Questions tagged [smiles]

Questions about or relating to SMILES (simplified molecular-input line-entry system) or related things such as SMARTS.

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How to parse GDB SMI file?

Reymond Research Group from Bern University has created [GDB-17][1], a compendium of molecules in SMILES format. The file is in smi format, how do I parse the molecular structure in xyz from this?
ananta's user avatar
  • 221
4 votes
0 answers
87 views

Is it possible to generate atom-mapped xyz files from reaction SMILES for NEB?

There are SMILES that represent reactions happening (e.g. C=C.O>>CCO representing water addition to ethylene). And I know that there are atom-mapping ...
S R Maiti's user avatar
  • 6,841
2 votes
1 answer
463 views

Create a SMILES from ASE Atoms

I am trying to create a SMILES representation starting from a .xyz molecule description (positions + symbols) read as ASE Atoms. How can I convert a given molecule as a SMILES string ?
Julien Blanchon's user avatar
5 votes
1 answer
743 views

Valence correction by adding formal charge in RDKit

I am modeling molecules as graphs, with nodes as atom types and edges as bond types (single, double, triple). I do not model formal charges or hydrogens explicitly (only heavy atoms). When trying to ...
Njw96's user avatar
  • 191
7 votes
2 answers
795 views

How to generate the SMILES for .cif files correctly and how do I generate .pkl or .pickle file out of these SMILES

I used openbabel to convert the .cif files to .smi. Here are parts of the .smi corresponding to two .cif files (I have many .cif files): ...
Rose Vanilla's user avatar
9 votes
1 answer
83 views

Is there a method or web API to get pricing from a SMILES string?

A variety of databases include "purchasability" (e.g., ZINC) and can be filtered as such. Or you can download just the purchasable compounds. I'm curious if there are methods or web APIs to ...
Geoff Hutchison's user avatar
4 votes
0 answers
53 views

Compositional SMILES data [closed]

I am interested to know if it is possible to encode compositional information in SMILES strings or other structural identifiers. For instance, in generating a SMILES string when combining two ...
shinyleaf's user avatar
6 votes
3 answers
1k views

Using OpenBabel's gen3d in a Python notebook

I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...
Meheret's user avatar
  • 93
4 votes
1 answer
147 views

How to create png files of right angle Lewis notation

I've recently begun experimenting with drawing molecules from smiles expressions for use in an educational website. I am looking for a way to create simple structural representations of various ...
Dr Acme Isme's user avatar
4 votes
1 answer
526 views

How to do SMARTS reaction substructure mapping with RDKit

I have been trying to use the RDKit's reaction substructure matching for some time. I want to match all reactions where a C-H bond is being broken to form a new C-C bond. This is my code: ...
S R Maiti's user avatar
  • 6,841
7 votes
1 answer
578 views

Rdkit: How can I get a weighted adjacency matrix where the weights are bond lengths, from the SMILES of my molecule?

Given the SMILES of my molecule, how can I get a weighted adjacency matrix where the weights are the bond lengths, using the Rdkit package and Python?
sriram's user avatar
  • 161
10 votes
1 answer
579 views

Node features matrix with Networkx

I built a function to generate graphs from smiles strings using networkx, inserting various features on the nodes. This is the code: ...
Gianmarco Luchetti 's user avatar
11 votes
2 answers
5k views

How to input 3D coordinates from xyz file and connectivity from SMILES in rdkit?

I am working on a QSAR project where the 3D structural descriptors are an input to a machine learning model. I am generating the descriptors using the python Mordred API (which uses rdkit). ...
S R Maiti's user avatar
  • 6,841
10 votes
2 answers
2k views

How to convert SMILES to Amino Acids sequence using RDKit

I have the following SMILES, wrapped in Python RDKit: ...
neversaint's user avatar
8 votes
2 answers
1k views

RDkit and PySmiles results differ on some SMILES strings

I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
nir shahar's user avatar
4 votes
0 answers
78 views

RDkit parse zero-order bonds (python) [closed]

I'm a computer scientist, helping with a chemistry project in python. I have been working with the library pysmiles in order to parse ...
nir shahar's user avatar
11 votes
2 answers
433 views

How to canonicalize SMILES written with aromatic bond symbols (:)?

I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols e.g. NC:1:N:N:C:[N]1N. RDKit does ...
Cody Aldaz's user avatar
  • 8,017
9 votes
1 answer
182 views

Excluding certain sp3-hybridized carbons with SMARTS

Let's say I have a compound shown above (SMILES: CCC(F)(F)F), and I want to exclude the trifluoromethyl group with SMARTS, how would I do that? I have tried ...
Theophylline's user avatar