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

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swift API to convert smiles strings to 2D chemical structures

Is there a method or free api written in swift for converting smiles strings to the corresponding 2D structures? I have used babel or ibabel with python, but how do i use it with swift?
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Finding vendor information programmatically

I have a large collection of structures (>10,000) that I've gathered from literature searches and I would like to find out which of those can be obtained from vendors. I know that eMolecules and ...
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Why do compounds with similar properties have different Stitch IDs?

I'm not from the Pharmacy or Chemistry background. I have been wondering why certain drug compounds have similar properties but each of them have different Stitch IDs in PubChem? For example: ...
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Inferring bond breakage in a reaction from InChI strings of reactans?

I'm currently confronting a problem: I would need to enumerate all chemical bond breakages that occur during a given chemical reaction, including the type of bond and the atoms participating in the ...
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1answer
38 views

How to quantize the shape of a molecule?

I am looking for numbers which tell you something about the 3D shape of the molecule, and is also easily calculated. One of these is the acentricity factor. I am aware of this one. My problem is you ...
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119 views

How to get 3D molecular structures for 270 compounds?

I need to calculate 10 properties for 270 molecules using Gaussian 09. Could you please suggest me what is the best and shortest way to have the structure of 270 molecules (in the format .com or .xyz)?...
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Why does rdkit's `AllChem.ReactionFromSmarts.RunReactants` return a tuple of tuples?

In rdkit, the function AllChem.ReactionFromSmarts.RunReactants returns a tuple of tuples. Does anyone know what the two dimensions are for? From the (admittedly few)...
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48 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 ...
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64 views

How can I search molecules by constituent atoms

Given a set of atoms, I would like to find (some / the most common) molecules that include only (some/all) atoms of the set. Is there any online search engine that can do this? E.g. Atoms={C,H} ...
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87 views

How to calculate hydrogen from SMILES string?

How to calculate the number of hydrogen atoms from SMILES string? For example, SMILES String: C1=CC(=C(C=C1C(CN)O)O)O The known result is C8H11NO3
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3answers
838 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? ...
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Determining reaction feasibility from SMILES representations [closed]

Consider the reaction of benzo-1,4-quinone with succinate to form hydroquinone and fumarate: $$ \ce{C6H4O2 + HOOC-(CH2)2-COOH <=> C6H4(OH)2 + HOOC-CH=CH-COOH} $$ The reaction written with each ...
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153 views

Pubchem: list all compounds for which Kovats retention indices are available

Pubchem recently started listing Kovats retention indices, e.g. for alpha ionone: https://pubchem.ncbi.nlm.nih.gov/compound/5282108 I was wondering though if there is a way to get a list of all ...
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1answer
47 views

Create combinatorial library of biologically plausible chemical compounds based on library of known compounds

I recently downloaded all the molecular structures (about 13,000) stored in Pherobase, an open library of insect pheromones. I would now like to create a derived, more extensive combinatorial library ...
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2answers
101 views

How to find the concentrations of the acid-base equilibrium between sulfuric acid and sulfur dioxide for a known pH using Octave?

The system is an aqueous solution of sulfuric acid and sulfur dioxide. I know how much sulfur there is and I know the pH. The system is in equilibrium. I would like to use Octave to solve the system....
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182 views

Trying to understand SMILES(?) patterns

In the example calculation from the conformer search package fafoom is a mysterious pattern that I'd like to understand. The SMILES code of the given example structure is: ...
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3answers
216 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)...
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2answers
91 views

Converting mol files to InChiKey in large batches

I want to convert mol files to InChiKey. I am using OpenBabel for the conversion but I have ...
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61 views

Questions regarding mol files

I have some questions regarding generation of mol files- For bond block the numbering can be done at random or it has to follow some order Also in the atom block the order in which atoms occur can ...
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458 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 ...
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134 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- ...
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1answer
51 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 ...
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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: ...
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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 ...
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2answers
384 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, ...
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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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65 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 implementation,...
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212 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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2answers
143 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
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1answer
255 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 ...
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139 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 ...
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907 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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2answers
63 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.
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1answer
232 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 ...
4
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1answer
121 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 ...
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1answer
271 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 ...
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How to store molecule data using SMILES when building a toy chemistry model

I'm currently building a toy chemistry model based around Gillespie's algorithm. Starting from a food set of {H,O,N,C} I let my system evolve, I have been storing my molecules as strings in SMILES ...