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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
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How to programmatically identify a chemical compound in my program?

I have a small set (a hundred of items) of chemical compounds in XYZ formats in my DB. How to quickly identify that a given chemical is or isn't in this DB? I don't want to just scan through them, or ...
4
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2answers
266 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,...
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0answers
64 views

Know if a molecule is viable with Python [closed]

I'm working with python and I'd like to know if someone knows a python module which is able to check if a molecule is chemically viable (valence, connectivity constraints ...), or not. I know there is ...
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0answers
29 views

Online list of water of crystallisation?

I was extremely happy to recently receive a copy of the Nuffield Revised Book of Data but was somewhat disappointed to find that it did not list data on the water of crystallisation for various ...
4
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1answer
80 views

Multiplication symbol in SMARTS

There is a SMARTS pattern that was published which looks like the following[1] [#6 × 4] and there are actually spaces around the ...
5
votes
1answer
114 views

How can I recognize aromatic rings in a connection table?

Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring? For reference, the aromatic rings in the ...
2
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0answers
87 views

Non central chirality in cheminformatics?

What are compact cheminformatics structural representations that allow to deal correctly with axial chirality, such as in binaphthyl compounds or metal complexes?
5
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0answers
110 views

Pseudo 3D skeletal structure style which emphasizes geometry

If one searches and navigates to a wiki page for, say, dichlorodifluoromethane one sees the 2D skeletal structure of the compound as below This representation appears to be of a particular style that ...
2
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1answer
62 views

Help on alternative terpene names and naming schemes

I am a software developer and currently parsing data involving terpene profiles of plant samples. The data in question uses different ways of naming the same terpenes in-between samples and since this ...
4
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2answers
483 views

How do I make a ZMAT or XYZ file from scratch?

From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file? The closest similar question asked here was about converting a PDB entry into XYZ, but ...
5
votes
1answer
109 views

Search by CAS Registry name to obtain trackable accession: ie InChi?

I'm updating a database and trying to move from CAS Registry names to InChiKeys. I have about ~800 compounds to track. Is there a way to do this mappings programatically? I'm looking for a web service ...
3
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0answers
45 views

Matchmol for substructure determination

I'm using Checkmol/Matchmol for substructure determination and retrieval, and I'm having problems determining whether a given molecule is the substructure of another molecule when they have the same ...
4
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5answers
293 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 ...
3
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0answers
79 views

In QSAR, what is the simplest (but most powerful) way to create an applicability domain model?

QSAR means Quantitative Structure Activity Relationship. An applicability domain model is a model that tells you how far you are from the domain where your model was trained. I.e. it is a kind of map ...
8
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2answers
372 views

Any program for conformational searching for sugars?

I want to estimate mean Gibbs free energy of formation of glucose and for that purpose I think conformers of ring flip should be taken into account. Do you know if some free program can find those ...
5
votes
2answers
479 views

What is the correct regular expression for InChI?

When I look for a regular expression for InChI, I succeed on EBI's MIRIAM Registery website: ...
8
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1answer
190 views

How to determine the correct InChI for a certain compound?

Let's say I have a compound L-xylulose 1-phosphate and I want to know its correct InChI, how to do this? The reason I ask is because when I go to different databases I get different results: ChEBI: $...
10
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3answers
425 views

How does a molecule search work by drawing in visual editor?

There are a lot of chemical search engines (such as ChemSpider's Structure search) that allow users to draw and search for a molecule. How does it work? Is the comparison of images used? Could you ...
2
votes
2answers
447 views

How to get Jmol to automatically determine and display bond order?

Some molecule file formats do not detail bond order and when I open these formats in Jmol implied (by the valency, of course) double bonds are not shown as double bonds but rather as single bonds. Is ...
2
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1answer
148 views

Openbabel: Generate random 3D geometry

Is it possible with openbabel to generate random 3D geometries (i.e. conformers) of a molecule without taking energy into account? Ideally with the property of being truly random, so that after ...
3
votes
1answer
185 views

Is it possible to export a rotating .gif format picture from chemapps.stolaf.edu?

I mainly use chemapps.stolaf.edu to get the 3D structure of a molecule from the SMILES. It renders the molecules as: I have the option to rotate the image by specifying the $x$, $y$, and $z$ spin ...
2
votes
1answer
226 views

How to find a chemical by its formula?

