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Recent Releases of plip

plip - Version 2.4.0

What's Changed

  • Workaround to fix and install openbabel bindings by @mestia in https://github.com/pharmai/plip/pull/161
  • Added Chains flag to command tool by @PhiCMS in https://github.com/pharmai/plip/pull/163
  • Update Dockerfile by @mestia in https://github.com/pharmai/plip/pull/162

New Contributors

  • @PhiCMS made their first contribution in https://github.com/pharmai/plip/pull/163

Full Changelog: https://github.com/pharmai/plip/compare/v2.3.1...v2.4.0

- Python
Published by mestia over 1 year ago

plip - v2.3.1

What's Changed

  • fixes NumPy DeprecationWarning by @QY0831 in https://github.com/pharmai/plip/pull/150
  • Fixes several mistakes in interaction detection with peptide ligands by @kalinni in https://github.com/pharmai/plip/pull/153
  • Fixes a mistake in hydrogen bond acceptor identification by @kalinni in https://github.com/pharmai/plip/pull/151
  • Fixes mistakes in waterbridge detection and filtering by @kalinni in https://github.com/pharmai/plip/pull/152

New Contributors

  • @QY0831 made their first contribution in https://github.com/pharmai/plip/pull/150

Full Changelog: https://github.com/pharmai/plip/compare/v2.3.0...v2.3.1

- Python
Published by mestia over 1 year ago

plip - Version 2.3.0

What's Changed

  • Fixes PDB file correction for multi-model structures by @kalinni in https://github.com/pharmai/plip/pull/120
  • Fixes a bug when using --nofix by @zrt in https://github.com/pharmai/plip/pull/126
  • fixes salt bridge detection for nucleic acid receptors by @sungekim in https://github.com/pharmai/plip/pull/127
  • Updates ImageMagick to version 7 and makes its use platform independent by @kalinni in https://github.com/pharmai/plip/pull/144

New Contributors

  • @zrt made their first contribution in https://github.com/pharmai/plip/pull/126
  • @sungekim made their first contribution in https://github.com/pharmai/plip/pull/127

Full Changelog: https://github.com/pharmai/plip/compare/v2.2.2...v2.3.0

- Python
Published by fkaiserbio almost 3 years ago

plip - Version 2.2.2

  • fixed a bug that cause encoding errors to be thrown on some systems and Docker images

- Python
Published by fkaiserbio about 5 years ago

plip - Version 2.2.1

  • streamlines citation information
  • adds new paper as standard reference

- Python
Published by fkaiserbio about 5 years ago

plip - Version 2.2.0

This minor release bundles a few things: - atom-level interaction detection for the receptor side - proper handling of multi-model structures incl. visualization - reports now contain information about the model that was analyzed

- Python
Published by fkaiserbio about 5 years ago

plip - Version 2.1.9

  • bug fixes in DNA handling

- Python
Published by fkaiserbio over 5 years ago

plip - Version 2.1.8 - Atom-level Interactions

  • PLIP now reports all individual atoms that engage in interactions
  • minor code optimizations

- Python
Published by fkaiserbio over 5 years ago

plip - Version 2.1.7 - Minor Bug Fixes

This is the PLIP Christmas release :christmas_tree: :santa: Thanks to all supporters and contributors.

  • fixes minor bugs when handling multiple models from command line
  • removes legacy compatibility code for MacOS
  • fixes issues when visualizing in PyMOL for other models than the first one

- Python
Published by fkaiserbio over 5 years ago

plip - Version 2.1.6 - RCSB API change compatibility

  • minor update to ensure working with upcoming API changes at RCSB PDB (see http://www.rcsb.org/news?year=2020&article=5f9714798807d067f8922116)
  • status checks for obsolete PDB files was removed as new RCSB GraphQL API does not yet support this (https://data.rcsb.org/migration-guide.html#pdb-file-description)

- Python
Published by fkaiserbio over 5 years ago

plip - PLIP v2.1.5 - Fixes Altloction Bug and Adds Model Handling

  • bug fixed that caused alt locations to be incorrectly parsed (see #80)
  • adds support to choose model in ensemble structures (--model)
  • resolves issues when downloading PDB files directly with PLIP

- Python
Published by fkaiserbio over 5 years ago

plip - PLIP v2.1.4 - Updates Dependencies and Static Functions

  • fixes invalid dependency of pymol on PyPi
  • makes use of static function declarations where possible

- Python
Published by fkaiserbio almost 6 years ago

plip - PLIP v2.1.3

This is the new major PLIP release, it brings you a ton of new features and fixes many bugs :smiley:

:exclamation: Finally, PLIP is fully compatible to Python 3 and OpenBabel 3 :exclamation:

The complete set of changes

  • maintainer changed to PharmAI GmbH
  • full compatibility to Python 3 and OpenBabel 3
  • many bug fixes
  • multi-architecture Docker and Singularity (Singularity on GitHub | Singularity Desktop for macOS) images, CI deployment to Docker Hub, PyPi
  • dropped support for OpenBabel 2, Python 2
  • reorganization of modules
  • migrates to proper logging pattern
  • code quality enhancements
  • adds option to disable non-deterministic protonation of structures (--nohydro)
  • protonated structures are now stored to guarantee consistent detection of interactions
  • new options to change verbosity levels

Enjoy the new PLIP.

- Python
Published by fkaiserbio almost 6 years ago

plip - PLIP v2.1.0-beta

This is the new major PLIP release, it brings you a ton of new features and fixes many bugs :smiley:

:exclamation: Finally, PLIP is fully compatible to Python 3 and OpenBabel 3 :exclamation:

The complete set of changes

  • maintainer changed to PharmAI GmbH
  • full compatibility to Python 3 and OpenBabel 3
  • Docker and Singularity support, CI deployment to Docker Hub
  • dropped support for OpenBabel 2, Python 2
  • reorganization of modules
  • migrates to proper logging pattern
  • code quality enhancements
  • adds option to disable non-deterministic protonation of structures (--nohydro)
  • protonated structures are now stored to guarantee consistent detection of interactions
  • new options to change verbosity levels

Enjoy the new beta release of PLIP.

Not yet fully tested and still experimental

- Python
Published by fkaiserbio about 6 years ago

plip - PLIP v1.4.4b

  • Improved parameters for water bridge detection
  • Added unit test for PDB structure 1HPX
  • PEP8 Changes
  • Improved imports

- Python
Published by ssalentin over 7 years ago

plip - PLIP v1.4.3b

  • adds covalent linkage information to XML result files
  • ready for deployment as Anaconda package
  • small improvements and bugfixes

- Python
Published by ssalentin over 7 years ago

plip - PLIP v1.4.2

  • Adds "--name" option to change name of output files
  • Adds "--nopdbcanmap" option to skip calculation of canonical->PDB mapping which can lead to segfaults with OpenBabel
  • Improved handling of ligand names

- Python
Published by ssalentin about 8 years ago

plip - PLIP v1.4.1

  • Improved import of modules
  • Corrections for README and documentation
  • Several improvements for error handling
  • independence from PyMOL when used without visualization features

- Python
Published by ssalentin about 8 years ago

plip - PLIP v1.4.0b

  • Full Python 3 Compatibility
  • Read PDB files from stdin with "-f -" and write to stdout with "-O" (capital "O")
  • Improves handling of fixed PDB files
  • Option to turn off writing fixed PDB structures to a file ("--nofixfile")

- Python
Published by ssalentin over 8 years ago

plip - PLIP v1.3.5

  • Preparation for Python 3: Imports
  • small correction for PDB fixing
  • includes TODO files with user suggestions
  • license adapted to GNU GPLv2

- Python
Published by ssalentin over 8 years ago

plip - PLIP v1.3.4b

  • DNA/RNA can be selected as receptor with --dnareceptor
  • Composite ligands and intra-protein mode: Annotation which part of the ligand interacts with the receptor
  • Improved handling of NMR structures
  • Filter for extremely large ligands
  • Speed-up for file reading and parallel visualization
  • More debugging messages

- Python
Published by ssalentin about 9 years ago

plip - PLIP v1.3.3

  • Adds XML Parser module for PLIP XML files
  • Detection of intramolecular interactions with --intra
  • improved error correction in PDB files

- Python
Published by ssalentin over 9 years ago

plip - PLIP v1.3.2

  • Processing of protein-peptide interactions via --peptides
  • option to keep modified residues as ligands (--keepmod)
  • Improved code for reports
  • Smart ordering of ligand in composite compounds
  • Fixes handling and visualization of DNA/RNA

