Cheminformatics involves the production, processing, filtering, and searching of chemical information. This includes chemical databases, computational screening, searching, etc.

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4
votes
3answers
173 views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
5
votes
1answer
51 views

mol files from structure

I have a question regarding mol files.For example I have this molecule- The mol file for this is- ...
-1
votes
1answer
40 views

What is the meaning of scores when comparing reaction classes in the KEGG database

With respect to related R class in KEGG website: http://www.genome.jp/tools-bin/relclass?RC00064 What is the biological or statistical relevance of the score? How is it computed? And does it signify ...
-3
votes
1answer
58 views

How are RDM patterns for reactions in the KEGG database constructed? [closed]

With respect http://www.genome.jp/dbget-bin/www_bget?rp:RP00167 can anyone tell me how the RDM pattern were obtained?? Information what RDM is given here: http://www.genome.jp/kegg/reaction/ Note: ...
8
votes
2answers
152 views

How do I create a spreadsheet containing the coordinates and predicted bond angles, molecular properties, torsion properties, etc of a molecule?

On a previous answer here (http://chemistry.stackexchange.com/a/30841/876) I was informed in the comments that OpenBabel & Python terminal could be used to print the data contained in the property ...
4
votes
2answers
85 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, ...
3
votes
1answer
85 views
1
vote
1answer
52 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
1
vote
0answers
26 views

Conversion of standard InChI to InChI with fixed-hydrogen-layer

I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer: Standard inChI for Uracil: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) Desired ...
2
votes
0answers
45 views

Obtaining chemical graph complexity index from SMILES or InChl

I wonder if anyone knows a readily available way to obtain some chemical graph complexity index (like the J index) from the SMILES or InChl representations?I'm looking for some existing ...
2
votes
1answer
101 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, chem spider closes property access to API calls, and toxnet only serves ...
1
vote
2answers
77 views

Confused about parity of atom and chirality

OK. I'm working in computational chemistry and the problem that bothers me is: Given a molecule, I know that it has a central asymmetric atom with some parity which is either "Anticlockwise" or ...
5
votes
1answer
143 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 ...
0
votes
1answer
75 views

MDLCT (Connection Table) Format specification

Is there a specification for MDL Connection Table format somewhere. At some places it is mentioned that the format writes the line length as a character then the actual line characters. If I save a ...
0
votes
1answer
280 views

How do I write a valid CIF, PDB or XYZ file from the coordinates listed below?

I want to create a 3D molecular file using coordinates taken from: Hrynchuk, RJ; Barton, RJ; Robertson, BE (1983). "The crystal structure of free base cocaine, C17H21NO4" (PDF). Canadian Journal of ...
0
votes
2answers
38 views

What is the official file extension for SMILES and SMARTS files

I want to know what is the officially used file extension for files containing SMILES and SMARTS strings. Somewhere I see .SMI/.SMA and somewhere its the full .SMILES/.SMARTS.
3
votes
1answer
143 views

Representation of chemical formulas as strings?

Is there a standard manner of representing chemical formulas as linear strings? For example, $H_2O$ can be represented with the string H2O. Isotopes are usually ...
6
votes
4answers
2k views

How many unique molecules exist? And how many exist only by synthesis?

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 ...
4
votes
1answer
108 views

Proton affinities in machine readable format?

Short: How to get proton affinities for a large list of chemicals? A database? A programming API? Longer: I have ca. 2000 chemicals (downloaded from MCM, mostly organics that occur in the atmosphere ...
8
votes
1answer
159 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 ...