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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Multidimensional Chemical Space - nD coordinate system

I have a dataset of many organic compounds. I would like to describe them using a set of coordinates. A 2D example of what I want to do is chemplot, this package lets you create a 2D coordinate system ...
Mirko's user avatar
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HOMO and LUMO energy levels diagrams

Good time of day. I want to draw the same beautiful pictures in my work as I will attach below taking from some articles. Are there any programms or scripts which can do this? I would be glad if ...
UserIn's user avatar
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1 answer
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What is the SMARTS string for a benzene ring (any substitution pattern)

I would like to use RDKit to highlight all benzene rings (regardless of substitution pattern - e.g. phenol, chlorobenene, benzoic acid type should all be highlighted) in any given molecule. I cannot ...
Guest's user avatar
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3 votes
1 answer
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Problem adding non-polar hydrogens whilst converting from pdbqt to pdb

I'm using OpenBabel 3.1.1 and the Python to C++ bindings to load pdbqt files and convert them to pdb with explicit hydrogens. Unfortunately, I can't add nonpolar hydrogens using OpenBabel. I can do ...
Anthony Nash's user avatar
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1 answer
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Transform raw atomic coordinate data into SDF file

I have raw data of the atom types and their coordinates. For example, water molecule is: O -0.034 0.977 0.007 H 0.064 0.020 0.001 H 0.871 1.300 0.0006 Here, I ...
neco's user avatar
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2 answers
172 views

Two compounds (not stereoisomers) have same SMILES code

Are there compounds that have the same SMILES code but are not stereoisomers? I am trying to find inconsistencies with SMILES code and currently I have that many compounds have multiples options for ...
xboxbot's user avatar
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2 votes
1 answer
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Difference between two forms of benzothiadiazole [closed]

Can someone please advise / point me to information regarding the difference between these two compounds: https://www.combi-blocks.com/cgi-bin/find.cgi?HC-3087 https://www.combi-blocks.com/cgi-bin/...
user6376297's user avatar
-2 votes
1 answer
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Substructure abbreviations with the SMILES format

I am trying to use the SMILES format for encoding molecules from handwritten logbooks. The molecules often contain abbreviations, such as "Ph" for a Phenyl group. Is there a way to have ...
finlay morrison's user avatar
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69 views

How does the canonization method of RDKit operate when valence is exceeded?

RDKit's canonization method1 allows nitrogen to bond with 3 hydrogen atoms and one oxygen atom ...
nightcod3r's user avatar
4 votes
0 answers
77 views

Molecule similarity measurement

I'm not a chemistry specialist, I'm more from informatics, and I have a question concerning molecule similarity measurement. Let's taking these two molecules: mol1: c1(cccnc1)C(O)=O mol2: O=C(O)...
user12910's user avatar
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776 views

How to convert SMILES to 3D (with higher accuracy than RDKit)?

I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
jasperhyp's user avatar
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1 answer
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"Best" way of referencing chemicals in databases [closed]

What is considered the "best" way of referencing chemicals in a database ? As far as I understand CAS nr. is a specific type of hash whereas something like smiles stores structural ...
Julien's user avatar
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Open MSDS (GHS/CLP) database API by CAS#

I am looking for an open API to a database that provides GHS/CLP classifications. I am aware this is a duplicate, however the post in question never provided an answer since, as far as I can tell ...
Julien's user avatar
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Defining SMARTS reaction template

I want to have a reaction template involves combination of 2 radicals such as this one O=C1CCC(=O)[N]1.[H]>>[H]N1C(=O)C([H])([H])C([H])([H])C1=O. A generic ...
Jung's user avatar
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Line Entry system like SMILES for metals?

