Contact Prediction ToolKit¶

Changelog¶

[0.12]

Fixed

• Resolve plotting of small contact maps

Changed

• Remove support for Python2.7
• Remove support for Python3.5
• Add support for Python3.8

[0.11.3]

Fixed

• Test cases ensure file removal regardless of failure

Changed

• Code formatting to adapt [Black](https://black.readthedocs.io/en/stable/) formatting

Added

• [map_align](https://github.com/sokrypton/map_align) contact file parser
• AppVeyor and TravisCI runs against Python3.7

[0.11.2]

Fixed

• Bug fix to avoid rare ZeroDivision

[0.11.1]

Changed

• conkit/core/ext/c_sequencefile.pyx removed print statement

[0.11]

Added

• conkit.io routines now accept keyword arguments
• SAINT2 and ROSETTA distance restraints can now be written, format keywords are saint2 and rosetta
• StructureSelector added to score protein structures by contact satisfaction

[0.10.2]

• MANIFEST.ini file required by PyPi

[0.10.1]

• Critical bug fix in installation procedure and Cython-code compilation

[0.10]

Added

• Support for Python 3.7
• Cython added as dependency and SciPy removed
• conkit.misc.deprecate decorator for easier tagging
• ContactMap.match provides keyword to add_false_negatives found in the reference but not in contact map
• ContactMap.remove_false_negatives allows convenient removal of false negatives
• ContactMap.recall to calculate the recall of a contact map
• SequenceFile.summary for quick alignment summaries
• A2mParser to read HH-suite A2M alignment files
• Automatic sphinx-apidoc generation for up-to-date index
• ClustalParser to read CLUSTAL formatted files

Changed

• SequenceFile.calculate_freq backend changed from numpy to Cython for faster computation
• SequenceFile.calculate_weights backend changed from numpy to Cython for faster computation
• SequenceFile.filter backend changed from numpy to Cython for faster computation
• SequenceFile.filter_gapped backend changed from numpy to Cython for faster computation
• SequenceFile.calculate_weights renamed to SequenceFile.get_weights
• SequenceFile.compute_freq renamed to SequenceFile.get_frequency
• ContactMap.singletons backend changed from numpy to Cython for faster computation
• Bandwidth backend changed from numpy to Cython for faster computation
• ContactMap.short_range_contacts renamed to ContactMap.short_range
• ContactMap.medium_range_contacts renamed to ContactMap.medium_range
• ContactMap.long_range_contacts renamed to ContactMap.long_range
• ContactMap.calculate_scalar_score renamed to ContactMap.set_scalar_score
• ContactMap.calculate_contact_density renamed to ContactMap.get_contact_density
• ContactMap.calculate_jaccard_index renamed to ContactMap.get_jaccard_index
• ContactMatchState provides options for true positive, true negative, false positive and false negative, which can be added to contacts in the map at will
• Contact.is_match and Contact.define_match renamed to attribute Contact.true_positive
• Contact.is_mismatch and Contact.define_mismatch renamed to attribute Contact.false_positive
• Contact.is_unknown and Contact.define_unknown renamed to attribute Contact.status_unknown
• Entity, Gap and Residue classes made public

Fixed

• Bug fix in SequenceFile.filter to remove Sequence entries reliably
• Bug fix in ContactMapMatrixFigure when gap variable was less than 1

Removed

• Python 3.4 support

[0.9]

Added

• conkit.plot subpackage refactored to allow matplotlib access of Figure instances. This provides functionality similar to seaborn, so matplotlib.Axes can be provided into which a plot is drawn.
• ContactMap.as_list function to represent the contact map as a 2D-list of residue indexes
• conkit.misc.normalize function to apply Feature scaling normalization
• CONTRIB.rst file to list all contributors
• SequenceFile.diversity property defined by \(\sqrt{N}/L\)
• ContactMap.reindex to reindex a contact map given a new starting index
• ContactMap.singletons returns a copy of the contact map with singleton contacts, i.e. ones without neighbors
• Sequence.seq_encoded to allow turning a sequence into an encoded list
• Sequence.encoded_matrix to give the entire alignment as encoded matrix
• SequenceFile.filter_gapped to filter sequences with a certain threshold of gaps
• SequenceFile.to_string and ContactMap.to_string methods
• ContactMapMatrixFigure added to illustrate prediction signal of entire ContactMap
• Added support for nebcon contact prediction format

