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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3
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0answers
84 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: ...
3
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1answer
34 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
50 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 ...
7
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1answer
184 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 a SMILES string. Is there a standard way to embed a SMILES string in 3D space? Are there other representations of ...
8
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1answer
529 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
60 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 ...
0
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1answer
29 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 ...
3
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2answers
102 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
134 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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0answers
32 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
74 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 ...
4
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2answers
454 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
145 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
76 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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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
80 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
125 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 ...
2
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0answers
90 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?
5
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0answers
155 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
85 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
760 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
169 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 ...
3
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0answers
51 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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5answers
413 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
81 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 ...
8
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2answers
405 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 ...
5
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2answers
538 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
198 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
429 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
538 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
158 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
votes
1answer
228 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
votes
1answer
245 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'...
3
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0answers
195 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?
14
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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
211 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
votes
1answer
262 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.
3
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1answer
187 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 ...
11
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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
votes
1answer
138 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
867 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?
5
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1answer
68 views

Change inchikey directly

Preamble: Now, I am aware that directly editing the inchikey is, generally speaking, a bad idea, but... Can I just change the 2nd block of an inchikey to "UHFFFAOY" to get the correct main-layer-...
3
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0answers
82 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?
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 ...
0
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1answer
230 views

How to calculate the charge distribution at the ortho/para or meta sites of a substituted benzene ring

I've modelled a few substituted benzene rings in avogadro and retrieved the partial charges of each atom; I've tried to sum the partial charges of the carbon and hydrogen atoms at the ortho/para and ...
14
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3answers
1k views

Portable library to render 2D structural formulas as vector graphics from SMILES or InChI

For a web-based project, I am looking for a piece of software to create a 2D vector graphics structural formula from a textual structure encoding scheme such as SMILES or InChI, running on the server ...
3
votes
1answer
262 views

Openbabel: Generate 3D depiction?

The process of creating 2D depictions is explained in detail here. This way, it is possible to create a 2D image via running e.g. obabel -O 2d_depiction.png However, how do I generate a ball and ...
3
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1answer
209 views

What workflow can I use on to extract cartesian coordinates of many molecules from both .spartan and .out (Gaussian) files?

I'm searching for a workflow for extracting cartesian coordinates for multiple moelcules from both a single file (e.g., several conformers from one .spartan file or one multiple molecules, each from ...
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0answers
128 views

is there a database of known chemical reactions? [duplicate]

I am looking for a complete directory of chemical reactions. It should be searchable by element or substance and also the various factors (pressure, temperature, catalyst, etc) should be mentioned. Is ...
16
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4answers
921 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 ...