public MoleCulePostion(string smiles)
{
Mol = MolImporter.importMol(smiles);
//将苯环的圈改为双线
Mol.dearomatize();
chemaxon.calculations.clean.Cleaner.clean(Mol, 2);
//重置类参数
InitPosition();
//重置原子垂直坐标
InitAtom();
}
private MemoryStream writeq()
{
//树绘图
MDocument md = new MDocument(MolImporter.importMol("O"));
MPoint p1 = new MPoint(1, 1);
MPoint p2 = new MPoint(1, 2);
MPolyline arrow = new MRectangle(p1, p2);
md.addObject(arrow);
MemoryStream stream = new MemoryStream(MolExporter.exportToBinFormat(md, "mrv"));
return(stream);
}
public static bool MoleculeComparisonTest(string mol1, string mol2)
{
bool blStatus = false;
try
{
string testMol1 = @"
ACCLDraw01081514282D
22 23 0 0 0 0 0 0 0 0999 V2000
8.7283 -2.9723 0.0000 C 0 0 0 0 0 0 0 0 0 8 0 0
5.6037 -2.9121 0.0000 C 0 0 0 0 0 0 0 0 0 11 0 0
6.7270 -2.5471 0.0000 O 0 0 0 0 0 0 0 0 0 10 0 0
7.6048 -3.3374 0.0000 C 0 0 0 0 0 0 0 0 0 9 0 0
5.9904 -6.0131 0.0000 C 0 0 0 0 0 0 0 0 0 14 0 0
6.2360 -4.8578 0.0000 O 0 0 0 0 0 0 0 0 0 13 0 0
7.3593 -4.4927 0.0000 C 0 0 0 0 0 0 0 0 0 12 0 0
8.8692 -7.2288 0.0000 C 0 0 0 0 0 0 0 0 0 17 0 0
7.9915 -6.4384 0.0000 O 0 0 0 0 0 0 0 0 0 16 0 0
8.2371 -5.2831 0.0000 C 0 0 0 0 0 0 0 0 0 15 0 0
9.3604 -4.9180 0.0000 C 0 0 0 0 0 0 0 0 0 18 0 0
9.6059 -3.7626 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
12.2755 -2.2744 0.0000 N 0 0 0 0 0 0 0 0 0 4 0 0
11.0943 -2.2744 0.0000 N 0 0 0 0 0 0 0 0 0 5 0 0
10.7293 -3.3978 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0
11.6848 -4.0921 0.0000 N 0 0 3 0 0 0 0 0 0 1 0 0
12.6405 -3.3978 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
13.7638 -3.7626 0.0000 S 0 0 0 0 0 0 0 0 0 3 0 0
14.6416 -2.9723 0.0000 C 0 0 0 0 0 0 0 0 0 20 0 0
16.0106 -4.4927 0.0000 O 0 0 0 0 0 0 0 0 0 22 0 0
15.7649 -3.3374 0.0000 C 0 0 0 0 0 0 0 0 0 21 0 0
16.6427 -2.5471 0.0000 O 0 0 0 0 0 0 0 0 0 23 0 0
12 1 1 0 0 0 2
1 4 2 0 0 0 2
3 2 1 0 0 0 2
4 3 1 0 0 0 2
4 7 1 0 0 0 2
6 5 1 0 0 0 2
7 6 1 0 0 0 2
7 10 2 0 0 0 2
9 8 1 0 0 0 2
10 9 1 0 0 0 2
10 11 1 0 0 0 2
11 12 2 0 0 0 2
15 12 1 0 0 0 2
17 13 2 0 0 0 8
13 14 1 0 0 0 8
14 15 2 0 0 0 8
15 16 1 0 0 0 8
16 17 1 0 0 0 8
17 18 1 0 0 0 8
18 19 1 0 0 0 4
19 21 1 0 0 0 2
21 20 2 0 0 0 2
21 22 1 0 0 0 2
M END
";
string testMol2 = @"
ACCLDraw01081514312D
21 22 0 0 0 0 0 0 0 0999 V2000
9.0242 -4.6483 0.0000 N 0 0 0 0 0 0 0 0 0 9 0 0
10.2054 -4.6483 0.0000 N 0 0 3 0 0 0 0 0 0 8 0 0
14.5726 -4.9211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
13.9404 -6.8668 0.0000 O 0 0 0 0 0 0 0 0 0 6 0 0
13.6947 -5.7114 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0
12.5714 -5.3464 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
11.6936 -6.1367 0.0000 S 0 0 0 0 0 0 0 0 0 3 0 0
10.5703 -5.7718 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
9.6148 -6.4660 0.0000 N 0 0 0 0 0 0 0 0 0 1 0 0
