Versioning

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.

Changelog

v0.7.23 (2024-03-27)

• Fixes bug in inter_chain_cc() for ldrs so conformers generated with -scm mcsce also work

v0.7.22 (2024-03-22)

• Fixes issue where clash-checking IDR combinations was not being performed between different chains

v0.7.21 (2024-03-13)

• When a given sequence overlaps with sequence from folded template in ldrs, ignore building on that chain

• Fixes issue #269

v0.7.20 (2024-02-01)

• Add a note for users in the README.rst regarding conformers generated with ldrs prior to version 0.7.17

v0.7.19 (2024-01-29)

• Update Sphinx requirement to v5 to fix docs workflow and tox error

v0.7.18 (2024-01-25)

• Correct case where multiple chains are given in a template and only some need ldrs

• Update documentation to clarify sequence formatting example for complexes

v0.7.17 (2024-01-20)

• Fix bug where torsion angles from ldrs would be swapped sometimes due to mirroring in rotation matrix

v0.7.16 (2024-01-11)

• Update citation for ldrs module to Bioinformatics paper

v0.7.15 (2024-01-05)

• Bug-fix for ldrs file processing during psurgeon stage for single IDR cases

v0.7.14 (2024-01-04)

• Correct reference hyperlink in usage documentation

v0.7.13 (2024-01-03)

• Update documentation for clarity

• Update example folder with processing AlphaFold structures

v0.7.12 (2023-11-17)

• Update documentation for DSSP due to clarity with version requirements

• Set default of -cmd in sscalc to mkdssp

v0.7.11 (2023-11-02)

• Update citing information.

v0.7.10 (2023-10-27)

• Correct reading CIF files without # end block.

• Fix minor bugs for reading CIF templates in ldrs

v0.7.9 (2023-10-27)

• Update libstructure.Structure documentation.

v0.7.8 (2023-10-02)

• Bug-fix in ldrs for input sequence recognition

v0.7.7 (2023-09-26)

• Bug-fix MC-SCE integration with force-field topology generation

v0.7.6 (2023-09-25)

• Update documentation for installation and usage

v0.7.5 (2023-09-11)

• Fix tests for cli_build.py that arose from #245

v0.7.4 (2023-09-11)

• Add --long and --long-ranges to the build subclient to build long (300+ AA) IDPs much quicker

• Change default backbone energy -etbb in build to 100.0

• Change default sidechain energy -etss in build to 250.0

v0.7.3 (2023-09-11)

• Add select ionic radii from CRC Handbook of Chemistry and Physics, 82nd Ed

• Update merge module 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 -etbb in ldrs to 100.0

• Change default sidechain energy -etss in ldrs to 250.0

v0.7.2 (2023-07-27)

• Correct documentation formatting reference to MC-SCE

v0.7.1 (2023-07-27)

• Update documentation formatting for LDRS

• Update README citations

• Temporarily removed MacOS GitHub actions tests

v0.7.0 (2023-07-25)

• Added new module ldrs to build IDRs in the context of a folded region

• Added new module resre to rename certain residue names of multiple PDB files

• Minor bug-fixes to numpy references (#231)

v0.6.17 (2023-06-12)

• Bug-fix for installation and tox build/pr

v0.6.16 (2022-11-08)

• Update citation to J Phys Chem A reference

v0.6.15 (2022-09-26)

• Added new subclient bgeodb to append to the database exact bgeos

• Implement exact bgeo-strategy

• Add documentation regarding new features with exact and bgeodb

• PR #220

v0.6.14 (2022-07-13)

• Add tests to cli_build.main (#225)

v0.6.13 (2022-07-13)

• Correct how some loops are written due to redundancies (#226)

v0.6.12 (2022-07-07)

• lint files

v0.6.11 (2022-06-14)

• Add option to build backbone conformers with fixed bond angle and distances. (#217)

v0.6.10 (2022-06-14)

• Implement boxplot plotting feature for bond angle distributions

• Append documentation for bgeo subclient

• Ability to use degrees for bgeo subclient

• Ability to change the name of the ouput file for bgeo subclient

• PR #219

v0.6.9 (2022-06-13)

• Correct CLI help for the --mem flag in the sethpc subclient (#218)

v0.6.8 (2022-06-13)

• Add bioRxiv citation

v0.6.7 (2022-05-31)

• update actions from master to main

• update install instructions for MC-SCE in GRAHAM (#215)

v0.6.6 (2022-05-27)

• Add pr env to tox

• Update CI workflows

• Update ReadTheDocs python version to 3.8

• Dropped python 3.7 after Numpy

v0.6.5 (2022-05-25)

• Correct typo bugs in fastext and bgeo

• General lints

v0.6.4 (2022-05-25)

