-
Notifications
You must be signed in to change notification settings - Fork 107
/
CHANGES.txt
200 lines (167 loc) · 6.89 KB
/
CHANGES.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
Changelog
---------
# 2.3.0
* fixes an issue that caused encoding errors to be thrown
* salt bridge interaction improved
* minor bugs fixed
# 2.2.2
* fixes an issue that caused encoding errors to be thrown
# 2.2.1
* updates citation information to latest paper: https://doi.org/10.1093/nar/gkab294
# 2.2.0
* new minor release
* increased detail level of report (individual atoms on protein side)
* improved handling of multi-model structures
* minor bug fixes and code optimizations
# 2.1.9
* fixes issues with DNA receptor handling
# 2.1.8
* report of individual binding site atoms
# 2.1.7
* bug fixes
# 2.1.6
* fetch URL for PDB files updated to avoid issues with RCSB API changes
# 2.1.5
* option added to handle specific model in NMR structures
* fixes a bug in alt-location handling
# 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
* bug fixes in code and deployment
* multi-architecture builds on https://hub.docker.com/r/pharmai/plip
* Docker build for Ubuntu 20.04 LTS
# 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__