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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,3 @@ | ||
| .settings | ||
| bin | ||
| .DS_Store |
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30 changes: 30 additions & 0 deletions
30
plugins/net.bioclipse.data.sampledata/data/Javascripts/buildmol.js
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| @@ -0,0 +1,30 @@ | ||
| /******************************************************************************* | ||
| * Bioclipse-script to iteratively build a molecule in JChemPaint | ||
| * Author: Ola Spjuth | ||
| * Author: Egon Willighagen | ||
| ******************************************************************************/ | ||
|
|
||
| //Start with a carbon and open in JCP | ||
| mol=cdk.fromSMILES("C") | ||
| mol2=cdk.generate2dCoordinates(mol) | ||
| ui.open(mol2) | ||
|
|
||
| //Add some atoms and bonds and wait 1 sec in between | ||
| atom=jcp.getModel().getAtomContainer().getAtom(0); | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| jcp.addPhenyl(atom) | ||
| js.delay(1) | ||
| molecule=jcp.getModel().getAtomContainer() | ||
| atom=molecule.getAtom(molecule.getAtomCount()-1); | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| atom=jcp.addAtom("C", atom) | ||
| js.delay(1) | ||
| jcp.addRing(atom,5) |
8 changes: 8 additions & 0 deletions
8
plugins/net.bioclipse.data.sampledata/data/Javascripts/dlPDBrotate.js
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|---|---|---|
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| //Download PDB | ||
| mol=ws.queryPDB("1d66") | ||
| ui.open(mol.get(0)) | ||
|
|
||
| //Do some jmol visualization | ||
| jmol.run("move 0 0 90 00 0 0 0 0 1;set selectionhalos off; select all; spacefill 0; cartoon on;") | ||
| jmol.run("select nucleic; isosurface dna1 solvent; delay 1; color isosurface red;"); | ||
| jmol.run("delay 1; color isosurface blue; delay 1; color isosurface translucent; move 0 360 90 90 0 0 0 0 4;"); |
8 changes: 8 additions & 0 deletions
8
plugins/net.bioclipse.data.sampledata/data/Javascripts/dnaiso.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| //Download PDB via Web service at EBI and open in Jmol | ||
| mol=ws.queryPDB("1d66") | ||
| ui.open(mol.get(0)) | ||
|
|
||
| //Execute some jmol script commands | ||
| jmol.run("select all; spacefill 0; wireframe off; cartoon on;select none") | ||
| jmol.run("select !dna; isosurface solvent; select none; color isosurface blue") | ||
| jmol.spinOn() |
3 changes: 2 additions & 1 deletion
3
plugins/net.bioclipse.data.sampledata/data/Javascripts/extractsmiles.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| //Output SMILES for all molecules in an SDFile | ||
| var mols = cdk.loadMolecules("/Sample Data/SDF/Fragments2.sdf"); | ||
| for (var i = 0; i < mols.size(); i++) { | ||
| print(cdk.calculateSMILES(mols.get(i)) + "\n"); | ||
| js.print(cdk.calculateSMILES(mols.get(i)) + "\n"); | ||
| } |
7 changes: 4 additions & 3 deletions
7
plugins/net.bioclipse.data.sampledata/data/Javascripts/extractsmilesAndMass.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,11 @@ | ||
| //Output SMILES and MASS for all molecules in an SDFile | ||
| var mols = cdk.loadMolecules("/Sample Data/SDF/Fragments2.sdf"); | ||
|
|
||
| for (var i = 0; i < mols.size(); i++) { | ||