• Re-licensed to Apache-2.0

v0.6.3 (2022-05-25)

v0.6.2 (2022-05-25)

• Update usage instructions for bgeo

v0.6.1 (2022-05-25)

• updated GRAHAM install instruction (#207)

v0.6.0 (2022-05-24)

• Add bond geometry option to build with Int2Cart software

• PR #203

v0.5.1 (2022-05-24)

• add plot functions to sscalc and torsions

• PR #198

v0.5.0 (2022-05-24)

• Add residue tolerance matrices: EDSS50

• Update/improve parameters to residue tolerance options

• PR #183

v0.4.10 (2022-05-23)

• Add documentation RTD format

• Add documentation for several features and examples

• PR #171

v0.4.9 (2022-05-23)

• Add sethpc client.

• Add merge client.

• PR #202

v0.4.8 (2022-05-23)

• Add stats client

• Add search client

• PR #200

v0.4.7 (2022-05-23)

• update CI methods

• PR #205

v0.4.6 (2022-04-22)

v0.4.5 (2022-04-21)

v0.4.4 (2022-03-29)

• Fixes MC-SCE integration when sidechain packing fails

• Corrects MC-SCE installation

• #190

v0.4.3 (2022-03-26)

v0.4.2 (2022-03-20)

v0.4.1 (2022-03-17)

• Adds support for single residues when not specified. Addresses #184

v0.4.0 (2022-03-15)

• Integrates the MC-SCE protocol in the building process as part of the sidechain packing method options.

v0.3.3 (2022-03-14)

• removes assert in 0.3.2

v0.3.2 (2022-03-14)

• improves regex creation to avoid silent bugs in possible parallel futures

v0.3.1 (2022-03-13)

• incorporates G in H when treating DSSP with reduced labels

v0.3.0 (2022-03-13)

• 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

v0.2.6 (2022-03-13)

• corrected sscalc from * input in command-line #175

v0.2.5 (2022-03-11)

• Implemented capacity to read PDBs with names different from cull #167

v0.2.4 (2022-03-11)

• implemented support for N-terminal Proline residues #166

v0.2.3 (2022-03-08)

• corrected energy.log #162

v0.2.2 (2022-03-07)

• incorporated libfuncpy internally

v0.2.1 (2022-03-03)

v0.2.0 (2022-02-10)

v0.1.0 (2021-07-24)

• Implements energy calculation to individual pairs. Energy threshold can now be compared to pairs or whole.

v0.0.24 (2021-07-01)

• Corrects make_folder function in cli_build.

v0.0.23 (2021-07-01)

• Added libfuncpy to requirements.yml

v0.0.22 (2021-06-30)

• Users are now able to fully configure the size of fragments and probabilities,

  via the flag -xp that expects a two column file.

v0.0.21 (2021-06-28)

• Now build prints log to terminal.

• improved other minor logging issues

v0.0.20 (2021-06-21)

• Decoupled energy-threshold parameters. Now Backbone and sidechains,

  can be configured separately.

v0.0.19 (2021-06-14)

• Saves a table with energy values per conformer.

• Crash reports now saved in execution folder (CLI build).

v0.0.18 (2021-06-10)

• 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.

v0.0.17 (2021-06-10)

• Corrects bug in Coulomb formula

v0.0.16 (2021-06-09)

• Add output-folder option for the build interface

v0.0.15 (2021-06-09)

• corrected typo in example/ commands

v0.0.14 (2021-06-05)

• Users can now select single residue fragment size

• -xp parameter was updated with checks and completion

v0.0.13 (2021-05-28)

• Added usage example and documentation.

v0.0.12 (2021-05-28)

• Corrects path suffix evaluation in cli_torsions.py

v0.0.11 (2021-05-28)

• corrects var name bug in ProgressBar

v0.0.10 (2021-05-27)

• Implements residue substitution/tolerance during conformer build

v0.0.9 (2021-05-27)

• user can now define the fragment size selection probabilities

v0.0.8 (2021-05-09)

• Expands try:catch to avoid index error when restarting conformer

v0.0.7 (2021-05-09)

• saves version number to file before running a client

v0.0.6 (2021-04-20)

• additional functions for logging

• add logging to build and other parts

v0.0.5 (2021-04-19)

• added --energy-threshold flag to control energy threshold after sidechain addition

v0.0.4 (2021-04-19)

• builder CLI now accepts .fasta files.

v0.0.3 (2021-04-19)

• added matplotlib in requirements.yml as dependency

v0.0.2 (2021-04-03)

• corrects variable name in libbuild that was breaking sidechain

  construction.

v0.0.1 (2021-04-02)

• added CI integration files

v0.0.0

• Any development previous to version 0.0.1 is registered in PRs up to #102.