Molecular alignment is very important procedure for drug design. There are lots of way to align molecules. RDKit has lots of function to align molecules. https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html I often use Open3DALIGN or other similar methods. And recently I found another useful alignment tool for pymol named ‘mcsalign’. If reader has already installed pymol, you can useContinue reading “MCS alignment with rdkit and pymol #chemoinformatics #pymol #RDKit”
Tag Archives: pymol
Coloring molecule with RESP charge on pymol #Pymol
To visualize 3D structure of molecule, PyMol is nice tool. What I would like to write on the post is how to visualize calculated RESP charge on pymol ;)One idea is embed calculated RESP charge to b_factor of molecule pdb. PDB file can make easily from rdkit mol object.A problem for me is how toContinue reading “Coloring molecule with RESP charge on pymol #Pymol”
tensorboard embeddings + RDKit #RDKit
Mainly I use Keras for deep learning. Because Keras is easy to use and easy to understand for me. Keras has callback function to call tensorboard. But It has difficulties in use tensorboard embeddings. You know, tensorboard embeddings is unique function to visualize future of word vectors. I want to use tensorboard embeddings for visualizationContinue reading “tensorboard embeddings + RDKit #RDKit”
Handle pymol via CUI.
I often use Pymol to visualize PDB files. Recently I want to merge some PDB files in one Pymol session file from CUI. Because I run the task as batch. So I searched API document and tried it. At first I need launch pymol in silent mode ( no GUI ). And then load pdbContinue reading “Handle pymol via CUI.”
Compile LeapPython and Manipulate protein structure with Leap Motion.
I was interested in Kinect as input device, because Kinect can detect motion as input it feels feature. ;-) And some days ago, I got new input device “Leap Motion”. The Leap Motion controller is a small USB peripheral device which is designed to be placed on a physical desktop, facing upward. ( from wikiContinue reading “Compile LeapPython and Manipulate protein structure with Leap Motion.”
Call rdkit from pymol
PyMol is one of major tool for visualisation of protein, ligand, etc. You know ‘Py’ means that pymol is written using python. I want to embed pymol to web app but it’s difficult for me (technical reason..) If anyone have advice to do it, please leave comment. ;-) Next, I have one question that, pymolContinue reading “Call rdkit from pymol”
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