This project follows strictly Semantic Versioning 2.0 for version control.
All additions to the master branch are done by PR followed by its respective version increment.
While in version 0, minor and patch upgrades converge in the patch number while major upgrades are reflected in the minor number.
- Update user install instructions to use only
miniconda3.
- Added first steps page to documentation.
- Fixes bug in
inter_chain_cc()forldrsso conformers generated with-scm mcscealso work
- Fixes issue where clash-checking IDR combinations was not being performed between different chains
- When a given sequence overlaps with sequence from folded template in
ldrs, ignore building on that chain - Fixes issue #269
- Add a note for users in the
README.rstregarding conformers generated withldrsprior to version 0.7.17
- Update Sphinx requirement to v5 to fix
docsworkflow andtoxerror
- Correct case where multiple chains are given in a template and only some need
ldrs - Update documentation to clarify sequence formatting example for complexes
- Fix bug where torsion angles from
ldrswould be swapped sometimes due to mirroring in rotation matrix
- Update citation for
ldrsmodule to Bioinformatics paper
- Bug-fix for
ldrsfile processing duringpsurgeonstage for single IDR cases
- Correct reference hyperlink in usage documentation
- Update documentation for clarity
- Update example folder with processing AlphaFold structures
- Update documentation for DSSP due to clarity with version requirements
- Set default of
-cmdinsscalctomkdssp
- Update citing information.
- Correct reading CIF files without # end block.
- Fix minor bugs for reading CIF templates in
ldrs
- Update libstructure.Structure documentation.
- Bug-fix in
ldrsfor input sequence recognition
- Bug-fix MC-SCE integration with force-field topology generation
- Update documentation for installation and usage
- Fix tests for
cli_build.pythat arose from #245
- Add
--longand--long-rangesto thebuildsubclient to build long (300+ AA) IDPs much quicker - Change default backbone energy
-etbbinbuildto 100.0 - Change default sidechain energy
-etssinbuildto 250.0
- Add select ionic radii from CRC Handbook of Chemistry and Physics, 82nd Ed
- Update
mergemodule to use multiprocessing - Increase efficiency of clash-checking algorithm in
ldrs_helper.py - Acceptance and automated processing of proteins with a membrane/bilayer
- Automated clash-checking between all combinations of IDRs built
- Added ability for multi-chain protein detection and processing
- Added ability to build IDRs on multi-chain complexes
- Change default backbone energy
-etbbinldrsto 100.0 - Change default sidechain energy
-etssinldrsto 250.0
- Correct documentation formatting reference to MC-SCE
- Update documentation formatting for LDRS
- Update README citations
- Temporarily removed MacOS GitHub actions tests
- Added new module
ldrsto build IDRs in the context of a folded region - Added new module
resreto rename certain residue names of multiple PDB files - Minor bug-fixes to numpy references (#231)
- Bug-fix for installation and tox build/pr
- Update citation to J Phys Chem A reference
- Added new subclient
bgeodbto append to the database exact bgeos - Implement
exactbgeo-strategy - Add documentation regarding new features with
exactandbgeodb - PR #220
- Add tests to
cli_build.main(#225)
- Correct how some loops are written due to redundancies (#226)
- lint files
- Add option to build backbone conformers with fixed bond angle and distances. (#217)
- Implement boxplot plotting feature for bond angle distributions
- Append documentation for
bgeosubclient - Ability to use
degreesforbgeosubclient - Ability to change the name of the ouput file for
bgeosubclient - PR #219
- Correct CLI help for the
--memflag in thesethpcsubclient (#218)
- Add bioRxiv citation
- update actions from
mastertomain - update install instructions for MC-SCE in GRAHAM (#215)
- Add
prenv totox - Update CI workflows
- Update ReadTheDocs python version to 3.8
- Dropped python 3.7 after Numpy
- Correct typo bugs in
fastextandbgeo - General lints
- Re-licensed to Apache-2.0
- Update usage instructions for bgeo
- updated GRAHAM install instruction (#207)
- Add bond geometry option to build with Int2Cart software
- PR #203
- add plot functions to
sscalcandtorsions - PR #198
- Add residue tolerance matrices: EDSS50
- Update/improve parameters to residue tolerance options
- PR #183
- Add documentation RTD format
- Add documentation for several features and examples
- PR #171
- Add
sethpcclient. - Add
mergeclient. - PR #202
- Add
statsclient - Add
searchclient - PR #200
- update CI methods
- PR #205
- Fixes MC-SCE integration when sidechain packing fails
- Corrects MC-SCE installation
- #190
- Adds support for single residues when not specified. Addresses #184
- Integrates the MC-SCE protocol in the building process as part of the sidechain packing method options.
- removes assert in 0.3.2
- improves regex creation to avoid silent bugs in possible parallel futures
- incorporates G in H when treating DSSP with reduced labels
- see #168
- Revisited the whole regex sampling machinery during conformer building
- A initial major part for preparing the regex database was dropped
- applied multiprocessing to the regex database preparation steps
- updated the cli_build API with 4 new command options
- dropped using regex in the cli_build command line
- corrected sscalc from * input in command-line #175
- Implemented capacity to read PDBs with names different from cull #167
- implemented support for N-terminal Proline residues #166
- corrected energy.log #162
- incorporated libfuncpy internally
- Implements energy calculation to individual pairs. Energy threshold can now be compared to pairs or whole.
- Corrects make_folder function in cli_build.
- Added libfuncpy to requirements.yml
- Users are now able to fully configure the size of fragments and probabilities,
- via the flag -xp that expects a two column file.
- Now build prints log to terminal.
- improved other minor logging issues
- Decoupled
energy-thresholdparameters. Now Backbone and sidechains, - can be configured separately.
- Decoupled
- Saves a table with energy values per conformer.
- Crash reports now saved in execution folder (CLI build).
- Improves sampling of multiple secondary structure regexes.
- Now, when given multiple regex, angle sampling will be biased towards the number of occurrences in each regex.
- Corrects bug in Coulomb formula
- Add output-folder option for the
buildinterface
- corrected typo in example/ commands
- Users can now select single residue fragment size
-xpparameter was updated with checks and completion
- Added usage example and documentation.
- Corrects path suffix evaluation in
cli_torsions.py
- corrects var name bug in ProgressBar
- Implements residue substitution/tolerance during conformer build
- user can now define the fragment size selection probabilities
- Expands try:catch to avoid index error when restarting conformer
- saves version number to file before running a client
- additional functions for logging
- add logging to build and other parts
- added
--energy-thresholdflag to control energy threshold after sidechain addition
builderCLI now accepts.fastafiles.
- added matplotlib in requirements.yml as dependency
- corrects variable name in
libbuildthat was breaking sidechain - construction.
- corrects variable name in
- added CI integration files
- Any development previous to version 0.0.1 is registered in PRs up to #102.