Supporting Information. Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit

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1 Supporting Information Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit Chen Jiang, *, Xi Jin, Ying Dong and Ming Chen Department of Organic Chemistry, China Pharmaceutical University, Nanjing , Jiangsu, China. Department of Foreign Languages, China Pharmaceutical University, Nanjing , Jiangsu, China * Corresponding Author, partridge@cpu.edu.cn S1

2 Table of Content Detailed Description of Unit Tests of Kekule.js S3 Comparison of Executing Speed between Native and Emscripten Compiled OpenBabel S5 Comparison of Composer Widget and Other Web Molecule Editors S6 Demos of Kekule.js Tutorial of Kekule.js Unit Test of Kekule.js demos.zip tutorial.zip unittest.zip S2

3 Detailed Description of Unit Tests of Kekule.js A series of unit tests are used to ensure the correctness of our molecule algorithm implementations. Most of those tests are directly borrowed from CDK or RDKit. For instance, an all-ring-finder test borrowed from CDK: /////////////////////////////////////////////////////////////// /// Java test code in CDK, /// which load molecule from porphyrin.mol /// and check if the ring number is 20. ////////////////////////////////////////////////////////////// public void testporphyrine() throws Exception { IRingSet ringset = null; AllRingsFinder arf = new AllRingsFinder(); String filename = "data/mdl/porphyrin.mol"; InputStream ins = this.getclass().getclassloader().getresourceasstream(filename); MDLV2000Reader reader = new MDLV2000Reader(ins); IChemFile chemfile = (IChemFile) reader.read(new org.openscience.cdk.chemfile()); IChemSequence seq = chemfile.getchemsequence(0); IChemModel model = seq.getchemmodel(0); // Getting molecule IAtomContainer molecule = model.getmoleculeset().getatomcontainer(0); // Finding all rings of molecule ringset = arf.findallrings(molecule); // Checking if the ring number is 20 Assert.assertEquals(20, ringset.getatomcontainercount()); } /////////////////////////////////////////////////////////////// /// JavaScript test code in our toolkit, almost translated directly from CDK. /////////////////////////////////////////////////////////////// it('ring test on external file: Porphyrine', function(done){ var MB = TestMolBuilder; // Loading molecule from external file MB.loadExternalData('mdl/porphyrin.mol', function(mol){ expect(mol).not.tobenull(); // Finding all rings of molecule var rings = mol.findallrings(); // Checking if the ring number is 20 S3

4 expect(rings.length).toequal(20); done(); }); }); Other algorithm tests, like aromatic detection and stereo identification, are formed in the same way. The source code of those unit tests can also be found at unittest.zip in supporting information of this manuscript or at Kekule.js GitHub site ( S4

5 Comparison of Executing Speed between Native and Emscripten Compiled OpenBabel The comparison tests are taken on a PC with Intel Xeon E3-1230V2 CPU, 8G DDR memory and Windows 8.1. The executing time of native code of OpenBabel is measured by obgen.exe shipped with OpenBabel Package for Windows. Compiled JavaScript code is tested in three web browsers: Firefox 48.0a2, Google Chrome m and IE Different molecules are used as input and OpenBabel force field calculation is performed to generate the 3D structures of molecule. The default parameters and force field MMFF94 are used for all of those tests. The result is shown in figure S1, executing times are in seconds: Figure S1. Executing time of force field calculation of Native and JavaScript code of OpenBabel It is obvious that Firefox is the fastest web browser to run the JavaScript code compiled by emscripten in this test, only about second slower than native code, nearly as fast as native code for long-time jobs. S5

6 Comparison of Composer Widget and Other Web Molecule Editors Composer, an encapsulated molecule editor, is one of the most important chemistry widgets shipped with Kekule.js. It is capable of handling both molecule structure and other objects such as text block and reaction symbols. It also supports unlimited undo/redo stack, clipboard operations and styles setting for individual chemical object, including (but not limited to) color, stroke width, font and text size of atom and bond. Table S1 is a feature matrix of composer widget and existing web molecule editors. The comparison mainly compares the basic ability of inputting molecules and does not involve in advanced features (e.g., mapping of reaction atoms). The features of other web editors are inspected by ourselves. If there exists mistakes, please let us know and we are happy to correct them. S6

7 Table S1. Comparison of Composer Widget and Other Web Molecule Editors ChemWriter c Marvin for JSDraw e MolSoft Editor Name JSME a ChemDoodle 2D Sketcher b JavaScript d HTML5 Molecule Editor f Molecule Structure Input Non-structure Input Style k Normal Bond Stereo Bond ICEdit g Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Atom Y Y Y Y Y Y Y Y Isotope N N Y Y Y N Y Y Atom Y Y N Y Y N Y Y Variations h Charge Y (1) Y Y Y Y Y Y Y Multiple N Y Y Y Y Y Y Y Molecules i Molecule Formula N N N N N N N Y Text N N N Y Y N Y Y Glyph j N N N Y Y N Y Y Text Formats N N N N N N N Y Color N N N N N N N Y Composer Widget Kekule.js in S7

8 Interaction Select l N Y Y Y Y Y Y Y I/O Remove m Y Y Y Y Y Y Y Y Move n Y Y N Y Y Y Y Y Scale o N N N N N N Y Y Rotate p N Y N Y N N N Y Copy/Paste N N N Y Y N Y Y Undo/Redo Y Y Y Y Y Y Y Y Load from String Save String to Load from File Save File Input Formats Output Formats to Y Y Y Y N Y N Y Y Y Y Y N Y N Y Y N N Y Y N N Y N Y N Y Y N N Y MDL (2), SMILES MDL (2), SMILES MDL (2) MDL (2) MDL (2), SMILES, MDL, ROSDAL, SK2, CDX, CML, InChI, JDX, InChi, CDX (3) CML, MDL (2) MDL (2), SMILES, InChi, CDX (3) CML, MDL (2), SMILES, SKC, CDX (4) CML, MDL (2), SMILES, SKC, CDX (4) CML, MOL, SMILES (3) - MDL (2), CML (5) MOL, SMILES (3) - MDL (2), CML, SMILES (5) SKC, MOL2, PDB, SLN, XYZ, SMILES (4) Require Backend Server q N Y N Y Y Y N N Price Free Free and Open Commercial Commercial Free Free for Unknown Free and Open S8

9 Source Personal and Academic Source a. b. c. d. e. f. g. h. Atom variations: including variable atom, pseudo atom, subgroup and so on. i. Multiple molecules: whether more than one molecule can be created and edited at once. j. Glyph: such as shapes and reaction symbols. k. Style: whether outlook style of individual element can be set in editor. E.g., font and size of atom symbol, color of atom or bond. l. Select: the ability to select a range of atoms and bonds. m. Remove: the ability to delete partial of atoms and bonds. n. Move: the ability to move selected atoms and bonds. o. Scale: the ability to scale the sizes of bonds and distances of atoms in selection. p. Rotate: the ability to rotate atoms and bonds in selection. q. Whether some functions of the editor depend on a backend server. (1) JME only supports charge of +1/-1. (2) MDL formats, a series connection table based formats proposed by MDL, including MOL2000, MOL3000, SDF and so on. (3) Formats other than MDL need a server side conversion. (4) All formats need a server side conversion. (5) Supports tens of more formats when OpenBabel-js module is used S9

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3D Molecule Viewer of MOGADOC (JavaScript)

3D Molecule Viewer of MOGADOC (JavaScript) Movement of the Molecule Rotation of the molecule: Use left mouse button to drag. Translation of the molecule: Use right mouse button to drag. Resize the molecule: