What’s new

v1.0.0 (May 2019)

  1. Added publications DOI.
  2. Added renumber, order, top_position cut and sampling to FragmentFrame.
  3. Added the ability to attach a source column to FragmentFrame.
  4. Adds write new Rosetta fragment format strictly from the fragment data.
  5. Adds highlight function to showcase rows following complex selection logics.
  6. Parse POSE_ENERGIES_TABLE from Rosetta-generated PDB files.
  7. Read MASTER files with parse_master_file.
  8. Adds function to get the sequence given certain residue labels.

v0.9.0 (January 2019)

  1. Patch bug that will crash FASTA sequence output when sequence identifier is a number.
  2. Adds utility function to change the text of a legend on plotting.
  3. Adds function to ensure logic in fragment data is properly kept.
  4. Adds function to mix fragment data.
  5. Adds function to concatenate fragment data.
  6. Adds function to generate qgrids as per the qgrid library. This is a simple wrapper that just makes sure that the html div overflows if the number of columns is too high. Adds a soft requirement to the library.
  7. Adds method DesignFrame.clean_rosetta_suffix() to clean Rosetta _0001 suffixes (use with caution)
  8. Adds ability to read from different single-chain Poses with different chain identifier into the same column.
  9. Add the ability to compare design populations with real data.
  10. Improved plotting control over axis in some multi-axis functions, notably in Ramachandran and LOGO plots.

v0.8.0 (September 2018)

  1. Patch bug when plotting positional_sequence_similarity_plot when a reference shift was added.
  2. Patch bug when calling get_sequence_with providing PDB-numbered selections.

v0.7.0 (August 2018)

  1. Command line scripts attached to the distribution.
  2. check_mutants script adapts itself to the number of sequences.
  3. DesignFrame function for sequence/structure global frequencies are key_residue aware.
  4. DesignFrame mutant functions can work with list-type key_residue.
  5. Added ability to read phi/psi angles from Rosetta output and plot Ramachandran.
  6. Added ability to read HMMsearch output.
  7. Descriptions to load silent files can be provided as YAML.
  8. Read json-formated Rosetta score files.
  9. Select a different seqID for fasta reading.
  10. Sequence distance can be calculated against a different DesignFrame.
  11. Plot data from a 96-well microplate.
  12. Read and plot SPR data.
  13. Read and plot CD spectra.
  14. Formatted plots for Thermal Melt, and MALS.
  15. Read and process Next Generation Sequencing data.
  16. Function to plot per residue score after applying a similarity matrix.
  17. Ability to execute the mutant variants to obtain scores for the new suggested mutations with apply_resfile.
  18. generate_mutant_variants allows to explore all residue types for a position with ‘*’.
  19. Keep silent file instead of minisilent after running get_sequence_and_structure allows better integration with apply_resfile.
  20. Function to plot per residue score after applying a similarity matrix
  21. Adding logo plot color schemes.
  22. Added population and positional enrichment for comparison between two sequence populations.

v0.6.0 (April 2018)

  1. First version of the documentation.
  2. Generate frequency and pssm matrix from FragmentFrame.
  3. Generate sequence transition networks for the frequency matrices.
  4. Fixed LOGO plot and added multi-line option.
  5. Labels are read as Selection.
  6. Write FASTA can generate multiple individual files.
  7. CLUSTALW format outputs
  8. Plot alignments with mutants highlight.
  9. New check_mutants script