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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1answer
545 views

Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
7
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5answers
4k views

Is there a database on chemical reactions, similar to NIST, but far more complete?

The only thing I'm interested in is to be able to search all reactions involving that compound in the database. Equilibrium constant, reaction rate and energy of activation would all be very welcome, ...
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? ...
12
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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 ...
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)...
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 ...
12
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3answers
905 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 ...
4
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5answers
547 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 ...
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 ...
14
votes
2answers
850 views

How should elements be colored? And how many bonds does an atom have?

I'm working on my own 3D molecule viewer for my AP Chem class. So far everything's going together nicely. There's a couple of things I'm not sure about though... Is there a certain rule of thumb or ...
5
votes
1answer
3k views

Internal (Z-Matrix) to Cartesian coordinates conversion

Is there any way to convert from Internal to Cartesian coordinates using simple formulas? I have studied and implemented: INTERNAL TO CARTESIAN by Jack D. Kunitz. But somehow the x, y and z values ...
4
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2answers
515 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,...
10
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1answer
564 views

What would be SMILES notation for a compound with delocalized bonding?

For example, the cyclopentadienyl rings in ferrocene $\ce{Fe(}\eta^5 \ce{-C5H5)2}$ are often drawn with delocalized electron circles in them instead of explicit pi bonds. The Wikipedia article for ...
5
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1answer
429 views

Generating mol files from a molecular structure image?

I have a question regarding mol files.For example I have this molecule- The mol file for this is- ...
4
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0answers
133 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 ...
3
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1answer
135 views

Is there an algorithm that counts Joback groups in a structure?

So I was wondering, there are a lot of cheminformatics tools (eg Babel) out there, to analyze and convert representations. I also saw some codes which counts certain groups, but ignores the carbon ...
3
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0answers
206 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?