8.6592 -5.7718 0.0000 C 0 0 0 0 0 0 0 0 0 10 0 0
6.6580 -5.3464 0.0000 C 0 0 0 0 0 0 0 0 0 12 0 0
7.5359 -6.1367 0.0000 C 0 0 0 0 0 0 0 0 0 11 0 0
7.2902 -7.2921 0.0000 C 0 0 0 0 0 0 0 0 0 22 0 0
5.9214 -8.8123 0.0000 O 0 0 0 0 0 0 0 0 0 20 0 0
6.1669 -7.6571 0.0000 C 0 0 0 0 0 0 0 0 0 19 0 0
3.9203 -8.3871 0.0000 C 0 0 0 0 0 0 0 0 0 18 0 0
4.1658 -7.2317 0.0000 O 0 0 0 0 0 0 0 0 0 17 0 0
5.2891 -6.8666 0.0000 C 0 0 0 0 0 0 0 0 0 16 0 0
5.5347 -5.7114 0.0000 C 0 0 0 0 0 0 0 0 0 13 0 0
4.6570 -4.9211 0.0000 O 0 0 0 0 0 0 0 0 0 14 0 0
3.5336 -5.2860 0.0000 C 0 0 0 0 0 0 0 0 0 15 0 0
10 1 2 0 0 0 2
1 2 1 0 0 0 2
2 8 1 0 0 0 2
5 3 1 0 0 0 4
5 4 2 0 0 0 2
6 5 1 0 0 0 2
7 6 1 0 0 0 2
8 7 1 0 0 0 2
8 9 2 0 0 0 2
9 10 1 0 0 0 2
10 12 1 0 0 0 2
11 19 2 0 0 0 2
12 11 1 0 0 0 2
13 12 2 0 0 0 2
15 13 1 0 0 0 2
15 14 1 0 0 0 2
18 15 2 0 0 0 2
17 16 1 0 0 0 2
18 17 1 0 0 0 2
19 18 1 0 0 0 2
19 20 1 0 0 0 2
20 21 1 0 0 0 2
M END
";
Molecule Molecule1 = MolImporter.importMol(testMol1);
Molecule Molecule2 = MolImporter.importMol(testMol2);
MolSearch s = new MolSearch();
s.setQuery(Molecule1);
s.setTarget(Molecule2);
if (s.isMatching())
{
}
}
catch (Exception)
{
throw;
}
return(blStatus);
}
public static bool ValidateReactantsAndProductsWithReactionScheme(DataTable rxnData, string rxnScheme, out string errMsg)
{
bool blStatus = true;
string strErrMsg = "";
try
{
if (!string.IsNullOrEmpty(rxnScheme) && rxnData != null)
{
RxnMolecule rxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(rxnScheme));
if (rxnMolecule != null)
{
int reactantsCnt = rxnMolecule.getReactantCount();
int productsCnt = rxnMolecule.getProductCount();
Molecule molReactant = null;
int rctMatchCnt = 0;
string schReactInchi = "";
string tblReactInchi = "";
Molecule molProduct = null;
int prodMatchCnt = 0;
string schProdInchi = "";
string tblProdInchi = "";
//Get Reactants count
int tblRctCnt = (from r in rxnData.AsEnumerable()
where r.Field <string>("PRPNT_TYPE") == "REACTANT"
select r).Count();
//Get Products Count
int tblProdCnt = (from r in rxnData.AsEnumerable()
where r.Field <string>("PRPNT_TYPE") == "PRODUCT"
select r).Count();
//Reactants
for (int rctIndx = 0; rctIndx < reactantsCnt; rctIndx++)
{
molReactant = rxnMolecule.getReactant(rctIndx);
schReactInchi = GetStructureInchiKey(molReactant.toFormat("mol"));
for (int rxnIndx = 0; rxnIndx < rxnData.Rows.Count; rxnIndx++)
{
if (rxnData.Rows[rxnIndx]["PRPNT_TYPE"].ToString() == "REACTANT")
{
tblReactInchi = GetStructureInchiKey(rxnData.Rows[rxnIndx]["PRPNT_STRUCTURE"].ToString());
if (schReactInchi == tblReactInchi)
{
rctMatchCnt++;
break;
}
}
}
}
//Products
for (int prodIndx = 0; prodIndx < productsCnt; prodIndx++)
{
molProduct = rxnMolecule.getProduct(prodIndx);
schProdInchi = GetStructureInchiKey(molProduct.toFormat("mol"));
for (int rxnIndx = 0; rxnIndx < rxnData.Rows.Count; rxnIndx++)
