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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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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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1answer
101 views

What are the disadvantages of using the InChI format?

What are the disadvantages (if any) in producing and using the InChI format of chemical compound representation in chemoinformatics? Are there any particular problem one can face when using InChI?
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4answers
1k views

Public API for physical properties

Is there a publicly available API that serves physical property data for organic molecules? Pubchem does not serve properties, ChemSpider closes property access to API calls, and Toxnet only serves ...
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0answers
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
100 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 ...
12
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5answers
10k views

Is there a way to use free software to convert SMILES strings to structures?

So far I've been unsuccessful in finding an open source tool that will convert a large number (>100k) of SMILES strings to a chemical structure. Is this really only solved by commercial applications? ...
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3answers
903 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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1answer
522 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 ...
8
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1answer
294 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 ...
4
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1answer
124 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 ...
5
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3answers
170 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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2answers
64 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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1answer
114 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
20 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 ...
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0answers
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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4answers
1k views

Is there a formula to tell how many conformers of a molecule to generate?

Let's say we want to generate conformers of molecules (e.g., ligands for docking in a protein pocket). Is there a formula, like a function of the number of rotatable bonds, to decide how many ...
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0answers
144 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
46 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
187 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
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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1answer
703 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 ...
2
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1answer
126 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 ...
3
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2answers
466 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 ...
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1answer
285 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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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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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
511 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
467 views

How to calculate hydrogen from SMILES string?

How to calculate the number of hydrogen atoms from SMILES string? For example, SMILES String: C1=CC(=C(C=C1C(CN)O)O)O The known result is C8H11NO3
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91 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 ...
5
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2answers
206 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
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0answers
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 ...
4
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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
142 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 ...
7
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2answers
3k views

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

Is there a way to easily extract all the structures and energies from an ADMP calculation done in Gaussian 09? GaussView can plot them but not export them in a useful way and babel just gives me the ...
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0answers
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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5answers
542 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 ...
5
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0answers
203 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
103 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 ...
4
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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
234 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 ...
13
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3answers
2k views

Pubchem, InChI, SMILES, and uniqueness

PubChem compound 6140 is L-phenylalanine in its neutral (not zwitterionic) form. According this PubChem, this molecule has the following SMILES and InChI indentifiers: SMILES: C1=CC=C(C=C1)CC(C(=O)O)...
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0answers
57 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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2answers
2k views

How to determine the Bravais lattice and atom basis vectors from a CIF file?

Say I have a CIF file describing some material in terms of its symmetry space group, lattice parameters and in-cell atom positions. A simple example might be, ...
5
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2answers
605 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: ...
5
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3answers
226 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 ...
10
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6answers
14k views

How many unique molecules exist? And how many exist only by synthesis? [closed]

I'm interested in How many unique molecules (of all types: organic and inorganic, etc), exist in the world accessible by man (let's exclude black holes and the centers of stars etc)? What subset ...
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0answers
88 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 ...
9
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2answers
439 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 ...
2
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1answer
193 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 ...
11
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3answers
938 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?