There are (obviously) a lot of chemical compounds. Wikipedia is able to translate names to molecular formulas for a lot of them. But is there a way to enter a molecular formula and find the chemical'...
3
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0answers
175 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?
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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 ...
5
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3answers
193 views

What is the best way to convert SMILES strings to file names?

I would like to convert SMILES strings into file names. There are many characters to avoid in file names, i.e. \/:*?"<>| or maybe even ...
2
votes
1answer
234 views

Obtaining number of functional groups in a compound from SMILES, SDF or MOL2 format

I'm looking for a tool that can give how many methyl groups, hydroxyl groups etc are in a compound's structure presented as SMILES, SDF or MOL2 format.
4
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1answer
169 views

In rdkit, how to preserve stereochemistry in a SMARTS subgraph?

In rdkit, when doing a MCS search for molecules bearing a chirality center, (how) is it possible to preserve the stereochemical information when exporting the subgraph to a SMARTS string? Consider ...
11
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3answers
910 views

Is converting SMARTS to SMILES a “lossless” operation?

The following three different SMARTS strings represent the same structure - at least when depicting it (e.g. at Uni Hamburg Smarts viewer). ...
5
votes
1answer
135 views

Algorithm used by PubChem to determine the 2D layout assignment for Compound entries?

The PubChem database provides 2D structures for entries in its Compounds database: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/ (ftp link to download examples) On the page linked below, under the "...
11
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3answers
643 views

List of functional groups in a molecule

Does anyone know if there's a tool for listing the functional groups present in a molecule?
5
votes
1answer
67 views

Change inchikey directly

Preamble: Now, I am aware that directly editing the inchikey is, generally speaking, a bad idea, but... Can I just change the 2nd block of an inchikey to "UHFFFAOY" to get the correct main-layer-...
4
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0answers
75 views

What are the disadvantages of using the InChI format?

What are the disadvantages (if any) in producing and using the InChI format of chemical compound representation in chemoinformatics? Are there any particular problem one can face when using InChI?
8
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2answers
2k 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 ...
0
votes
1answer
222 views

How to calculate the charge distribution at the ortho/para or meta sites of a substituted benzene ring

I've modelled a few substituted benzene rings in avogadro and retrieved the partial charges of each atom; I've tried to sum the partial charges of the carbon and hydrogen atoms at the ortho/para and ...
14
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3answers
1k views

Portable library to render 2D structural formulas as vector graphics from SMILES or InChI

For a web-based project, I am looking for a piece of software to create a 2D vector graphics structural formula from a textual structure encoding scheme such as SMILES or InChI, running on the server ...
4
votes
1answer
232 views

Openbabel: Generate 3D depiction?

The process of creating 2D depictions is explained in detail here. This way, it is possible to create a 2D image via running e.g. obabel -O 2d_depiction.png However, how do I generate a ball and ...
3
votes
1answer
188 views

What workflow can I use on to extract cartesian coordinates of many molecules from both .spartan and .out (Gaussian) files?

I'm searching for a workflow for extracting cartesian coordinates for multiple moelcules from both a single file (e.g., several conformers from one .spartan file or one multiple molecules, each from ...
0
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0answers
128 views

is there a database of known chemical reactions? [duplicate]

I am looking for a complete directory of chemical reactions. It should be searchable by element or substance and also the various factors (pressure, temperature, catalyst, etc) should be mentioned. Is ...
14
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3answers
818 views

Is there a formula to tell how many conformers of a molecule to generate?

Let's say we want to generate conformers of molecules (e.g., ligands for docking in a protein pocket). Is there a formula, like a function of the number of rotatable bonds, to decide how many ...
2
votes
1answer
117 views

SMARTS for cis amide

Is there a SMARTS pattern for cis (and trans) amide bonds? This seems to be the SMARTS for any amide: [NX3][CX3](=[OX1])[#6] But I am not sure whether or not ...
7
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5answers
3k 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, ...
5
votes
1answer
2k 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 ...
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1answer
44 views

Disease predicting software for small molecules [closed]

Can anyone please help me in finding softwares for predicting diseases from small molecules?
2
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3answers
2k views

Open Source SDF (Chemical Table File) Parser in any language

I'm looking to parse a large .sdf file and put it into a .csv file. The only software I could find that parses ...
-1
votes
1answer
148 views

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?
6
votes
1answer
88 views

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 ...
2
votes
1answer
209 views

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: Stitch ...
3
votes
1answer
50 views

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 ...
3
votes
1answer
54 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 ...
2
votes
1answer
378 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)?...