{
if (rxnData.Rows[rxnIndx]["PRPNT_TYPE"].ToString() == "PRODUCT")
{
tblProdInchi = GetStructureInchiKey(rxnData.Rows[rxnIndx]["PRPNT_STRUCTURE"].ToString());
if (schProdInchi == tblProdInchi)
{
prodMatchCnt++;
break;
}
}
}
}
//Reactants count matching
if (tblRctCnt != reactantsCnt)
{
blStatus = false;
strErrMsg = "Scheme reactants count not matching with reaction reactants";
}
//Products count matching
if (tblProdCnt != productsCnt)
{
blStatus = false;
strErrMsg = "Scheme products count not matching with reaction products";
}
if (rctMatchCnt != reactantsCnt)
{
blStatus = false;
strErrMsg = "Scheme reactants are not matching with reaction reactants";
}
if (prodMatchCnt != productsCnt)
{
blStatus = false;
strErrMsg = strErrMsg.Trim() + "\r\n" + "Scheme products are not matching with reaction products";
}
}
}
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
errMsg = strErrMsg.Trim();
return(blStatus);
}
public static string GetReactionSchemeFromReactionTable(DataTable rxnData, bool atomAutoMap)
{
string strMolFile = "";
try
{
if (rxnData != null)
{
RxnMolecule rxnMol = new RxnMolecule();
MolHandler mHandler1;
//Add Reactants to RxnMol
for (int i = 0; i < rxnData.Rows.Count; i++)
{
if (rxnData.Rows[i]["PRPNT_TYPE"].ToString().ToUpper() == "REACTANT")
{
mHandler1 = new MolHandler(rxnData.Rows[i]["PRPNT_STRUCTURE"].ToString());
rxnMol.addComponent(mHandler1.getMolecule(), 0, true);
}
}
//Add Products to RxnMol
for (int i = 0; i < rxnData.Rows.Count; i++)
{
if (rxnData.Rows[i]["PRPNT_TYPE"].ToString().ToUpper() == "PRODUCT")
{
mHandler1 = new MolHandler(rxnData.Rows[i]["PRPNT_STRUCTURE"].ToString());
rxnMol.addComponent(mHandler1.getMolecule(), 1, true);
}
}
//string strSmiles = rxnMol.exportToFormat("smiles");
RxnMolecule rxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(rxnMol.toFormat("mol")));
//If Auto mapping is checked
if (atomAutoMap)
{
AutoMapper mapper = new AutoMapper();
mapper.setMappingStyle(AutoMapper.MATCHING);
try
{
mapper.map(rxnMolecule);
}
catch
{
}
}
//MolHandler mh = new MolHandler(rxnMolecule.toFormat("mol"));
//mh.clean(true, "2D");
//strMolFile = mh.toFormat("mol");// reaction.toFormat("mol");
strMolFile = rxnMolecule.toFormat("mol");
#region Code commented
//AutoMapper mapper = new AutoMapper();
////Molecule mol = MolImporter.importMol(rxnMol.exportToFormat("smiles"));
//// RxnMolecule rm = RxnMolecule.getReaction(mol);
//mapper.setReaction(rxnMol);
//mapper.setMappingStyle(AutoMapper.CHANGING);
//mapper.map(rxnMol, true);
//AutoMapper.mapReaction(rxnMol);
//MolImporter importer = new MolImporter("unmapped.smiles");
//MolExporter exporter = new MolExporter("mapped.mol", "sdf");
//AutoMapper.mapReaction(importer, exporter);
//importer.close();
//exporter.close();
//MDL.Draw.Modules.Editor.Actions.Calcs.