| var mol = mols.get(i); | ||
|
|
||
| print(cdk.calculateMass(mol) + | ||
| "\t" + | ||
| cdk.calculateSMILES(mol) + | ||
| js.print( cdk.calculateSMILES(mol) + | ||
| ": \t" + | ||
| cdk.calculateMass(mol) + | ||
| "\n" ); | ||
| } |
40 changes: 40 additions & 0 deletions
40
plugins/net.bioclipse.data.sampledata/data/Javascripts/gencoords.js
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| /******************************************************************************* | ||
| * Bioclipse-script to generate different coordinates on a list of molecules. | ||
| * Author: Ola Spjuth | ||
| ******************************************************************************/ | ||
|
|
||
| //Create list of molecules | ||
| mols=cdk.createMoleculeList(); | ||
| mols.add(cdk.fromSMILES("CCC")); | ||
| mols.add(cdk.fromSMILES("CCCNCC")); | ||
| mols.add(cdk.fromSMILES("CCNCCOC(C)CC")); | ||
|
|
||
| //Print out molecules with no coordinates | ||
| js.print("\n\nWe have " + mols.size() + " mols in list: mols\n"); | ||
| for (i=0; i<mols.size();i++){ | ||
| js.print( i +" has 2D: " + cdk.has2d(mols.get(i)) + " , has 3D:" + cdk.has3d(mols.get(i)) +" \n"); | ||
| } | ||
|
|
||
| //Generate 2D coordinates from no coordinates | ||
| mols2=cdk.generate2dCoordinates(mols); | ||
| js.print("\nWe have " + mols2.size() + " mols in list: mols2\n"); | ||
| for (i=0; i<mols2.size();i++){ | ||
| js.print( i +" has 2D: " + cdk.has2d(mols2.get(i)) + " , has 3D:" + cdk.has3d(mols2.get(i)) +" \n"); | ||
| } | ||
|
|
||
| //Generate 3D coordinates from no coordinates | ||
| mols3=cdk.generate3dCoordinates(mols); | ||
| js.print("\nWe have " + mols3.size() + " mols in list: mols3\n"); | ||
| for (i=0; i<mols3.size();i++){ | ||
| js.print( i +" has 2D: " + cdk.has2d(mols3.get(i)) + " , has 3D:" + cdk.has3d(mols3.get(i)) +" \n"); | ||
| } | ||
|
|
||
| //Generate 3D coordinates from 2D coordinates | ||
| mols4=cdk.generate3dCoordinates(mols2); | ||
| js.print("\nWe have " + mols4.size() + " mols in list: mols4\n"); | ||
| for (i=0; i<mols4.size();i++){ | ||
| js.print( i +" has 2D: " + cdk.has2d(mols4.get(i)) + " , has 3D:" + cdk.has3d(mols4.get(i)) +" \n"); | ||
| } | ||
|
|
||
| //Test open MolTable on Molecules with 5D | ||
| ui.open(mols); |
5 changes: 5 additions & 0 deletions
5
plugins/net.bioclipse.data.sampledata/data/Javascripts/jcpcustom.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| //Create a molecule from SMILES, open in JCP and customize rendering | ||
| mol=cdk.fromSMILES("C1CCCCC1CC(CCO)CCNC") | ||
| mol2=cdk.generate2dCoordinates(mol) | ||
| ui.open(mol2) | ||
| jcpglobal.setShowAromaticity(true) |
19 changes: 19 additions & 0 deletions
19
plugins/net.bioclipse.data.sampledata/data/Javascripts/jmolExample.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| //Generate molecule from SMILES and generate 3D coordinates with CDK | ||
| mol = cdk.fromSMILES("C(C1C(C(C(C(O1)O)O)O)O)O"); | ||
| mol = cdk.addExplicitHydrogens(mol); | ||
| cdk.generate3dCoordinates(mol); | ||
|
|
||
| //Save to file in CML | ||
| fileName = "/Virtual/" + cdk.molecularFormula(mol) + ".cml"; | ||
| if ( ui.fileExists(fileName) ) { | ||
| ui.remove(fileName); | ||
| } | ||
| cdk.saveCML(mol, fileName); | ||
|
|
||
| //Open file and do some Jmol scripting | ||
