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diff --git a/CHANGES.txt b/CHANGES.txt new file mode 100644 index 0000000..529636e --- /dev/null +++ b/CHANGES.txt @@ -0,0 +1,164 @@ +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__ |