I would like to convert smiles string which has Cl or Br atoms convert to new one which has L as Cl and R as Br. I wrote simple code for my note. Result was.. OK. If I use vectrize function the performance will be increased.
I visited India this week and I came back to Japan today. When I went to Narita Air Port day before departure, the weather chill came to Japan and trains were disrupted due to a snow. The Bus from Air port to hotel was also stacked so I went to hotel by walk. It wasContinue reading “Business trip to India”
Last year researcher who is in Bio MedX published following article. https://chemrxiv.org/articles/Mol2vec_Unsupervised_Machine_Learning_Approach_with_Chemical_Intuition/5513581 And recently the article was published from ACS. The concept of mol2vec is same as word2vec. Word2vec converts word to vector with large data set of corpus and showed success in NLP. Mol2Vec converts molecules to vector with ECFP information. Fortunately Mol2Vec sourceContinue reading “mol2vec analogy of word2vec #RDKit”
To convert SDF to SMILES I write like a following code. In this way, to write smiles strings with properties it is needed to get properties by using GetProp(“some prop”). If I need several properties my code tend to be long. Greg who is developer of RDKit advised me to use SmilesMolWriter. ;) I haveContinue reading “Simple way for making SMILES file #RDKit”
Association of drug targets with diseases are important information for drug discovery. There are lots of databases to provide these information I think. I like python. ;-) So, I am interested in following article. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210543/ Opentargets is a ” a data integration and visualization platform that provides evidence about the association of known and potentialContinue reading “API for opentargets”