Questions tagged [smiles]
Questions about or relating to SMILES (simplified molecular-input line-entry system) or related things such as SMARTS.
21 questions
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QUICK energy calculations in Amber Tools, vs Gaussian 16, vs Open Babel MMFF94
I am just getting back into molecular modeling, and looking for an open-source tool for generating some conformers from various SMILES to use in binding simulations.
Way back when I used Gaussian for ...
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4
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Creating RDkit script to show how SMILES strings translate from the structure like the wikipedia image
I would like to start using SMILES strings for some research, and I'd like to show my colleagues how SMILES works. They aren't do much computation, so I want to keep it simple, but the molecules I ...
5
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83
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Butina cluster over a 300 million SMILES
I have a dataset with approximately 300 million SMILES strings, for which I want to apply Butina clustering and extract the Tanimoto similarity matrix to visualize the PCA of this matrix.
Since I have ...
Manuel Ravasqueira
2
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1
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39
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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?
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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 ...
- 7,171
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762
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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 ?
5
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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 ...
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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):
...
- 145
9
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90
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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 ...
- 9,395
4
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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 ...
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1k
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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 ...
- 103
4
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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 ...
- 43
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1
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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:
...
- 7,171
7
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911
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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?
- 161
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620
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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:
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11
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2
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6k
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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).
...
- 7,171
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How to convert SMILES to Amino Acids sequence using RDKit
I have the following SMILES, wrapped in Python RDKit:
...
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RDkit and PySmiles results differ on some SMILES strings
I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
- 223
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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 ...
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11
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2
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529
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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 ...
- 8,025
9
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218
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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 ...
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