Questions tagged [cheminformatics]

Cheminformatics involves the production, processing, filtering, and searching of chemical information. This includes chemical databases, computational screening, searching, etc.

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OpenBabel: how to get correct SMILES from Gaussian output?

I would like to get the molecular structure as SMILES from Gaussian output files. OpenBabel seems to be the tool made for such tasks. However, the structure is not always correct. One example: ...
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138 views

What is the dataset with the largest number of molecules?

In computational chemistry we often apply techniques to all molecules of a "dataset". Recently it was asked which dataset contains the largest molecules, and a user accidentally misinterpreted this ...
5
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231 views

Pseudo 3D skeletal structure style which emphasizes geometry

If one searches and navigates to a wiki page for, say, dichlorodifluoromethane one sees the 2D skeletal structure of the compound as below This representation appears to be of a particular style that ...
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42 views

Illegal valence meaning

I'm using the rdkit package to process some molecules. I noticed that when creating a molecule from a SMILES string the library does some syntactic and some semantic checks. This question regards the ...
3
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0answers
75 views

Is there a Python module for calculating Ovality of a molecule?

Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
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38 views

Bioinformatics tools for predicting synthetic reaction for identified drugs?

We are aware of many bioinformatics open source tools like AUTODOCK, Smina for drug discovery through structure based virtual screening. I was wondering if there are validated bioinformatics tools ...
3
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25 views

Validity of graph-based molecular representation in ML

I was reading about molecular graph based generative models, which attempt to generate new molecules by training on a subset of a molecular dataset, such as QM9. In these works, there are 2 types of ...
3
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0answers
314 views

Open Babel: conversion to SMILES. How to delete H?

OpenBabel is a convenient converter between different chemical formats. If I convert to SMILES, however, although I checked the option "Delete hydrogens (make implicit)". I still have ...
3
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0answers
64 views

Matchmol for substructure determination

I'm using Checkmol/Matchmol for substructure determination and retrieval, and I'm having problems determining whether a given molecule is the substructure of another molecule when they have the same ...
3
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0answers
94 views

In QSAR, what is the simplest (but most powerful) way to create an applicability domain model?

QSAR means Quantitative Structure Activity Relationship. An applicability domain model is a model that tells you how far you are from the domain where your model was trained. I.e. it is a kind of map ...
3
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0answers
214 views

How to get the SMILES from structure without software?

Usually I use online programs and structure drawing tools to find the SMILES of a compound. How to find the SMILES without software? Where to find resources to learn it?
3
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157 views

Obtaining chemical graph complexity index from SMILES or InChl

I wonder if anyone knows a readily available way to obtain some chemical graph complexity index (like the J index) from the SMILES or InChl representations?I'm looking for some existing implementation,...
2
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40 views

On drug-like criteria and QM9 dataset

According to the book Machine Learning Meets Quantum Physics QM9 is built up from $\sim 134 \mathrm{k}$ drug-like molecules with up to nine heavy atoms (C, N, O, or F). I'm assuming that drug-like ...
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44 views

Getting warnings during SDF to PDB conversion using obabel?

I did batch conversion of SDF to PDB for the Maybridge Screening library (containing ~50000 ligands) using obabel batch conversion tool using the following code. <...
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30 views

Order of features in chemical descriptors

ECFP are small-molecule descriptors, which are usually represented as a bit vector. I wonder if order of elements of this vector matters, in other words, if this vector encodes any positional ...
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98 views

Non central chirality in cheminformatics?

What are compact cheminformatics structural representations that allow to deal correctly with axial chirality, such as in binaphthyl compounds or metal complexes?
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1answer
49 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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14 views

How to calculate Wiener index for aromatic and cyclic organic compounds?

I have been searching for literature on calculating the Wiener index for aromatic and cyclic organic compounds. For acyclic aliphatic compounds the methodology is straightforward obtained from ...
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83 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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40 views

What is molecular potency?

In the paper Junction Tree Variational Autoencoder for Molecular Graph Generation, the authors propose a ML model that is based on the message passing neural network, variational auto-encoder, the ...
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0answers
33 views

Online list of water of crystallisation?

I was extremely happy to recently receive a copy of the Nuffield Revised Book of Data but was somewhat disappointed to find that it did not list data on the water of crystallisation for various ...
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94 views

Conversion of standard InChI to InChI with fixed-hydrogen-layer

I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer: Standard InChI for Uracil: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) Desired ...
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100 views

How to store molecule data using SMILES when building a toy chemistry model

I'm currently building a toy chemistry model based around Gillespie's algorithm. Starting from a food set of {H,O,N,C} I let my system evolve, I have been storing my molecules as strings in SMILES ...
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45 views

Graph representation of polymer nanocomposites

Graph theory has been used as a means of representing molecules for decades. For a single molecule, a graph representation assigns a vertex for every atom in the molecule and the covalent bonds are ...
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47 views

How to create .CIF file from DRX data in a paper, for compound not found in crystallographic database

I tried to recover a .CIF file with the crystal structure for the compound discussed in this 2006 paper, strontium hydroxide octahydrate - $\ce{Sr(OH)2·8H2O}$ - from Cambridge Crystallographic Data ...
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28 views

How to determine if ChEMBL compound is an `agonist` or `antagonist` in assay?

In the ChEMBL database, there is an assays table that contains a standard_type column. In our case, we care only about ...