Answers.Body: <p>It looks like various chemical software toolkits can export SMILES, for example <a href="http://openbabel.org/wiki/SMILES" rel="nofollow noreferrer">OpenBabel</a>, using the <a href="http://openbabel.org/wiki/Babel" rel="nofollow noreferrer">babel command line tool.</a> I am not readily seeing the best way to read e.g. a FASTA, though. Another option would be <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwi52YLa98r9AhVPMTQIHT8QCRkQFnoECAwQAQ&amp;url=https%3A%2F%2Fperkinelmerinformatics.com%2Fproducts%2Fresearch%2Fchemdraw&amp;usg=AOvVaw0BmVb9fWH4mKXs22TzVe39" rel="nofollow noreferrer">ChemDraw</a>.</p>
  <p><a href="https://www.researchgate.net/post/How_do_I_convert_my_peptides_into_SMILES_strings" rel="nofollow noreferrer">This researchgate thread</a> has a lot of information on peptide-&gt;SMILES conversion, I don't see nucleotides though.</p>
  <p>One option, though it would be a little finicky, would be to look up the nucleotides SMILES strings on <a href="https://pubchem.ncbi.nlm.nih.gov/#query=adenosine" rel="nofollow noreferrer">PubChem</a> and then write a script to string them together (with a monophosphate) based on an input sequence. It seems like <a href="https://github.com/rdkit/rdkit/issues/3080" rel="nofollow noreferrer">there is some related tooling already in rdkit</a>, but a convenient API doesn't seem to exist yet. <a href="https://Born,%20Jannis.%20(2020).%20Re:%20How%20do%20I%20convert%20my%20peptides%20into%20SMILES%20strings?.%20Retrieved%20from:%20https://www.researchgate.net/post/How_do_I_convert_my_peptides_into_SMILES_strings/5eaff1007b75ea5bbf031b32/citation/download." rel="nofollow noreferrer">The developer does have one suggestion for peptides</a>, which would translate into something like this for nucleotides:</p>
  <pre><code>from rdkit import Chem
  
  nt_mol = Chem.MolFromFASTA(&quot;ACATATAT&quot;, flavor=9)  # flavor param notes as DNA
  Chem.MolToSMILES(nt_mol)
  </code></pre>
  <p>To do this across many nucleotides you could hook it up to biopython to iterate across a FASTA file.</p>
  <p>The nucleotide <code>flavor</code> option exists, but there is a note that only peptide is supported. I don't know whether that means the feature is experimental or is not implemented.</p>
  
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Answers.CreationDate: 2023-03-07T23:10:17.930Z
Answers.LastActivityDate: 2023-03-07T23:10:17.930Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I want to use physico chemical descriptors of single stranded DNA/RNA-Oligonucleotides in order to model certain properties. To generate these descriptors i need a computer understandable representation of these oligonucleotides, e.g. the SMILES representation. So far i could not find of any method to generate these SMILES representations out of the primary structure of these oligonucleotides.
  I am wondering if someone knows of a software, that takes the primary sequence of a single stranded DNA-Oligonucleotide with e.g. 50 nts as input and gives the SMILES representation as output.
  So far i could find nothing that would accomplish this task, although, at least to me, it seems like a straight forward task.</p>
  <p>I will appreciate every constructive thought on that.</p>
  <p>Thanks!</p>
  <p><strong>EDIT:</strong> Add some form of input and output file</p>
  <p>As requested here an example of input and output pair:</p>
  <p>input should be primary sequence:
  TCA</p>
  <p>output should be the corresponding SMILES string:
  O=C(C(C)=CN1[C@@]2([H])C([H])([H])C@@([H])C@([H])O2)NC1=O</p>
  <p>This example was generated with chemdraw 20.1.1.</p>
  <p>For my use case i need a software, that convert many (like 50k - 1000k) primary sequences of single stranded DNA/RNA with a length of about 50 nts into the corresponding SMILES string. Ideally would be some sort of python package but anything else would help also a lot!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-26T16:26:56.513Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-27T19:39:45.443Z
Comments.Text: Can you please provide an example input file and example output file?
Comments.UserDisplayName: gringer
Tags: <rna>
Title: Is it possible to create SMILES representation out of DNA/RNA-Oligonucleotides (~50 nts)?
ThreadText: # Is it possible to create SMILES representation out of DNA/RNA-Oligonucleotides (~50 nts)?
  
