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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14 views

Where to find DFT Datasets with 3D Electron Density values?

This may be dumb question. Please bear with me. Where can I find datasets with 3D electron density values and any related physical property. I have looked up the QM9 dataset as well, but since I am ...
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1answer
44 views

SMART string for alkyl group excluding alcohols

I'm quite new to the usage of SMARTS strings. I would like to find all alkyl groups (but no $\ce{CH3})$ in a component, here e.g. cyclohexanol (C1CCC(CC1)O). My ...
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111 views

Are molecular properties robust towards manipulations? [closed]

Machine learning algorithms analyze molecules by looking at their molecular representations (e. g. SMILES and graph) and turning them into feature maps that help the algorithm to distinguish them. In ...
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1answer
40 views

Using RDKit to determine “nonring, nonterminal atoms”

I am a non-chemist using RDKit to determine the number of "nonring, nonterminal atoms" in a molecule. I can't find anything in the RDKit documentation that helps with "nonterminal"....
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1answer
46 views

Using RDKit to count “RR, the number of rigid single or fused ring systems in the molecule”

I am a computer scientist, not a chemist, working with RDKit. I need to compute something described to me as "RR, the number of rigid single or fused ring systems in the molecule." I know I ...
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1answer
47 views

Best Cheminformatics API for drawing SMARTS reactions?

I have a need to automatically draw SMARTS reactions. Rdkit's drawings are suboptimal. OpenBabel's drawings don't work properly on macOS. Indigo's drawings are cut off half the page. I would love to ...
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2answers
130 views

Why don’t we have a list of all compounds yet?

With only three basic particles making up atoms, and their interaction fairly well understood (we can even predict the chemical properties of elements we have not yet discovered) atoms seem to be like ...
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16 views

SMARTS string matching an aldehyde or a ketone where the target alpha carbon is less substituted than the other carbon

I need a SMARTS string that matches the following critereon: It makes an aldehyde or a ketone only The target carbon is an alpha carbon The other alpha carbon must be more substituted (or be an ...
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1answer
66 views

Representing conformers using SMILES and Graph representations

I was wondering if either of SMILES or graph representations (in their vanilla form) can distinguish between two conformers of the same molecule. Can this be enhanced by adding additional metadata on ...
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1answer
81 views

How to convert Excel comments to ChemDraw .cdx?

Not sure whether this might be a Superuser or StackOverflow question... but I hope some Chemist can help me with this. I have an Excel table with cells which contain comments "by Cambridge Soft&...
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1answer
24 views

How to interpret BRICS fragments

I have a molecule with a SMILES string as given below. smi='c1ccccc1OCCOC(=O)CC' I want to obtain BRICS based fragments which I did as follows. ...
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1answer
159 views

Converting SMILES string into valid sub-strings

I have a SMILES string as follows. smi= 'CCOC(=O)C1=C(COCCN)NC(C)=C(C(=O)OC)C1c1ccccc1Cl' Is there anyway that I convert this SMILES string into valid sub-strings ...
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1answer
29 views

Why should duplicates compounds be removed from compound libraries before screening/activity prediction?

This is one of the first steps to be done while analysing chemical data or applying training models to predict chemical activity. However, I am unclear as to why is this done. Doe sit have a major ...
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364 views

How to convert an XYZ file to Z-matrix?

I would like to generate a Z-matrix from the following XYZ file (C2H6dimer.xyz): ...
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2answers
105 views

How to compare three or more molecular structures? [closed]

Let's say you have three or more different geometry files (xyz) for the same structure and you want to compare them. What would be best way for that?
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45 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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2answers
227 views

SMILES string convertors

I'm new to SMILES strings, and have noticed that they're not standardised. Firstly, what is the reason for different structures of SMILES strings to represent the same compound? Why not have a ...
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1answer
94 views

Naming a synthetic molecule from QM9 dataset [closed]

I was trying to write a name for a synthetic molecule in QM9 dataset. The molecule is: is 3-aminooxolane-2-carbonitrile a correct name for this?
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48 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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94 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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1answer
94 views

Openbabel is not converting Gaussian Z-matrix

I ran into an issue when OpenBabel (a great and extremely useful problem) could not convert my custom-generated Gaussian Z-matrix to XYZ format. The problem is that probably major flaw of OpenBabel ...
4
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1answer
312 views

Alternative python modules to RDKit to convert SMILES to structure

Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment. I am wondering that if ...
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43 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 ...
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1answer
127 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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117 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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41 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 ...
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29 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 ...
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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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50 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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1answer
170 views

Molecular similarity using Tanimoto coefficient

I'm trying to use a method for evaluating similarity of molecules. I have seen many publications in the machine learning community have used Tanimoto coefficient. However, when I read about it, it ...
5
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1answer
188 views

How to search substructures with explicit hydrogen in RDKit?

For a substructure search I would like to search for structures containing unfused benzyl. The idea was to explicitly add hydrogen. But apparently this does not give the expected results. So, I ...
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2answers
436 views

Substructure search with RDKit

I'm trying to search for substructures with RDKit. I would like to search for structure 1 as substructure in other structures. I don't understand why it doesn't find this structure in structures 3 ...
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2answers
57 views

Syntactic vs Semantic validity of molecular graphs

While reading this paper on molecular graph generators using deep learning algorithms, I encountered the terms syntactically and semantically valid molecular graphs: $\dots$ to ensure the ...
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2answers
674 views

SMILES vs. Graph representation in deep learning

I have been reading papers on machine learning and deep learning methods for learning molecular space and generating molecules. These methods use different representations of the molecules. The most ...
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2answers
137 views

What is maximum energy level of molecules?

I have been reading about the relation of molecular graph spectrum, that is, the set of eigenvalues of the Laplacian matrix of the molecular graph, and molecular properties. Recently, I came across a ...
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1answer
69 views

Simple QM9 properties for prediction

I was looking into an article (doi: 10.1063/1.5058063) which presented a histogram of radius of gyration for samples of different configurations of alanine dipeptide. This property is fairly simple to ...
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95 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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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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2answers
136 views

Computing force fields using Open Babel

I am trying to use Open Babel (OB) to compute universal force field (UFF) given an xyz file. I read each xyz file and turn it ...
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1answer
2k views

How to get the SMILES of all compounds on PubChem?

I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the ...
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1answer
248 views

QM9 dataset with chirality

I am trying to find chiral centers of molecules in QM9 dataset. Browsing their SMILES representation, I noticed SMILES yield using datasets.get_qm9(GGNNPreprocessor(), return_smiles=True) don't ...
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1answer
383 views

Euclidean distance between atoms using RDKit

I'm trying to find the Euclidean distance between two atoms in the molecule with SMILES representation O=CC1OC12CC1OC12 using the ...
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2answers
192 views

Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
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145 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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1k views

Are there any datasets containing molecules with more than 38 heavy atoms?

I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if ...
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260 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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1answer
75 views

Red Squares in RDKit?

I'm newish to RDKit and couldn't find an answer to this online. The following is a minimal representation of how I drew a molecule ...
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358 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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1answer
649 views

Is it possible to build or embed the SMILES representation of compounds in 3D?

I would like to know if there is a proper way to get the 3D information from the SMILES string of a molecule. Is there a standard way to embed a SMILES string in 3D space? Are there other ...
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1answer
2k views

What is kekulization (in RDKit)?

It's been a while since I've studied chemistry. Now, I am reading the documentation of RDKit. At a certain point, the term "kekulization" is mentioned. What is kekulization (in RDKit, if this is not a ...