,IRDMolecule)15 NS_IMPL_ISUPPORTS1(RDMolecule, IRDMolecule)
16
17 RDMolecule::~RDMolecule() {
18 if (this->dp_mol) {
19 delete dp_mol;
20 dp_mol = 0;
21 }
22 }
23
24 /* double GetMW (); */
GetMW(double * _retval)25 NS_IMETHODIMP RDMolecule::GetMW(double *_retval) {
26 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
27 RDKit::PeriodicTable *pt = RDKit::PeriodicTable::getTable();
28 *_retval = 0.0;
29 for (RDKit::ROMol::AtomIterator atIt = dp_mol->beginAtoms();
30 atIt != dp_mol->endAtoms(); atIt++) {
31 *_retval += (*atIt)->getMass() +
32 (*atIt)->getNumImplicitHs() * pt->getAtomicWeight(1);
33 }
34 return NS_OK;
35 }
36
37 /* string GetSmiles (); */
GetSmiles(char ** _retval)38 NS_IMETHODIMP RDMolecule::GetSmiles(char **_retval) {
39 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
40 std::string smi = RDKit::MolToSmiles(*dp_mol);
41 *_retval =
42 (char *)nsMemory::Clone(smi.c_str(), sizeof(char) * (smi.size() + 1));
43 return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
44 }
45
46 /* unsigned long GetSmartsMatchCount (in string smarts); */
GetSmartsMatchCount(const char * smarts,PRUint32 * _retval)47 NS_IMETHODIMP RDMolecule::GetSmartsMatchCount(const char *smarts,
48 PRUint32 *_retval) {
49 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
50 RDKit::ROMol *patt = RDKit::SmartsToMol(std::string(smarts));
51 if (!patt) return NS_ERROR_FAILURE;
52
53 std::vector<RDKit::MatchVectType> matches;
54 int res = RDKit::SubstructMatch(dp_mol, patt, matches);
55 *_retval = res;
56 return NS_OK;
57 }
58
59 /* double LogP (); */
LogP(double * _retval)60 NS_IMETHODIMP RDMolecule::LogP(double *_retval) {
61 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
62 double logp;
63 if (dp_mol->hasProp(common_properties::_CrippenLogP)) {
64 dp_mol->getProp(common_properties::_CrippenLogP, logp);
65 } else {
66 double mr;
67 RDKit::Descriptors::CalcCrippenDescriptors(dp_mol, logp, mr);
68 dp_mol->setProp(common_properties::_CrippenLogP, logp, true);
69 dp_mol->setProp(common_properties::_CrippenMR, mr, true);
70 }
71 *_retval = logp;
72 return NS_OK;
73 }
74
75 /* double MR (); */
MR(double * _retval)76 NS_IMETHODIMP RDMolecule::MR(double *_retval) {
77 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
78 double mr;
79 if (dp_mol->hasProp(common_properties::_CrippenMR)) {
80 dp_mol->getProp(common_properties::_CrippenMR, mr);
81 } else {
82 double logp;
83 RDKit::Descriptors::CalcCrippenDescriptors(dp_mol, logp, mr);
84 dp_mol->setProp(common_properties::_CrippenLogP, logp, true);
85 dp_mol->setProp(common_properties::_CrippenMR, mr, true);
86 }
87 *_retval = mr;
88 return NS_OK;
89 }
90
91 /* string GetMolBlock (); */
GetMolBlock(char ** _retval)92 NS_IMETHODIMP RDMolecule::GetMolBlock(char **_retval) {
93 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
94 std::string molB = RDKit::MolToMolBlock(dp_mol);
95 *_retval =
96 (char *)nsMemory::Clone(molB.c_str(), sizeof(char) * (molB.size() + 1));
97 return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
98 }
99
100 /* void Generate3DCoords (); */
Generate3DCoords()101 NS_IMETHODIMP RDMolecule::Generate3DCoords() {
102 if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
103 bool embedded = RDKit::DGeomHelpers::EmbedMolecule(*dp_mol);
104 if (!embedded) return NS_ERROR_FAILURE;
105
106 ForceFields::ForceField *ff = RDKit::UFF::constructForceField(dp_mol);
107 if (!ff) return NS_ERROR_FAILURE;
108 ff->initialize();
109 int needsMore = ff->minimize();
110 delete ff;
111 if (needsMore) return NS_ERROR_FAILURE;
112 return NS_OK;
113 }
114