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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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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2answers
95 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 ...
9
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1answer
296 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
97 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
85 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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0answers
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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 ...
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2answers
57 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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130 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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3answers
872 views

What are 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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124 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: ...
4
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1answer
43 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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0answers
102 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 ...
8
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1answer
250 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
645 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 ...
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1answer
104 views

What is a molecule’s smallest set of smallest rings?

It is been a while since I've studied chemistry. Now, I am reading the documentation of RDKit, where they mention the expression "smallest set of smallest rings" (SSSRs). I understand that a ring is a ...
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1answer
33 views

Is there a way to export detailed data about atom connectivity, dihedral angle, etc from GaussView?

As far as I know, opening the .com files as .txt files (with a text editor like simple notepad) yields a nicely formatted table ...
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2answers
343 views

Converting SMILES to .sdf files

I have around 1000 SMILES entries in Excel and I have to generate .sdf file for all. Is there any way to automate this whole process, preferably with an offline ...
7
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1answer
234 views

converting SMILES (or .mol2) to SMARTS

The conversion between different chemical structure formats, e.g. from .mol2 to .xyz, by openbabel may tied to conditions to be met. One example of such a filter is to allow such a conversion only ...
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34 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 ...
3
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1answer
80 views

How to programmatically identify a chemical compound in my program?

I have a small set (a hundred of items) of chemical compounds in XYZ formats in my DB. How to quickly identify that a given chemical is or isn't in this DB? I don't want to just scan through them, or ...
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2answers
497 views

Finding all Chemical Reactions Given Products and Reactants

Suppose only a set of chemical formulas is given. How can you find all mathematically possible chemical equations whose educts and products are only from this set? Take e.g. the set $\{ \ce{C, H2, O2,...
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3answers
168 views

How to index molecules in computer programs?

Is there a standard way how can the index over a molecular structure be kept in the computer? A molecule is a graph, where nodes have labels (chemical element type), and edges are chemical bonds. ...
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0answers
87 views

Know if a molecule is viable with Python [closed]

I'm working with python and I'd like to know if someone knows a python module which is able to check if a molecule is chemically viable (valence, connectivity constraints ...), or not. I know there is ...
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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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1answer
82 views

Multiplication symbol in SMARTS

There is a SMARTS pattern that was published which looks like the following[1] [#6 × 4] and there are actually spaces around the ...
5
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1answer
140 views

How can I recognize aromatic rings in a connection table?

Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring? For reference, the aromatic rings in the ...
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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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193 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 ...
2
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1answer
100 views

Help on alternative terpene names and naming schemes

I am a software developer and currently parsing data involving terpene profiles of plant samples. The data in question uses different ways of naming the same terpenes in-between samples and since this ...
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2answers
1k views

How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...
5
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1answer
217 views

Search by CAS Registry name to obtain trackable accession: ie InChi?

I'm updating a database and trying to move from CAS Registry names to InChiKeys. I have about ~800 compounds to track. Is there a way to do this mappings programatically? I'm looking for a web service ...
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0answers
53 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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5answers
503 views

Free API to view 2D representation of Molecules

I'm looking for a free API that can accept a SMILE and produce the 2D structure of a molecule. I would like to include this in a web page. I have collection of SMILES and would like to have the 2D ...
3
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0answers
84 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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2answers
433 views

Any program for conformational searching for sugars?

I want to estimate mean Gibbs free energy of formation of glucose and for that purpose I think conformers of ring flip should be taken into account. Do you know if some free program can find those ...
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2answers
588 views

What is the correct regular expression for InChI?

When I look for a regular expression for InChI, I succeed on EBI's MIRIAM Registery website: ...
8
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1answer
210 views

How to determine the correct InChI for a certain compound?

Let's say I have a compound L-xylulose 1-phosphate and I want to know its correct InChI, how to do this? The reason I ask is because when I go to different databases I get different results: ChEBI: $...
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3answers
433 views

How does a molecule search work by drawing in visual editor?

There are a lot of chemical search engines (such as ChemSpider's Structure search) that allow users to draw and search for a molecule. How does it work? Is the comparison of images used? Could you ...
2
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2answers
610 views

How to get Jmol to automatically determine and display bond order?

Some molecule file formats do not detail bond order and when I open these formats in Jmol implied (by the valency, of course) double bonds are not shown as double bonds but rather as single bonds. Is ...
2
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1answer
185 views

Openbabel: Generate random 3D geometry

Is it possible with openbabel to generate random 3D geometries (i.e. conformers) of a molecule without taking energy into account? Ideally with the property of being truly random, so that after ...
3
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1answer
287 views

Is it possible to export a rotating .gif format picture from chemapps.stolaf.edu?

I mainly use chemapps.stolaf.edu to get the 3D structure of a molecule from the SMILES. It renders the molecules as: I have the option to rotate the image by specifying the $x$, $y$, and $z$ spin ...
2
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1answer
259 views

How to find a chemical by its formula?

There are (obviously) a lot of chemical compounds. Wikipedia is able to translate names to molecular formulas for a lot of them. But is there a way to enter a molecular formula and find the chemical'...
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0answers
202 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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2answers
2k views

How do I make 3d molecular graphics similar to those shown on Wikipedia?

I want to make 3d molecular graphics similar to those found on Wikipedia. In the page for benzene, you can see the structure looks like this: However, if I go to the interactive image as shown in ...
5
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3answers
219 views

What is the best way to convert SMILES strings to file names?

I would like to convert SMILES strings into file names. There are many characters to avoid in file names, i.e. \/:*?"<>| or maybe even ...
2
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1answer
282 views

Obtaining number of functional groups in a compound from SMILES, SDF or MOL2 format

I'm looking for a tool that can give how many methyl groups, hydroxyl groups etc are in a compound's structure presented as SMILES, SDF or MOL2 format.
4
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1answer
197 views

In rdkit, how to preserve stereochemistry in a SMARTS subgraph?

In rdkit, when doing a MCS search for molecules bearing a chirality center, (how) is it possible to preserve the stereochemical information when exporting the subgraph to a SMARTS string? Consider ...
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3answers
1k views

Is converting SMARTS to SMILES a “lossless” operation?

The following three different SMARTS strings represent the same structure - at least when depicting it (e.g. at Uni Hamburg Smarts viewer). ...
5
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1answer
142 views

Algorithm used by PubChem to determine the 2D layout assignment for Compound entries?

The PubChem database provides 2D structures for entries in its Compounds database: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/ (ftp link to download examples) On the page linked below, under the "...
11
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3answers
913 views

List of functional groups in a molecule

Does anyone know if there's a tool for listing the functional groups present in a molecule?