Syed Asad Rahman asad
asad
/ SMSD Paper Test Cases
Created
July 28, 2010 06:01
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| KEGG MSD | |
| C02447 3257 | |
| C02668 37992 | |
| C02668 121250 | |
| C04054 1137 | |
| C04382 37992 | |
| C04480 3257 | |
| C04804 3257 | |
| C06185 121251 | |
| C06544 121745 |
asad
/ MCS search
Created
April 26, 2010 18:54
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| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | |
| // Benzene | |
| IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1"); | |
| // Napthalene | |
| IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2"); | |
| //{ 0: Default SMSD Algorithm, 1: MCSPlus Algorithm, 2: VFLibMCS Algorithm, 3: CDKMCS Algorithm} | |
| //Bond Sensitive is set true | |
| SMSD comparison = new SMSD(Algorithm.DEFAULT, true); | |
| // set molecules and remove hydrogens | |
| comparison.init(A1, A2, true); |
asad
/ Substructure search
Created
April 26, 2010 18:52
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| SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); | |
| // Benzene | |
| IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1"); | |
| // Napthalene | |
| IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2"); | |
| //Turbo mode search | |
| //Bond Sensitive is set true | |
| SMSD comparison = new SMSD(Algorithm.SubStructure, true); | |
| // set molecules and remove hydrogens | |
| comparison.init(A1, A2, true); |
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| EBI 11210921182D | |
| 3 3 0 0 0 0 999 V2000 | |
| 0.5048 2.1204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 0.0923 1.4060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 0.9173 1.4060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 1 2 1 0 0 0 0 | |
| 2 3 1 0 0 0 0 | |
| 1 3 1 0 0 0 0 |
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| 3292 | |
| Marvin 07240902122D | |
| 82 87 0 0 0 0 999 V2000 | |
| 7.0737 -0.4431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 6.3592 -2.2845 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
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| 4.5429 -0.1272 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
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| 4.1032 -0.4133 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 3292 | |
| Marvin 07210922142D | |
| 52 57 0 0 0 0 999 V2000 | |
| 9.2616 1.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 8.5472 1.5125 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 8.1347 2.2270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 8.9597 0.7980 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 7.8327 1.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 7.1182 1.5125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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