  (Asked by: username_0 on 2023-01-26)
  
  I want to use physico chemical descriptors of single stranded DNA/RNA-Oligonucleotides in order to model certain properties. To generate these descriptors i need a computer understandable representation of these oligonucleotides, e.g. the SMILES representation. So far i could not find of any method to generate these SMILES representations out of the primary structure of these oligonucleotides.
  I am wondering if someone knows of a software, that takes the primary sequence of a single stranded DNA-Oligonucleotide with e.g. 50 nts as input and gives the SMILES representation as output.
  So far i could find nothing that would accomplish this task, although, at least to me, it seems like a straight forward task.
  
  I will appreciate every constructive thought on that.
  
  Thanks!
  
  **EDIT:** Add some form of input and output file
  
  As requested here an example of input and output pair:
  
  input should be primary sequence:
  TCA
  
  output should be the corresponding SMILES string:
  O=C(C(C)=CN1[C@@]2([H])C([H])([H])C@@([H])C@([H])O2)NC1=O
  
  This example was generated with chemdraw 20.1.1.
  
  For my use case i need a software, that convert many (like 50k - 1000k) primary sequences of single stranded DNA/RNA with a length of about 50 nts into the corresponding SMILES string. Ideally would be some sort of python package but anything else would help also a lot!
  
  **Tags:** rna
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: Can you please provide an example input file and example output file?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-03-07. Score: 3 | Accepted answer
  
  It looks like various chemical software toolkits can export SMILES, for example [OpenBabel](http://openbabel.org/wiki/SMILES), using the [babel command line tool.](http://openbabel.org/wiki/Babel) I am not readily seeing the best way to read e.g. a FASTA, though. Another option would be [ChemDraw](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwi52YLa98r9AhVPMTQIHT8QCRkQFnoECAwQAQ&url=https%3A%2F%2Fperkinelmerinformatics.com%2Fproducts%2Fresearch%2Fchemdraw&usg=AOvVaw0BmVb9fWH4mKXs22TzVe39).
  
  [This researchgate thread](https://www.researchgate.net/post/How_do_I_convert_my_peptides_into_SMILES_strings) has a lot of information on peptide->SMILES conversion, I don't see nucleotides though.
  
  One option, though it would be a little finicky, would be to look up the nucleotides SMILES strings on [PubChem](https://pubchem.ncbi.nlm.nih.gov/#query=adenosine) and then write a script to string them together (with a monophosphate) based on an input sequence. It seems like [there is some related tooling already in rdkit](https://github.com/rdkit/rdkit/issues/3080), but a convenient API doesn't seem to exist yet. [The developer does have one suggestion for peptides](https://Born,%20Jannis.%20(2020).%20Re:%20How%20do%20I%20convert%20my%20peptides%20into%20SMILES%20strings?.%20Retrieved%20from:%20https://www.researchgate.net/post/How_do_I_convert_my_peptides_into_SMILES_strings/5eaff1007b75ea5bbf031b32/citation/download.), which would translate into something like this for nucleotides:
  
  ```
  from rdkit import Chem
  
  nt_mol = Chem.MolFromFASTA("ACATATAT", flavor=9)  # flavor param notes as DNA
  Chem.MolToSMILES(nt_mol)
  
  ```
  
  To do this across many nucleotides you could hook it up to biopython to iterate across a FASTA file.
  
  The nucleotide `flavor` option exists, but there is a note that only peptide is supported. I don't know whether that means the feature is experimental or is not implemented.
  
  
  ---
  
  