This is an attempt to improve the CDK HashFingerprint (Fingerprinter class). The idea behind the improved version is borrowed from my blog improvised hashing function and their impact on the fingerprints.
http://chembioinfo.com/2011/10/30/revisiting-molecular-hashed-fingerprints/
Compile with dependencies
mvn clean compile assembly:single
Test improved CDK FP
java -jar target/fingerprinter-1.0-SNAPSHOT-jar-with-dependencies.jar mol scaffold 250
Improved CDK HashedFingerprinter class with 1024 size FP
| CASES | TP | FP | TN | FN | ACCURACY | TPR | FPR | Time (mins) |
|---|---|---|---|---|---|---|---|---|
| 25*25 | 25 | 1 | 597 | 2 | 0.996 | 0.926 | 0.002 | 0 |
| 50*50 | 51 | 9 | 2433 | 7 | 0.994 | 0.880 | 0.004 | 0 |
| 75*75 | 76 | 21 | 5502 | 26 | 0.992 | 0.746 | 0.004 | 0 |
| 100*100 | 101 | 47 | 9784 | 68 | 0.989 | 0.598 | 0.005 | 0.01 |
| 125*125 | 129 | 71 | 15337 | 88 | 0.990 | 0.595 | 0.005 | 0.01 |
| 150*150 | 154 | 79 | 22155 | 112 | 0.992 | 0.579 | 0.004 | 0.01 |
| 175*175 | 183 | 106 | 30070 | 266 | 0.988 | 0.408 | 0.004 | 0.01 |
| 200*200 | 210 | 137 | 39330 | 323 | 0.989 | 0.394 | 0.004 | 0.02 |
| 225*225 | 236 | 149 | 49875 | 365 | 0.990 | 0.393 | 0.003 | 0.02 |
| 250*250 | 266 | 225 | 61489 | 520 | 0.989 | 0.339 | 0.004 | 0.02 |
Test CDK default FP
java -jar target/fingerprinter-1.0-SNAPSHOT-jar-with-dependencies.jar mol cdk 250
CDK Default Fingerprinter class with 1024 size FP
| CASES | TP | FP | TN | FN | ACCURACY | TPR | FPR | Time (mins) |
|---|---|---|---|---|---|---|---|---|
| 25*25 | 25 | 4 | 863 | 2 | 0.991 | 0.926 | 0.007 | 0 |
| 50*50 | 51 | 20 | 2422 | 7 | 0.990 | 0.880 | 0.009 | 0 |
| 75*75 | 76 | 68 | 5455 | 26 | 0.984 | 0.746 | 0.013 | 0 |
| 100*100 | 101 | 181 | 9650 | 68 | 0.976 | 0.598 | 0.019 | 0.01 |
| 125*125 | 129 | 257 | 15151 | 88 | 0.978 | 0.595 | 0.017 | 0.01 |
| 150*150 | 154 | 325 | 21909 | 112 | 0.981 | 0.579 | 0.015 | 0.01 |
| 175*175 | 183 | 648 | 29528 | 266 | 0.971 | 0.408 | 0.022 | 0.01 |
| 200*200 | 210 | 810 | 38657 | 323 | 0.972 | 0.394 | 0.021 | 0.02 |
| 225*225 | 236 | 928 | 49096 | 365 | 0.975 | 0.393 | 0.019 | 0.02 |
| 250*250 | 266 | 1240 | 60474 | 520 | 0.972 | 0.339 | 0.021 | 0.03 |
Note: New Scaffold fingerprinter reduces number of False Positives (FP) - High Accuracy