SMILES is not designed for metallic compounds. Is there a similar ASCII line entry notation for metallic compounds, including repeating structure in space, &c.?
Sam's user avatar
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Rotating molecule representations with rdkit

I'm trying to display some molecules in rdkit and save them as png files. Simple enough. However, when I display them, most of them are drawn at a weird angle (shown below) or even completely upside ...
apvn's user avatar
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1 answer
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accessing the ZINC15 and ZINC20 databases

I'm trying to access the ZINC15 and ZINC20 databases but I've been at it the whole morning and I can not figure out how to do it. I am not that experienced with programming so maybe there's something ...
apvn's user avatar
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Python implementation of the Lilly Medchem Rules code? [closed]

As the title suggests, I am looking for a Python implementation of the Lilly filter from the paper: https://pubs.acs.org/doi/full/10.1021/jm301008n. The shared code on GitHub (https://github.com/...
mac179's user avatar
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1 answer
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SMARTS: distinguish between alcohol and carboxylic acid

I'm new to SMARTS and have to identify substructures with the Python package rdkit, so far so good. Let's say I have a SMILES with an carboxylic acid and a alcohol ...
dideldideldum's user avatar
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1 answer
110 views

Are there tools or algorithms to detect organic molecules from 3D crystal structures?

The task I'm thinking of is to detect entire molecules from structures, such as in a crystallographic information file (CIF) or from the XYZ file generated in a molecular dynamics simulation. ...
QGent's user avatar
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SMILES vs. Graph for generating molecules

I have seen this question, but mine is slightly different, focusing on generating molecules. There are many published methods for generating molecules; some of which generate SMILES and others ...
Hossein's user avatar
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1 answer
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How to use Python RDKit to remove stereochemistry, salts and molecules with undesirable atoms or groups?

I am not a chemist, I come from a computer science background. Bung et al. [1] say in the Data preprocessing part that they used Python RDKit to remove stereochemistry, salts, and molecules with ...
mac179's user avatar
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2 votes
1 answer
2k views

Python and RDKit to extract sub-structures in a SMILES

I am not a chemist, I come from a computer science background. I am involved in a cheminformatics project. I have a list of molecules in SMILES format, which I want to extract sub-structures from. I ...
mac179's user avatar
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Machine learning-based drug design: how to determine the desired properties given a target?

I am working on a machine learning-based drug design project. The machine learning part was easily understood for me being from a computer science background. However, the biochemistry part is what I ...
mac179's user avatar
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4 votes
1 answer
118 views

Forming conjugate acid of borate anion via protonation

I am a biologist so please forgive me as I likely won't be as rigorous as a professional chemist. I am using the RDKit package to extract organic molecules from salts, where one ion is organic and the ...
atevm's user avatar
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0 answers
537 views

Is chemAxon check of validity of a smiles the same as RDKit check?

I am working on an AI-based drug design application, I want to verify the validity of the produced molecules (which are in smiles representation). I found a solution to this using the RDKit library ...
mac179's user avatar
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7 votes
1 answer
587 views

Listing all possible structures for a given Markush structure automatically

I have Markush formulas described as mol blocks, v3000, even if that does not matter that much because I could convert it into another format if needed. I need the possibility to automatically list ...
bfalk's user avatar
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0 answers
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Handling of tautomerism in QSAR modelling

This article from 2009: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776169/ mentions the potential impact of tautomerism on QSAR modelling, and concludes that more work is needed to address it. 12 ...
user6376297's user avatar
-1 votes
1 answer
916 views

How to get smiles from pubchem CID

I have downloaded about 10k compounds of interest from pubchem. Im using pubchempy to get smiles for all those structures . I am able to get smiles for each compound one by one but while fetching two ...
vemaparna's user avatar
5 votes
1 answer
436 views

SMARTS pattern for amines with connected carbons only having bonds to carbon or hydrogen

I'm trying to find a SMARTS pattern that matches primary and secondary amines, where the connected carbon atoms only have connections to other carbon atoms or hydrogens (to exclude amides, guanidines, ...
snurden's user avatar
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3 votes
1 answer
186 views

What Chemical Database Extensions for Structure and Similarity Search are there?

I am looking for extensions/add-ons for relational databases (RDBMS) that enable storing and handling chemical structures including the possibility for substructure searches and similarity search. I ...
buddemat's user avatar
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2 votes
2 answers
810 views

How to highlight the substructure of a molecule with thick red lines in RDKit as SVG (high res)

I have the following code: ...
littleworth's user avatar
4 votes
2 answers
146 views

Why do two programs assign different SMILES to one amino acid sequence?

