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

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Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
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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 ...
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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 ...
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82 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 ...
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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 ...
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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 ...
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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 ...
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138 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 ...
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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.
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116 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 ...
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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 ...
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103 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 ...