//GenericEditorModule mod = RenditorRxnScheme;
//MDL.Draw.Modules.Editor.Actions.Calcs.AutoMapAction mp = new MDL.Draw.Modules.Editor.Actions.Calcs.AutoMapAction();
//mp.Editor.AppendStructureToEditor(rxnMol.toFormat("mol"));
//RenditorRxnScheme.Preferences.AtomAtomDisplayMode = MDL.Draw.Renderer.Preferences.AtomAtomMappingDisplayMode.On;
//RenditorRxnScheme.Preferences.AtomChargeDisplay = true;
//RenditorRxnScheme.Preferences.StereoChemistryMode = MDL.Draw.Renderer.Preferences.StereoChemistryModeEnum.Absolute;
//RenditorRxnScheme.Preferences.ReactionCenterSize = 5.5;
//RenditorRxnScheme.Preferences.
//RenditorRxnScheme.MolfileString = rxnMol.toFormat("mol");
#endregion
}
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
return(strMolFile);
}
private static bool CompareProductsAndReactantsInTables(DataTable productData, DataTable reactantData)
{
bool blStatus = true;
try
{
int productsCnt = 0;
int reactantsCnt = 0;
RxnMolecule prodRxnMolecule = null;
RxnMolecule rctRxnMolecule = null;
Molecule molReactant = null;
Molecule molProduct = null;
MolSearch srchMol = new MolSearch();
MolSearchOptions so = new MolSearchOptions();//SearchConstants.DUPLICATE
so.setQueryAbsoluteStereo(true);
so.setChargeMatching(SearchConstants.__Fields.CHARGE_MATCHING_EXACT);
so.setDoubleBondStereoMatchingMode(StereoConstants.__Fields.DBS_ALL);
so.setImplicitHMatching(SearchConstants.__Fields.IMPLICIT_H_MATCHING_ENABLED);
so.setExactBondMatching(true);
so.setStereoSearchType(SearchConstants.__Fields.STEREO_EXACT);
so.setTautomerSearch(true);
so.setAttachedDataMatch(1);
so.setOrderSensitiveSearch(true);
so.setSearchType(5);
srchMol.setSearchOptions(so);
string rctInchi = "";
string prodInchi = "";
for (int prIndx = 0; prIndx < productData.Rows.Count; prIndx++)
{
if (!string.IsNullOrEmpty(productData.Rows[prIndx]["REACTION_SCHEME"].ToString()))
{
prodRxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(productData.Rows[prIndx]["REACTION_SCHEME"].ToString()));
productsCnt = prodRxnMolecule.getProductCount();
}
for (int rctIndx = 0; rctIndx < reactantData.Rows.Count; rctIndx++)
{
if (!string.IsNullOrEmpty(reactantData.Rows[rctIndx]["REACTION_SCHEME"].ToString()))
{
rctRxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(reactantData.Rows[rctIndx]["REACTION_SCHEME"].ToString()));
reactantsCnt = rctRxnMolecule.getReactantCount();
}
int rctLoopCnt = productsCnt < reactantsCnt ? productsCnt : reactantsCnt;
for (int p = 0; p < productsCnt; p++)
{
molProduct = prodRxnMolecule.getProduct(p);
for (int r = 0; r < rctLoopCnt; r++)
{
molReactant = rctRxnMolecule.getReactant(r);
rctInchi = ChemistryOperations.GetStructureInchiKey(molReactant.toFormat("mol"));
prodInchi = ChemistryOperations.GetStructureInchiKey(molProduct.toFormat("mol"));
if (rctInchi == prodInchi)
{
srchMol.setQuery(molReactant);
srchMol.setTarget(molProduct);
if (!srchMol.isMatching())
{
blStatus = false;
return(blStatus);
}
}
}
}
}
}
}
catch (Exception)
{
throw;
}
return(blStatus);
}