Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

Dear JP, To confuse you even more, you can also have a look at the ChEMBL open-source molecular standardizer: https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py No need to thank me. :D On 18/06/2021 03:12, JP Ebejer wrote: Dear all, I

Re: [Rdkit-discuss] Autodock Vina

Hi Valik, I do this on a regular basis for our generators here. Basically what you will need is to: 1. Generate 3D structures for the molecules (RDKit can do that) 2. Save to SDF files (again, RDKit) 3. Convert to PDBQT (I use OpenBabel: "$ obabel -isdf structures.sdf -opdbqt -Oname-.pdbqt -m")

Re: [Rdkit-discuss] [ext] Re: Autodock Vina

Hi Velik, though unrelated to RDKit ... in our TeachOpenCADD platform - though still living in an PR to be released soon (PR #74) - we talk about protein-ligand docking using smina (starting

Re: [Rdkit-discuss] Autodock Vina

Hi Velik, This is a discussion list for the RDKit, not for Autodock Vina. Here's the link for getting help about Autodock Vina: http://vina.scripps.edu/questions.html Best, -greg On Tue, Jun 22, 2021 at 10:08 AM Velik Velikov wrote: > Dear all, > > > > I am constructing new molecules (de

[Rdkit-discuss] Autodock Vina

Dear all, I am constructing new molecules (de novo design) that are drug-like with RDKit. I have my molecules in SMILES now and I need to check them with AutoDock Vina. I have never used it and I have been trying since last week but I kind of don’t know where to go from here. What is my config

Re: [Rdkit-discuss] Searching in (Downloaded) Databases

Hi Philipp, It looks like the supplier thinks the line index has gone past the end of file. 1) How large is the SMILES file which leads to this error (ls -l)? 2) Does it consistently happen at the same line number? You can check this with something like: suppl = Chem.SmilesMolSupplier(infile,

[Rdkit-discuss] Searching in (Downloaded) Databases

Hey you lovely people, as I am creating a set of building blocks for my in-silico reaction, I downloaded various accessible databases (ChemBL28, GDB13, GDB17, Pubchem, emolecules and mcule) and want to just work through them with "HasSubstructMatch". Unfortunately I run into a "File parsing error: