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Commits on May 11, 2026

• Update dca_analysis.py

  AlbertodelaPaz

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Commits on May 5, 2026

• Updated clean_pfam and filter_pfam functions to be significantly faster. Also added in filter_pfam the option to specify percent contiguous gaps in the function (instead of the number of gaps you w…

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  jmart-n

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Commits on Nov 19, 2025

• Calculate Frobenius norm for couplings

  AlbertodelaPaz

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• Change default symbolDict to use specific alphabet

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  AlbertodelaPaz

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• updated .gitignore

  AlbertodelaPaz

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• Added a Frobenius method for the dca object and a function to translate adabm unto our format in dca_functions

  

  de la Paz

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• Minor changes on alignment with nucleotides

  

  de la Paz

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Commits on Aug 26, 2025

• Update pyproject to 1

  

  de la Paz

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• I added a function called MapMSA2hmmProfile to align a list of sequences to an existing MSA profile

  

  de la Paz

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Commits on Jul 29, 2025

• Update dca_functions.py

  AlbertodelaPaz

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• Update dca_functions.py

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  AlbertodelaPaz

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• Trying to fix license error

  jmart-n

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Commits on Jul 14, 2025

• Merge branch 'master' of github.com:utdal/py-mfdca

  jmart-n

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• changed map_filter_DI so that it can take pairs without the DI attached

  jmart-n

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Commits on Jul 8, 2025

• I modified the get_all_contacts to ignore author numbering and chains when using mmCIF

  

  de la Paz

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Commits on Jul 4, 2025

• Update dca_analysis.py

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  jmart-n

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Commits on Jul 3, 2025

• Updated the plotting function. finding hits and misses of DI pairs now

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  jmart-n

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Commits on Jun 17, 2025

• We added a function to take a nucleotide sequence, map it to an hmm and create the inputs for seec-nt

  

  de la Paz

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Commits on Jun 13, 2025

• Corrected .toml

  

  de la Paz

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• New hmm_tools.py module included with the respective change in the .toml and Readme

  

  de la Paz

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Commits on May 29, 2025

• updated README

  jmart-n

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Commits on May 28, 2025

• Added new cdist function, which for large MSA should be considerably faster

  jmart-n

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• Updated to pyproject.toml format, some formatting changes in other files

  jmart-n

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Commits on May 27, 2025

• Update helper_functions.py

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  AlbertodelaPaz

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Commits on May 7, 2025

• Now you can use mmCIF in get_allatom_contacts and I included a line to clear the cache at backmap_alignmnet

  

  de la Paz

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• Update helper_functions.py

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  jmart-n

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Commits on Mar 25, 2025

• I included some decorators for jit at function related to effective alphabet and included the necessary dependencies

  

  de la Paz

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Commits on Mar 21, 2025

• Initial Commit: I included a function to get the conditional single site distribution from the Potts model expression, another function to compute the effective alphabet and the corresponding metho…

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  de la Paz

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Commits on Jan 10, 2024

• Update Readme.md

  jmart-n

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Commits on Dec 19, 2023

• updated class function so that variables are actually passed correctly

  

  Jonathan Martin

  authored and

  Jonathan Martin

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• Updated hamiltonian function to allow inter-domain scoring. Added unit tests for Hamiltonian and this new functionality.

  

  Jonathan Martin

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  Jonathan Martin

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Commits on Dec 18, 2023

• Added variable for removing self.sequences variable after performing mean_field(). Added some descriptions of mean_field() options.

  

  Jonathan Martin

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  Jonathan Martin

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Commits on Jan 19, 2023

• Update dca_functions.py

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  jmart-n

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Commits on Aug 18, 2022

• Update readme.md

  jmart-n

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• Update Readme.md

  jmart-n

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