Cheminformatics2011-11-22T12:34:51+00:00/groups/1252017-04-28T21:00:41+00:00jayadeepa rajamani murugesan joined the Cheminformatics groupurn:uuid:7fe50f7b-4e8f-4a7f-bb1d-547494c44d7djayadeepa rajamani murugesan2017-02-05T14:17:02+00:00Dr Kaveh Ostad Ali Askari joined the Cheminformatics groupurn:uuid:60e76e1a-296c-459a-ab3b-09d59f19e790Dr Kaveh Ostad Ali Askari2016-10-26T20:14:01+00:00Derek Essegian joined the Cheminformatics groupurn:uuid:29400d6f-5e78-4f84-a527-47e87a03e49fDerek Essegian2016-10-17T12:09:19+00:00José Teófilo Filho joined the Cheminformatics groupurn:uuid:17447134-73a8-459e-81fe-203821e95136José Teófilo Filho2016-01-05T11:22:48+00:00Paul Boardman joined the Cheminformatics groupurn:uuid:084f0057-f3ee-439f-94fa-7a65a50d880bPaul Boardman2014-05-30T07:18:34+00:00Dr. Suneel Kumar BVS joined the Cheminformatics groupurn:uuid:2c80489b-dbb2-454b-a826-8334a17660e2Dr. Suneel Kumar BVS2013-08-13T08:06:44+00:00sauberns shared Indigo-pains-recursive*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries *** The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list. Using the WEHI-10k reference set (embedded in the workflow), I get ~10% time reduction. Not as good as parallelizing the process, but welcome nonetheless. At the end of the process, the list of failures indicates only the first PAINS query that was matched, rather than multiple PAINS queries that were matched to that structure. Otherwise, exactly the sam …urn:uuid:be16cfbb-31f3-4bef-9d69-e93533f9479dsauberns2013-07-30T20:53:34+00:00Egon Willighagen shared Find isotopes with a certain exact matchThis script lists all isotopes matching a certain exact mass (given a certain error) and outputs the symbol, atomic number, and exact match of the search hits.urn:uuid:c528aa6f-adfd-434c-8a6c-a714d119255fEgon Willighagen2013-05-14T23:54:22+00:00sauberns shared Chemical structure extractor - img2structureExtracts images of chemical structures from PDFs and converts them to usable structure data using the OSRA binaries. An in-progress (incomplete) workflow. This workflow makes use of the External Tool node to access the OSRA structure recognition binaries. So you must have a functioning installation of OSRA and it's dependencies. This may require advanced compiler knowledge on your platform, and may not be a trivial task. OSRA 1.4 is free for both the source & binary distribution. OSRA 2.0 source is free, but the binaries require a small fee. Requirements: KNIME 2.7.4 Community Nodes - RDKit (to view structures) See http://tech.knime.org/community OSRA 1.4 http://osra.sourceforge.net/   Start by creating a working directory where you can put the test PDF and some other files. Then try t …urn:uuid:ad52b08d-e116-4291-8133-2fd9afc04d87sauberns2013-05-08T14:51:56+00:00Paul Dobson shared CDK ExampleThis workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five. It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Lipinski, and creates PNG images of those structures that contain the substructure. The image results will be found in your Taverna Data folder.urn:uuid:5a5e47a9-2ef5-4e96-9895-ef1aba30aff8Paul Dobson2013-04-23T11:23:29+00:00sauberns shared Chemical term extractor - text2structureThis workflow demonstrates how to extract biological and chemical terms (text!) from a PDF file using the KNIME text processing nodes and attempts to convert the chemistry terms to structures. Requirements: KNIME 2.7.4 KNIME Labs nodes - Text Processing Community Nodes - RDKit (to view structures) See http://tech.knime.org/community Start by selecting the folder containing the PDF documents. Alternatively, you can use a folder with Word docs.urn:uuid:305ecdbf-1b8e-4636-a180-fd6184f56390sauberns2012-09-24T11:49:08+00:00Giribio joined the Cheminformatics groupurn:uuid:8fc65fe4-5a98-4ac3-9ab4-9af035dfc66dGiribio