I have an amino acids string "MKGK" and I would like to convert it into SMILES format. I tried two approaches. First with PepSMI which gives me: ...
littleworth's user avatar
5 votes
1 answer
166 views

What do sequence numbers in PDB files actually mean and why don't they match the sequence?

I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
Gunther Schadow's user avatar
0 votes
1 answer
59 views

Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry showing both reactant ligands?

I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have ...
Gunther Schadow's user avatar
1 vote
0 answers
121 views

What is an enzymatic reaction for which a detailed tertiary structure showing all ligands is available on the PDB?

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate ...
Gunther Schadow's user avatar
2 votes
2 answers
137 views

How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
2 votes
1 answer
359 views

How to "draw" a coordination bond (dashed bond) in MOLFILE?

How can we "draw" a coordination bond (dashed bond) in MOLFILE? I cannot find a bond property or option that would allow me to choose such a thing. So many drawings of organo-metallic ...
Gunther Schadow's user avatar
1 vote
0 answers
39 views

Classification model from biological assays with different compounds

If I want to use an undersampling approach to construct the machine learning model (classification model predicting whether the target compounds are active or inactive, using chemical fingerprint as ...
tassaneel's user avatar
5 votes
1 answer
198 views

InChI issue with organic salts, inconsistent approach?

I am wondering why there is the following inconsistency in InChI: penicillin G vs. penicillin G potassium salt uses the /p layer to drop a proton but chloramine-T vs. tosylchloramide drops an H from ...
Gunther Schadow's user avatar
3 votes
1 answer
179 views

How to implement SDF format?

I have a program that returns a file with SDF format molecule. Now I want to transfer it to SMILES with Open Babel. But I don't get the result I expect. I have visited different websites that show how ...
Tim Schneider's user avatar
6 votes
1 answer
297 views

Can cis-trans isomers have same InChI?

From all we know only tautomers should get the same InChI key, or, in case of the second block, if there are lots of stereo centers. However these cases are just collisions, they still have different ...
Ralf Stephan's user avatar
6 votes
1 answer
228 views

Discrepancy when calulating mol weights with ChemSketch and Python RDKit

I am an IT guy with little knowledge of Chemistry, so please bear with me... For context: I am working with a system that has a lot of structures, their .mol files ...
buddemat's user avatar
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5 votes
1 answer
1k views

How to find the largest cyclic substructure with RDKit?

I have a bunch of structures and of each I would like to find the largest cyclic substructure. I'm not a chemist, so I don't know if there is a common terminology for this. I hope, I made it clear ...
theozh's user avatar
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4 votes
0 answers
66 views

Why is the reported melting point of formaldehyde so different from the triple point?

All of the (believable) sources at PubChem and most of the sources at NIST give 181 K for the melting point. The one source I can find for the triple point is NIST, which gives 155 K. There are two ...
MackTuesday's user avatar
12 votes
3 answers
2k views

Does the SDF format have any benefit over SMILES?

The eMolecules page for example offers a complete dataset containing ~26 million structures. They're providing it either as a 300 MB SMILES archive or 6 GB SDF archive (1.5 GB and 50 GB uncompressed ...
Marc Wittke's user avatar
2 votes
1 answer
153 views

INCHI-1 software input format(s)?

I am looking at the latest INCHI-1 software which supports molecules with 32 thousand atoms. I work with macro-molecules and want to use that to generate humongous InChIs. I've never used that INCHI-1 ...
Gunther Schadow's user avatar
6 votes
1 answer
100 views

Are atom coordinates in molfile necessary to produce a valid InChI identifier

I took this molfile of benzoic acid: ...
Paul Jurczak's user avatar
6 votes
0 answers
476 views

Are there any ADME predictions tools available for Python/RDKit?

Is there any Pythonic way (a.k.a: a module, an rdkit package, etc) or an API I can use for ADME predictions? I need to prioritize some compounds for purchase/synthesis and some sort of ADME scoring ...
Leitouran's user avatar
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4 votes
1 answer
108 views

How to draw xenon hexafluoride in rdkit from SMILES?

In SMILES I would think that $\ce{XeF6}$ would be F[Xe](F)(F)(F)(F)F or F[Xe](F)(F)(F)(F)(F). A quick Wikipedia search showed ...
Sohil Kollipara's user avatar