Changed

• Changed API interface for conkit.plot in accordance to necessary changes for above
• ContactMapFigure now accepts lim parameters for axes limits
• ContactMapFigure and ContacctMapChordFigure improved to better space marker size
• Typos corrected in documentation
• THREE_TO_ONE and ONE_TO_THREE dictionaries modified to Enum objects
• SequeneFile.neff renamed to SequenceFile.meff
• ContactMapChordFigure.get_radius_around_circle moved to conkit.plot.tools.radius_around_circle
• AmiseBW.curvature renamed to AmiseBW.gauss_curvature

Fixed

• A3mParser keyword argument mismatch sorted

[0.8.4]

Added

• Entity.top property to always return the first child in the list
• ContactMap.find function accepts strict keyword argument to find contact pairs with both residues in register
• PdbParser takes a distance cutoff of 0 to include all Cb-Cb contacts in the protein structure
• ContactMatchState enumerated type for definitions of state constants for contact
• SequenceAlignmentState enumerated type for definitions of state constants for each sequence file
• NcontParser added to extract contact pairs identified by NCONT (CCP4 Software Suite)

Changed

• Optimized some functions and comparisons according to the recommended Python optimization instructions
• ContactMap.match does __not__ modifiy other by default anymore. Specify match_other=True as kwarg!
• ContactMap.calculate_kernel_density renamed to ContactMap.calculate_contact_density
• ContactDensityFigure draws domain boundary lines instead of symbols

[0.8.3]

Added

• requirements.txt file re-added for easier dependency installation
• LinearBW calculator added for linear bandwidth calculation in analysis
• seq_ascii property to Sequence for encoded sequence
• ascii_matrix property to SequenceFile for encoded alignment
• SequenceFile and ContactFile classes have new empty properties
• flib format for ContactFile classes to allow easier conversions for the Flib-Coevo fragment picking library

Changed

• Distance definitions accept floating point values
• _BandwidthCalc class renamed to BandwidthBase
• Abstractified BandwidthBase, and Parser with all subparser classes
• Refactored conkit/io/__init__.py to avoid duplication of code

Fixed

• PconsParser class accepts negative raw_score values
• SequenceFile.neff returns float instead of int
• CCMpredParser.read() returns empty ContactFile when matrix file empty

[0.8.2]

Added*

• Test function skipping added for SequenceFile.filter() when SciPy not installed

Changed

• Renamed conkit/io/tests files for filenames to agree with modules in conkit/io
• Performance of write() in parsers improved by construction of string and single call to write() of filehandle

Fixed

• Critical bug fix for automated opening of filehandle in Python2.7

[0.8.1]

Changed

• Revoked catching of SystemExit(0) exception in scripts when invoked with --help flag

Fixed

• Bug fix relating to Python3 automatic opening of file handles - Thanks to Miguel Correa for reporting this bug

[0.8]

Added

• Logging message coloring according to message level
• filter() function added for redundancy/distant homolog removal from SequenceFile
• License text added to each module
• io sub-package caches modules and imports upon request

Changed

• Default value in calculate_meff() and calculate_weights() changed from 0.7 to 0.8 [more commonly used in literature]
• core classes extracted to individual module files

Fixed

• Bug fix with PyPi installation where requirements.txt not found; fix includes removal of requirements.txt and addition of install_requires to setup.py instead. - Thanks to Miguel Correa for reporting this bug