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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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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132 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 ...
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143 views

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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56 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 ...
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87 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 ...
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206 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?
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151 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,...
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27 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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185 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 ...
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91 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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62 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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37 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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31 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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91 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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99 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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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 ...