Draw scaffold tree as network with molecular image #RDKit #Cytoscape

I posted new function about scaffold tree which is implemented in rdkit 2020 03 before. In previous my post, I showed example to draw scaffold tree with networkx. It could draw the scaffold tree as a network but molecular structures are not shown on the node. For chemist, structure image is important so I tried

Handling chemoinformatics data with pandas #RDKit #chemoinformatics

I often use Pandas for data analysis. RDKit provides useful method named PandasTools. The method can load sdf and return data as pandas dataframe. By using dataframe, It isn’t needed to do something with for loop. I found an interesting information in rdkit issues. A package named pyjanitor. The package wraps pandas and provides useful

New version of openforcefield supports RDKit! #RDKit #chemoinformatics #openforcefield

In this morning I found great news on my tiwtter TL that openforcefield supports RDKit! Older version of openforcefiled is required openeyeTK which is commercial license for industry. I had interested in the package but could not install because I’m not academia and our company does not OETK license now. https://open-forcefield-toolkit.readthedocs.io/en/latest/releasehistory.html I can’t wait to

Make Graph convolution model with geometric deep learning extension library for PyTorch #RDKit #chemoinformatics #pytorch

In the chemoinformatics area, QSAR by using molecular graph as input is very hot topic. Examples of major implementations are deepchem and chainer-chemistry I think. I also have interest about Graph based QSAR model building. Recently I am using pytorch for my task of deeplearning so I would like to build model with pytorch. Fortunately

Generate possible heteroaromatic cores from query molecule #RDKit #chemoinformatics

Hetero shuffling is the approach which replace atoms of scaffold and generate new molecule with atom replaced scaffold. For example benzene as core, examples of shuffled cores will be pyridine, pyrimidine etc. The approach is often used medicinal chemistry project to improve ADMET properties, biological activities and also used for substance patent claim strategy. Native

Draw molecular network on Jupyter notebook with rdkit and cytoscape.js-2 #RDKit #cytoscape

Yesterday, I posted about cyjupyter. And got comment how to render the compound name on each node. I think it is possible to use context attribute in style settings. Let’s try. Code is almost same as yesterday Networkx is easy to make network with many attributes. I set smiles as name attribute. OK let’s draw

Draw molecular network on Jupyter notebook with rdkit and cytoscape.js #RDKit #cytoscape

I use cytsocape and cytoscape.js when I would like to draw molecular network. Molecular network can be made from similarity, matched molecular pair etc. In cytoscape there is a plug in for drawing chemical structures named ‘chemviz‘. There is no plugin for cytoscape.js. So it is needed for drawing function which draw chemical structures as

Make MMP network and send to cytoscape #chemoinfo

Recently I use cytoscape in my laboratory. You know Cytoscape is nice tool for network visualization. I often make data with python and import data from cytoscape. The work flow is not so bad but I am thinking that it will be nice if python can communicate with cytoscape. Fortunately cytocape has REST plugin called

Cytoscape and MMP

I posted an example about cytoscape.js using molecular similarity. Cytoscape.js is cool but not good for lots of data. I tried to make network that has 1000 nodes. My PC freeze…. So I go back to cytoscape. Today I made network from mmpa data for example. If you had rdkit, make mmp is very easy.

similarity network using cytoscape.js.

Lots of relationships are presented as graph. For example, if I set molecule as node, and similarity as edge, I could make molecular networks. Cytoscape.js is one of the good tool. It is an open-source JavaScript graph theory library for analysis and visualisation. And works on server side. So, Not depend on client machine. I