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• 22:15, 20 February 2024 Mtsukanov talk contribs created page Covalent Library Preparation 2024 (Created page with "Modify warhead to covalent adduct with SiH3 added. == Prepare “SMILES ID” file. == ssh n-1-17 (or another development node) Source environment with RDkit source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh conda activate base3.7 python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes...")
• 18:51, 10 August 2023 Mtsukanov talk contribs created page CLI Enumeration (Created page with "== Coding the Reactions == Step 1. Pick out the reactions that you want to enumerate. This can be done either through already-made reactions that are in commons.docking.org or you can use those reaction SMARTS and inclusion/exclusion SMARTS as examples/guidelines to make your own reaction/s. We recommend using the daylight SMARTS as a resource if you plan on doing this: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. Once you have your reaction we recomme...")
• 21:20, 23 May 2023 Mtsukanov talk contribs created page Particle Shape Calculator for CCDC/Mercury (Created page with "This tutorial will introduce you to the morphology calculation features included with Mercury under the CSD-Particle toolset, namely BFDH Morphology and VisualHabit. BFDH crystal morphology is an approximation based on crystallographic geometrical considerations. For a given structure, the BFDH algorithm will predict the habit or shape of a crystal using the corresponding unit cell and symmetry operator information. The VisualHabit tool calculates a morphology for your m...")
• 18:50, 21 March 2023 Mtsukanov talk contribs created page AB3 Developer Notes (Created page with "'''UNDER DEVELOPMENT''' The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first...")
• 05:13, 29 August 2022 Mtsukanov talk contribs created page Bioisostere Tool (Created page with "BAT or Bioisostere Analoging Tool is a tool designed by the Irwin Lab for the purpose of analoging molecules. The tool creates analogs through interchanging the substructures...")
• 23:31, 27 August 2022 Mtsukanov talk contribs created page ABBB (Created page with "ABBB or Analog By Building Block is a tool designed by the Irwin Lab for the purpose of analogizing molecules. The molecules that are given to the tool are first retrosynthesi...")