WebJul 5, 2024 · The current RDKit implementation assigns E/Z instead of using cis/trans. Re: methods There is unfortunately very little documentation available for this. You kind of just have to look at the functions/classes that are defined and “guess” (or use the RDKit C++ documentation linked from rdkit.org) Re: R/S WebMay 11, 2024 · If you are not using conda: how did you install the RDKit? Some tricks: you can split the result here using "Chem.GetMolFrags" or simply smiles.split ("."). The isotope will be the atom index of the split bond, here the bond was split between atom index 3 and 4 autodataming closed this as completed on May 13, 2024
Editing, merging, and replacing molecules in RDKit
Webdef remove_hs (self, ** kwargs): """Remove hydrogen atoms. Args: ... List of identifiers for properties to retrieve from bonds, or a callable object that receives `RDkit` bond class and returns list or value. encoder (dict): A dictionary of … WebSep 1, 2024 · This is the approach taken in the RDKit. Instead of using patterns to match known aromatic systems, the aromaticity perception code in the RDKit uses a set of rules. The rules are relatively straightforward. Aromaticity is a property of atoms and bonds in rings. An aromatic bond must be between aromatic atoms, but a bond between aromatic … chinese tapered tray qing
Getting Started with the RDKit in Python
WebApr 22, 2024 · 1 Assume that I have a molecule as below. smile = 'C (CN)SS' mol = Chem.MolFromSmiles (smile) As can be seen, N has two Hydrogen atoms and S has one Hydrogen atom. I would like to replace those Hydrogens with Carbon. I can find neighbor atoms by the following code. But, it only returns non-Hydrogen atoms. http://rdkit.org/docs/cppapi/classRDKit_1_1Bond.html WebSep 1, 2024 · I was expecting the output to be [CH2]=[CH][CH3], (three carbons, no hydrogens, no double bond stereochem). Instead I find that the output still has a hydrogen as well as double bond stereochem. Is there a proper way to remove that lingering hydrogen? Interestingly, if the input is s = 'C\C=C\*', I find that the output is C=CC. grandview yvcc