Releases: LBC-LNBio/pyKVFinder
pyKVFinder v0.9.0
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings, hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH]: Expand cavity tags by @jvsguerra in #194
- Bump swig to 4.4.1 by @jvsguerra and @r1ckhdk in #194
- Update macOS runners by @jvsguerra and @r1ckhdk in #194
Full Changelog: v0.8.4...v0.9.0
Contributors
Assets 3
pyKVFinder v0.8.4
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings, hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH] Add compatilibility to Python 3.14 by @jvsguerra in #187
- Improve performance for Deploy workflow by @jvsguerra
Full Changelog: v0.8.3...v0.8.4
Contributors
Assets 3
pyKVFinder v0.8.3
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [BUG] fix for probe In smaller than step size by @jvsguerra in #180
- Bump pytest-cov from 6.2.1 to 7.0.0 by @dependabot[bot] in #179
Full Changelog: v0.8.2...v0.8.3
Contributors
Assets 3
pyKVFinder v0.8.2
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH] Add ARM64 Linux build by @jvsguerra in #177
- Bump pytest from 8.3.5 to 8.4.0 by @dependabot[bot] in #167
- Bump tomlkit from 0.13.2 to 0.13.3 by @dependabot[bot] in #168
- Bump pytest-cov from 6.1.1 to 6.2.1 by @dependabot[bot] in #170
- Bump flake8 from 7.2.0 to 7.3.0 by @dependabot[bot] in #172
- Bump pytest from 8.4.0 to 8.4.2 by @dependabot[bot] in #176
- Update plotly requirement from ~=6.0.1 to >=6.0.0,<6.4.0 by @dependabot[bot] in #174
Full Changelog: v0.8.1...v0.8.2
Contributors
Assets 3
pyKVFinder v0.8.1
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH] Add MacOS intel (x86_64) build by @jvsguerra in #166
Full Changelog: v0.8.0...v0.8.1
Contributors
Assets 3
pyKVFinder v0.8.0
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Migrate to tomlkit and improve build system by @jvsguerra in #163
Full Changelog: v0.7.3...v0.8.0
Contributors
Assets 3
pyKVFinder v0.7.3
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bug fix: delete temp file for exporting cavities to string by @jvsguerra in #155
- Bump black from 24.10.0 to 25.1.0 by @dependabot in #148
- Bump flake8 from 7.1.1 to 7.1.2 by @dependabot in #151
- Bump sphinxcontrib-video from 0.3.2 to 0.4.1 by @dependabot in #152
- Bump pytest from 8.3.4 to 8.3.5 by @dependabot in #153
Full Changelog: v0.7.2...v0.7.3
Contributors
Assets 3
pyKVFinder v0.7.2
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in #138
- Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 by @dependabot in #140
- Bump sphinxcontrib-video from 0.2.1 to 0.3.2 by @dependabot in #144
- Bump pytest from 8.3.3 to 8.3.4 by @dependabot in #141
- Update matplotlib requirement from ~=3.9.2 to ~=3.10.0 by @dependabot in #143
- Update numpy requirement from ~=2.1.2 to ~=2.2.1 by 80bc7a2
- [MNT] Update pyKVFinder build with cibuildwheel by @jvsguerra in #145
Full Changelog: v0.7.1...v0.7.2
Contributors
Assets 3
pyKVFinder v0.7.1
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump black from 24.8.0 to 24.10.0 by @dependabot in #136
- Add compatibility for Python 3.13
Full Changelog: v0.7.0...v0.7.1
Contributors
Assets 3
pyKVFinder v0.7.0
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH] Add PyMOL plugin for pyKVFinder by @jvsguerra and @wapablos in #132
Full Changelog: v0.6.16...v0.7.0