- Python
Published by ssalentin over 9 years ago

plip - PLIP v1.3.1a

Hotfix Release

- Python
Published by ssalentin about 10 years ago

plip - PLIP v1.3.1

  • Support for amino acids as ligands
  • Plugin-ready for PyMOL and Chimera
  • Refactores code and optimized input
  • Improved verbose and debug log system
  • Bugfixes for problems affecting some structures with aromatic rings

- Python
Published by ssalentin about 10 years ago

plip - PLIP v1.3.0a

Bugfix Release - Fixes problem with segmentation fault in at least one structure (PDB ID 1U6B) - Typing of aromatic rings has been changed from using OpenBabel to manual (discriminating 5-membered and 6-membered rings)

- Python
Published by ssalentin over 10 years ago

plip - PLIP v1.3.0

  • Batch processing
  • Improvements to verbose mode and textual output

- Python
Published by ssalentin over 10 years ago

plip - PLIP v1.2.3

  • Better support for files from MD and docking software
  • Fixes issues with large and complex structures
  • Speed optimizations

- Python
Published by ssalentin over 10 years ago

plip - PLIP v1.2.2

  • Option to consider alternate atom locations (e.g. for ligands with several conformations)
  • Automatic fixing of missing ligand names
  • Improved handling of broken PDB files and non-standard filenames
  • Improved error handling

- Python
Published by ssalentin over 10 years ago

plip - PLIP v1.2.1

  • Mapping of canonical atom order to PDB atom order for each ligand
  • Introduction of debug mode (--debug)
  • More robust visualization
  • Handling of negative residue numbers for more cases
  • Composite members in alphabetical order
  • Fixes errors in aromatic ring detection
  • Code improvements

- Python
Published by ssalentin over 10 years ago

plip - PLIP v1.2.0

  • Support for DNA and RNA as ligands
  • Detection of metal complexes with proteins/ligands, including prediction of geometry
  • Extended result files with detailed information on binding site residues and unpaired atoms
  • Support for zipped and gzipped files
  • Rich verbose mode in command line with information on detected functional groups and interactions
  • Automatic fixing of common errors in custom PDB files
  • Refined binding site selection
  • Better overall performance
  • Initial test suite for metal coordination
  • Classification of ligands
  • Improves detection of aromatic rings and interactions involving aromatic rings
  • Single nucleotides and ions not excluded anymore as ligands
  • Generation of canonical smiles for complete (composite) ligands
  • Generation of txt files is now optional
  • Basic support for PDBQT files
  • Correct handling of negative chain positions of ligands
  • Improved check for valid PDB IDs
  • Fixes several bugs

- Python
Published by ssalentin almost 11 years ago

plip - PLIP v1.1.1

  • Detailed information on binding site residues in XML files
  • Improved extraction of binding site residues
  • Information whether halogen bonds are made with side- or main chain of protein

- Python
Published by ssalentin almost 11 years ago

plip - PLIP v1.1.0

  • Folder structure and setup.py for automatic installation using pip
  • H-Bond Donor Prioritization (see documentation for details)
  • Adds separate changelog
  • Updated documentation and citation information
  • Reduction of blacklist usage
  • Information on excluded ligands in result files

- Python
Published by ssalentin about 11 years ago

plip - PLIP v1.0.2

  • Automatic grouping of composite ligands (e.g. polysaccharides)
  • Proper handling of alternative conformations in PDB structures
  • Exclusion of modified residues as ligands
  • Improved detection of hydrogen bonds
  • Prioritization of hydrogen bonds
  • Adds atom type description in the output files
  • Basic support for usage on Windows (without multithreading)
  • Option to turn multithreading off by setting maxthreads to 0
  • Improved detection of hydrogen bond donors in ligands
  • Adaption of standard parameters
  • Fixes a bug in PyMOL visualization script leading to missing or wrong interactions with pseudoatoms
  • Fixes a bug leading to duplicate or triplicate detection of identical pi-cation interactions with guanidine
  • Adds now unit tests
  • Small changes to existing unit tests for new features

- Python
Published by ssalentin over 11 years ago

plip - PLIP v1.0.1

Changes

  • Option to change detection thresholds permanently or for single runs
  • Option to (de)activate output for images, PyMOL session files and XML files
  • Changed standard behaviour to output of RST report only
  • Information on sidechain/backbone hydrogen bond type
  • Sorted output
  • Detection of more flavors of halogen bonds
  • Fixed bug leading to duplicate interactions with quartamine groups

- Python
Published by ssalentin over 11 years ago