Changelog --------- # 2.1.0 * maintainer changed to PharmAI GmbH * full compatibility to Python 3 and OpenBabel 3 * Docker and Singularity support, 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 interaction detection * new options to change verbosity levels # 1.4.5 * Updates contact info # 1.4.4 * Improved parameters for water bridge detection * Added unit test for PDB structure 1HPX * PEP8 Changes * Improved imports # 1.4.3 * Adds information on covalent linkages to XML files * __Anaconda package__ (provided by `Ikagami`) # 1.4.2 * 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 # 1.4.1 * Improved import of modules * Corrections for README and documentation * Several improvements for error handling * independence from PyMOL when used without visualization features # 1.4.0 * __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") ### 1.3.5 * Preparation for Python 3: Imports * small correction for PDB fixing * includes TODO files with user suggestions * license adapted to GNU GPLv2 ### 1.3.4 * __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 ### 1.3.3 * __Adds XML Parser module for PLIP XML files__ * Detection of intramolecular interactions with --intra * improved error correction in PDB files ### 1.3.2 * __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 ### 1.3.1 * __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 ### 1.3.0 * __Batch processing__ * Improvements to verbose mode and textual output ### 1.2.3 * __Better support for files from MD and docking software__ * __Fixes issues with large and complex structures__ * Speed optimizations ### 1.2.2 * __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 ### 1.2.1 * __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 ### 1.2.0 * __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 ### 1.1.1 * __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 #### 1.1.0 * __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 #### 1.0.2 * __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 #### 1.0.1 * __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 #### 1.0.0 * __Initial Release__