| ui.open(fileName); | ||
| jmol.run("background black"); | ||
| jmol.run("set echo botom left; echo Mass: " + cdk.calculateMass(mol)) | ||
| jmol.run("select all; dots on; select none"); | ||
| jmol.minimize(); | ||
| jmol.run("move 60 360 30 -45 0 0 0 0 7"); |
7 changes: 7 additions & 0 deletions
7
plugins/net.bioclipse.data.sampledata/data/Javascripts/multimol.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| //Demonstrates basic manipulation of multiple molecules in Bioclipse | ||
| //Requires sample data installed in default location | ||
| mols=cdk.loadMolecules("/Sample Data/SDF/Fragments2.sdf") | ||
| mols.size() | ||
| mol=mols.get(3) | ||
| cdk.calculateSMILES(mols.get(4)) | ||
| ui.open(mols) |
30 changes: 30 additions & 0 deletions
30
plugins/net.bioclipse.data.sampledata/data/SMILES/sample30.smi
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| C(=O)N(Cc1ccco1)C(c1cc2ccccc2cc1)C(=O)NCc1ccccc1 1 | ||
| C(=O)(C=CC)N(CCCCCCC)C(c1cc2c(cccc2)c2ccccc12)C(=O)NC(C)(C)C 2 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1oc(C(F)(F)F)cc1)C(c1ccccc1)C(=O)NCc1ccccc1 3 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccco1)C(c1ccccc1)C(=O)NCc1ccccc1 4 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccc(o1)C)C(c1ccc(OC)c(c1)OC)C(=O)NCc1ccccc1 5 | ||
| C(=O)(C=CC)N(Cc1ccccc1)C(c1cc2c(cccc2)c2ccccc12)C(=O)NC(C)(C)C 6 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccc(o1)C)C(c1ccccc1)C(=O)NC(C)(C)C 7 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccco1)C(c1ccccc1)C(=O)NC(C)(C)C 8 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccc(o1)C)C(c1ccc2OCOc2c1)C(=O)NC(C)(C)C 9 | ||
| C(=O)(CNC(=O)OC(C)(C)C)N(Cc1ccco1)C(c1ccc(OC)c(c1)OC)C(=O)NC(C)(C)C 10 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCC)C(c1cccc(c1O)OC)C(=O)NCc1ccccc1 11 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCCC)C(c1cccc(c1O)OC)C(=O)NCc1ccccc1 12 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCC 13 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCC 14 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCC 15 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCC)C(c1cccc(c1O)OC)C(=O)NCCCC 16 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(Cc1ccco1)C(c1ccc(OC)c(c1)OC)C(=O)NCCCC 17 | ||
| C(=O)N(Cc1ccco1)C(c1cc2ccccc2cc1)C(=O)NCCCC 18 | ||
| C(=O)N(Cc1ccc(o1)C)C(c1cc2ccccc2cc1)C(=O)NCCCC 19 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCCC 20 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCCC 21 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCCCCCCC)C(c1cccc(c1O)OC)C(=O)NCCCCC 22 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(CCC)C(c1cccc(c1O)OC)C(=O)NCCCCC 23 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(Cc1ccc(o1)C)C(c1ccc(OC)c(c1)OC)C(=O)NCCCCC 24 | ||
| C(=O)(C(NC(=O)OC(C)(C)C)CC1c2ccccc2NC1)N(Cc1ccco1)C(c1ccc(OC)c(c1)OC)C(=O)NCCCCC 25 | ||
| C(=O)N(CCCCCC)C(c1cc2ccccc2cc1)C(=O)NCCCCC 26 | ||
| C(=O)(CCCc1ccc2ccc3cccc4ccc1c2c34)N(C)C(c1cc2ccccc2cc1)C(=O)NC(C)(C)C 27 | ||
| C(=O)(c1cccc(O)c1O)N(C)C(c1ccc(c2ccc(OC)cc12)OC)C(=O)NCS(=O)(=O)c1ccc(cc1)C 28 | ||
| C(=O)(c1c(cc(O)cc1O)O)N(C)C(c1ccc(O)c(c1)O)C(=O)NCS(=O)(=O)c1ccc(cc1)C 29 | ||
| C(=O)N(Cc1ccc(o1)C)C(c1ccccc1)C(=O)NCS(=O)(=O)c1ccc(cc1)C 30 |
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