What’s new
v1.0.0 (May 2019)
- Added publications DOI.
- Added renumber, order, top_position cut and sampling to FragmentFrame.
- Added the ability to attach a source column to FragmentFrame.
- Adds write new Rosetta fragment format strictly from the fragment data.
- Adds
highlight
function to showcase rows following complex selection logics.
- Parse
POSE_ENERGIES_TABLE
from Rosetta-generated PDB files.
- Read MASTER files with
parse_master_file
.
- Adds function to get the sequence given certain residue labels.
v0.9.0 (January 2019)
- Patch bug that will crash FASTA sequence output when sequence identifier is a number.
- Adds utility function to change the text of a legend on plotting.
- Adds function to ensure logic in fragment data is properly kept.
- Adds function to mix fragment data.
- Adds function to concatenate fragment data.
- 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.
- Adds method
DesignFrame.clean_rosetta_suffix()
to clean Rosetta _0001
suffixes (use with caution)
- Adds ability to read from different single-chain Poses with different chain identifier into the same column.
- Add the ability to compare design populations with
real data
.
- Improved plotting control over axis in some multi-axis functions, notably in Ramachandran and LOGO plots.
v0.8.0 (September 2018)
- Patch bug when plotting
positional_sequence_similarity_plot
when a reference shift was added.
- Patch bug when calling
get_sequence_with
providing PDB-numbered selections.
v0.7.0 (August 2018)
- Command line scripts attached to the distribution.
check_mutants
script adapts itself to the number of sequences.
DesignFrame
function for sequence/structure global frequencies are key_residue
aware.
DesignFrame
mutant functions can work with list-type key_residue
.
- Added ability to read phi/psi angles from Rosetta output and plot Ramachandran.
- Added ability to read HMMsearch output.
- Descriptions to load silent files can be provided as YAML.
- Read json-formated Rosetta score files.
- Select a different
seqID
for fasta reading.
- Sequence distance can be calculated against a different
DesignFrame
.
- Plot data from a 96-well microplate.
- Read and plot SPR data.
- Read and plot CD spectra.
- Formatted plots for Thermal Melt, and MALS.
- Read and process Next Generation Sequencing data.
- Function to plot per residue score after applying a similarity matrix.
- Ability to execute the mutant variants to obtain scores for the new suggested mutations with
apply_resfile
.
generate_mutant_variants
allows to explore all residue types for a position with ‘*’.
- Keep silent file instead of minisilent after running
get_sequence_and_structure
allows better integration with apply_resfile
.
- Function to plot per residue score after applying a similarity matrix
- Adding logo plot color schemes.
- Added population and positional enrichment for comparison between two sequence populations.
v0.6.0 (April 2018)
- First version of the documentation.
- Generate frequency and pssm matrix from
FragmentFrame
.
- Generate sequence transition networks for the frequency matrices.
- Fixed LOGO plot and added multi-line option.
- Labels are read as
Selection
.
- Write FASTA can generate multiple individual files.
- CLUSTALW format outputs
- Plot alignments with mutants highlight.
- New check_mutants script