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19 votes
Accepted

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

I haven't seen any rigorous benchmarking or guidelines. Consider that the total number of conformers goes up like $3^n$, where $n$ is the number of rotatable bonds, and ~3 is the approximate number ...
Geoff Hutchison's user avatar
18 votes

What is kekulization (in RDKit)?

This is a method to generate alternate Lewis structures of the same molecule. Here are two examples from the cumulative dissertation by Sascha Urbaczek[1]: If you were to search for the left molecule ...
Karsten's user avatar
  • 40.7k
15 votes

How to get the SMILES of all compounds on PubChem?

The best way to download bulk data from PubChem is actually FTP, as documented in their documentation. For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp....
Geoff Hutchison's user avatar
14 votes
Accepted

Is it possible to build or embed the SMILES representation of compounds in 3D?

SMILES is insufficient SMILES strings do not encode 3D structure information. They only convey atom type, connectivity and bond types. InChI is like SMILES in this regard. Thus, you will need ...
Curt F.'s user avatar
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14 votes

Are there any datasets containing molecules with more than 38 heavy atoms?

This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing ...
Buttonwood's user avatar
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13 votes

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

You might want to have a look at Open Babel. It is licensed under GNU GPLv2 It has bindings for Python It has bindings for PHP It has bindings for Ruby It can read (and write) SMILES It can read (...
Klaus-Dieter Warzecha's user avatar
13 votes

How do I make 3d molecular graphics similar to those shown on Wikipedia?

You can generate the geometry for your molecule of choice by drawing it in Avogadro. More often than not, you want to refine the geometry through a force field calculation. Avogadro supports ...
Klaus-Dieter Warzecha's user avatar
12 votes

List of functional groups in a molecule

Norbert Haider from the University of Vienna has been working on the identification of functional groups for quite a while. You might want to have a look at his checkmol/matchmol tool, which natively ...
Klaus-Dieter Warzecha's user avatar
12 votes

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

Usually, structure search is implemented using a graph model. For example, let's take cyclohexane. On screen this is a hexagon - but this is converted on the server to a simple atom/bond graph model ...
gilleain's user avatar
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12 votes
Accepted

Rotating molecule representations with rdkit

You can use SetPreferCoordGen(True) ...
rapelpy's user avatar
  • 839
11 votes

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

You should also look at RDKit, which is at its core is C++ code for manipulating molecular structures, but which also has Python and Java bindings. Most people use it via its Python bindings. Here's ...
Curt F.'s user avatar
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11 votes
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How to determine the correct InChI for a certain compound?

One of the goals of the InChI project was to ensure uniqueness: [1] Strict uniqueness of identifier The same label always means the same substance, and the same substance always receives the same ...
NotEvans.'s user avatar
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11 votes
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Are there any datasets containing molecules with more than 38 heavy atoms?

The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms! The other answer says that there's a database called "OE" with ...
user1271772's user avatar
  • 1,452
11 votes
Accepted

Discrepancy when calulating mol weights with ChemSketch and Python RDKit

In first place, you must clarify with the users of the database the purpose of the entries about molecular weight because average molecular weight and exact molecular weight differ in their meaning ...
Buttonwood's user avatar
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9 votes
Accepted

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

The best known databases are Beilstein and Chemical Abstracts with around 22 millions reactions each since the end of the 19th century but they are commercial. Organic Syntheses has made available ...
SteffX's user avatar
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9 votes

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

To extend on Philipp's excellent answer, I'd like to offer some advice on judging bond orders. Pekka Pyykkö and Michiko Atsumi published covalent (single-, double-, triple-) bond radii for (almost) ...
Martin - マーチン's user avatar
9 votes
Accepted

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

If you have the latest copy of cclib installed, it can extract both the energies and geometries and write the geometries to an XYZ trajectory file that you can open with Avogadro or VMD. To print the ...
pentavalentcarbon's user avatar
9 votes
Accepted

Is converting SMARTS to SMILES a "lossless" operation?

SMARTS is deliberately designed to be a superset of SMILES. That is, any valid SMILES depiction should also be a valid SMARTS query, one that will retrieve the very structure that the SMILES string ...
R.M.'s user avatar
  • 4,934
9 votes
Accepted

How do I make 3d molecular graphics similar to those shown on Wikipedia?

Have a look at Molcalc. It's fully online and uses JSmol as a visualiser. Alternatively you can browse the Pitt Quantum Repository for structures that have already been calculated.
Martin - マーチン's user avatar
9 votes

Substructure search with RDKit

I'm not sure about why it's not matching but when I carry out substructure matches in rdkit I use SMARTS instead https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Here is what I would ...
Unskilled's user avatar
  • 371
9 votes
Accepted

Alternative python modules to RDKit to convert SMILES to structure

I am not aware of any other Python tool not mentioned in the question @Mithoron linked to. Openbabel is available via pip by the way. That RDKit is not available on PyPi should not hinder you from ...
Jan Joswig's user avatar
9 votes
Accepted

Does the SDF format have any benefit over SMILES?

In my experience, the most relevant type of information that a (classic) SMILES does not encode, whereas a SDF does, is about stereochemistry. Most commonly, the explicit stereocenters in a molecular ...
user6376297's user avatar
8 votes

How to calculate hydrogen from SMILES string?

Other answers have done a good job of providing a description of the concepts and algorithms needed to answer the question. Here I'll demonstrate the opposite: a black-box empirical approach. In ...
Curt F.'s user avatar
  • 21.9k
8 votes
Accepted

Openbabel: Generate 3D depiction?

Open Babel does not generate "ball and stick 3D depictions" directly, because it's not a molecular visualization program. That's why we started Avogadro. There are a few formats supported in Open ...
Geoff Hutchison's user avatar
8 votes
Accepted

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

Chemical Identifier Resolver can convert several identifiers and has an API so you can convert with a script. A Python example for CAS to InChIKey: ...
rapelpy's user avatar
  • 839
8 votes

SMILES string convertors

SMILES doesn't define a particular order in which the atoms show up in the string. Hence the position in the molecule where software starts printing will determine the string. E.g. for CO2: Ketcher ...
Stanislav Bashkyrtsev's user avatar
8 votes
Accepted

How to convert an XYZ file to Z-matrix?

According to the manual of the newzmat utility of Gaussian 16, it accepts unadorned Cartesian coordinates (G16 online manual). The format you have posted is ...
Martin - マーチン's user avatar
8 votes
Accepted

Listing all possible structures for a given Markush structure automatically

Preface: Since you mention familiarity with/access to Python, and I assume you want to process batches from .sdf from a script rather than from a GUI (note, ...
Buttonwood's user avatar
  • 30.1k
8 votes
Accepted

Line Entry system like SMILES for metals?

Representing organometallics by ASCII is notoriously difficult. Neither InChI nor SMILES does it well. The most common approach that I've seen is to shoehorn organometallics into the SMILES system by ...
Curt F.'s user avatar
  • 21.9k
7 votes

How to get 3D molecular structures for 270 compounds?

There are a few resources that can get you what you want, but you'll probably want to consider some level of scripting automation. A search for 270 molecules isn't enormous, but doing it by hand would ...
Geoff Hutchison's user avatar

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