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Releases: LBC-LNBio/parKVFinder

parKVFinder v1.2.0

28 Feb 17:47
@jvsguerra jvsguerra
v1.2.0
85815e9
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parKVFinder v1.2.0 Latest
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The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure, using a dual probe system.

The description includes spatial, depth, constitutional and hydropathy characterization. The spatial description includes shape, volume, and area. The depth description defines depths for each cavity point, shown in the B-factor, and calculates the average and maximum depth per cavity. The constitutional description includes amino acids that form the identified cavities. The hydropathy description maps Eisenberg & Weiss hydrophobicity scale at surface points, shown in the Q-factor, and estimates average hydropathy per cavity.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

What's Changed

  • Integrate depth and hydropathy characterization to parKVFinder by @jvsguerra in #3

New Contributors

Full Changelog: v1.1.4...v1.2.0

Contributors

jvsguerra
Assets 3
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parKVFinder v1.1.4

15 Mar 16:01
@jvsguerra jvsguerra
v1.1.4
ca65824
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parKVFinder v1.1.4

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

Changes (v.1.1.4):

  • Fix compilation warning

Changes (v1.1.3):

  • Update the installation of Python packages in the Makefile

Changes (v1.1.2):

  • Minor bug fixes in plugin
  • Plugin accepts .toml results from other LBC's software

Changes (v1.1.1):

  • Bug fix in a plugin error message

Changes (v1.1):

  • Added a new PyMOL v2.x plugin with Qt interface: PyMOL2 parKVFinder Tools
  • Updated documentation/wiki

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility

Full Changelog: v1.1.3...v1.1.4

Assets 3
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parKVFinder v1.1.3

12 May 18:44
@jvsguerra jvsguerra
v1.1.3
b0d8093
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parKVFinder v1.1.3

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

Changes (v1.1.3):

  • Update the installation of Python packages in the Makefile

Changes (v1.1.2):

  • Minor bug fixes in plugin
  • Plugin accepts .toml results from other LBC's software

Changes (v1.1.1):

  • Bug fix in a plugin error message

Changes (v1.1):

  • Added a new PyMOL v2.x plugin with Qt interface: PyMOL2 parKVFinder Tools
  • Updated documentation/wiki

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility
Assets 3
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parKVFinder v1.1.2

17 Mar 19:30
@jvsguerra jvsguerra
v1.1.2
bf7c8d0
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parKVFinder v1.1.2

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

Changes (v1.1.2):

  • Minor bug fixes in plugin
  • Plugin accepts .toml results from other LBC's software

Changes (v1.1.1):

  • Bug fix in a plugin error message

Changes (v1.1):

  • Added a new PyMOL v2.x plugin with Qt interface: PyMOL2 parKVFinder Tools
  • Updated documentation/wiki

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility
Assets 3
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parKVFinder v1.1.1

23 Feb 15:02
@jvsguerra jvsguerra
v1.1.1
baa2316
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parKVFinder v1.1.1

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

Changes (v1.1.1):

  • Bug fix in a plugin error message

Changes (v1.1):

  • Added a new PyMOL v2.x plugin with Qt interface: PyMOL2 parKVFinder Tools
  • Updated documentation/wiki

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility
Assets 3
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parKVFinder v1.1

12 Feb 18:25
@jvsguerra jvsguerra
v1.1
963a388
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parKVFinder v1.1

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugins with a graphical user interface:
    • PyMOL2 parKVFinder plugin (PyMOL v2.x-compatible; Qt interface);
    • PyMOL parKVFinder plugin (PyMOL v1.8-compatible; tk interface);
  • Integrated command-line interface (CLI).

Changes(v1.1):

  • Added a new PyMOL v2.x plugin with Qt interface: PyMOL2 parKVFinder Tools
  • Updated documentation/wiki

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility
Assets 3
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parKVFinder v1.0.1

07 Jan 15:02
@jvsguerra jvsguerra
v1.0.1
5098a8d
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parKVFinder v1.0.1

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugin with a graphical user interface, PyMOL parKVFinder plugin (Python2- and Python3-compatible);
  • Integrated command-line interface (CLI).

Changes (v1.0.1):

  • Bug fix in the area estimation
  • GCC10 compiler compatibility
Assets 2
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parKVFinder v1.0

10 Oct 18:39
@jvsguerra jvsguerra
v1.0
83e6134
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parKVFinder v1.0

The parallel KVFinder (parKVFinder) software identifies and describes cavities in a target biomolecular structure using a dual probe system.

The description includes spatial and constitutional characterization. The spatial description includes shape, volume, and area. The constitutional description includes amino acids that form the identified cavities.

Main features:

  • Multi-threaded parallelization;
  • New approach to area estimation;
  • New space segmentation strategies;
  • New approach to control cavity ceiling and segmentation;
  • PyMOL plugin with a graphical user interface, PyMOL parKVFinder plugin (Python2- and Python3-compatible);
  • Integrated command-line interface (CLI).
Assets 2
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