Menu
▾
▴
[Cdk-commits] SF.net SVN: cdk: [6488] trunk/cdk/src/org/openscience/cdk/test/tools/GenerateFragmentsTest.java
|
From: <ch...@us...> - 2006-06-19 11:35:23
|
Revision: 6488 Author: chhoppe Date: 2006-06-19 04:35:14 -0700 (Mon, 19 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6488&view=rev Log Message: ----------- new test case for the exclusion of small ring system (e.g. in the case if 3mem rings should be not part of the scaffold) Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/test/tools/GenerateFragmentsTest.java Modified: trunk/cdk/src/org/openscience/cdk/test/tools/GenerateFragmentsTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/tools/GenerateFragmentsTest.java 2006-06-19 11:33:08 UTC (rev 6487) +++ trunk/cdk/src/org/openscience/cdk/test/tools/GenerateFragmentsTest.java 2006-06-19 11:35:14 UTC (rev 6488) @@ -55,7 +55,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -76,7 +76,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -97,7 +97,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; @@ -122,7 +122,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; @@ -160,7 +160,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -180,7 +180,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; @@ -206,7 +206,7 @@ GenerateFragments gf=new GenerateFragments(); try { - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -229,7 +229,7 @@ GenerateFragments gf=new GenerateFragments(); try { - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -251,7 +251,7 @@ GenerateFragments gf=new GenerateFragments(); try { - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -297,7 +297,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; @@ -323,7 +323,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; @@ -354,7 +354,7 @@ GenerateFragments gf=new GenerateFragments(); try { - gf.generateMurckoFragments(mol,false,false); + gf.generateMurckoFragments(mol,false,false,4); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; for (int i =0;i<smiles.length;i++){ @@ -385,7 +385,7 @@ GenerateFragments gf=new GenerateFragments(); try { - gf.generateMurckoFragments(mol,false,false); + gf.generateMurckoFragments(mol,false,false,4); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); boolean found=false; for (int i =0;i<smiles.length;i++){ @@ -410,7 +410,7 @@ try { MDLReader reader = new MDLReader(ins); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -432,7 +432,7 @@ try { MDLReader reader = new MDLReader(new InputStreamReader(ins)); Molecule mol = (Molecule)reader.read(new Molecule()); - gf.generateMurckoFragments(mol,true,true); + gf.generateMurckoFragments(mol,true,true,4); //System.out.println("Murcko Fragments generated"); String[] smiles=gf.getMurckoFrameworksAsSmileArray(); for (int i =0;i<smiles.length;i++){ @@ -445,6 +445,26 @@ e.printStackTrace(); } } - + public void testGenerateMurckoFragments17() throws ClassNotFoundException, CDKException, java.lang.Exception { + String filename = "data/mdl/murckoTest11.mol"; + //System.out.println("\nMurckoTesting: " + filename); + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); + GenerateFragments gf=new GenerateFragments(); + try { + MDLReader reader = new MDLReader(new InputStreamReader(ins)); + Molecule mol = (Molecule)reader.read(new Molecule()); + gf.generateMurckoFragments(mol,true,true,4); + //System.out.println("Murcko Fragments generated"); + String[] smiles=gf.getMurckoFrameworksAsSmileArray(); + for (int i =0;i<smiles.length;i++){ + //System.out.println("MF"+i+" :"+smiles[i]); + } + assertEquals("C1CCc2ccccc2(C1)",smiles[0]); + assertEquals(1,smiles.length); + }catch (Exception e){ + System.out.println("Error in testGenerateMurckoFragments5:"); + e.printStackTrace(); + } + } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |