Release 3.0.0 by mestia · Pull Request #195 · pharmai/plip

mestia · 2025-10-27T11:26:26Z

No description provided.

Keep modified residues in protein ligands

…ceptor.

Keepmod flag keeps modified residues in the receptor

Detection of charged functional groups in modified residues

…mbering to the structure preparation process

* Update README.md, adding colab link

Adding flag to check if pdb was corrected in PDBParser class

fix for loading PDB as files for PDBComplex - setting the default value for pdb_file_was_corrected flag before pdb is parsed

making this shift so that the loading into pymol GUI is simpler

Fix for loading corrected PDB string in PDBComplex object

* Fix for #186 pdb as text as_sting=True argument fixed * Fix for #185 changed acc <-> don coords in halogen_info --------- Co-authored-by: Philipp Schake <philipp@bioinf-mbp4.biotec.tu-dresden.de>

….g., domains)

Regions Feature

Fix handling of TER entries without numbering

citation information update to latest PLIP publication.

…, new option to gzip-compress the report files, and proper filenaming for batch processing.

Report filenaming and compression

Update module packaging

Update CHANGES.txt

Update version in plip/basic/config.py

Update version in setup.py

snbolz and others added 30 commits January 13, 2025 17:17

fixed handling of modified residues in protein ligands.

c2bb26f

Merge pull request #168 from snbolz/bug/keepmod

fcf8da8

Keep modified residues in protein ligands

if the keepmod flag is used, keep modified residues as part of the re…

427704d

…ceptor.

Merge pull request #169 from snbolz/bug/modres_bs

ea15bc3

Keepmod flag keeps modified residues in the receptor

enables the detection of charged functional groups in modified residues.

0504276

Merge pull request #170 from snbolz/bug/modres_charged

1876230

Detection of charged functional groups in modified residues

added handling of pdb files that have TER lines without continuing nu…

accf551

…mbering to the structure preparation process

Updated Readme (#176)

93f7fbc

* Update README.md, adding colab link

dev: adding flag pdb_file_was_corrected

54188c9

Adding flag to check if pdb was corrected in PDBParser class

fix: condition for as_string in read_pdb

1612786

fix: pdb complex as string source file for visualizer data

7797f0f

fix: broken test suite for using PDBComplex

d174c65

fix for loading PDB as files for PDBComplex - setting the default value for pdb_file_was_corrected flag before pdb is parsed

fix: using pdb file as string for VisualizerData

0860903

making this shift so that the loading into pymol GUI is simpler

fix: typo in attribute

6041ea3

Update remote.py

d20949c

Merge branch 'development' into bugfix/load-pdb-as-string-fix

a900834

Merge pull request #178 from CtrlShanya/bugfix/load-pdb-as-string-fix

eda5482

Fix for loading corrected PDB string in PDBComplex object

Fix for #186, #185

0f39424

* Fix for #186 pdb as text as_sting=True argument fixed * Fix for #185 changed acc <-> don coords in halogen_info --------- Co-authored-by: Philipp Schake <philipp@bioinf-mbp4.biotec.tu-dresden.de>

fix: missing attribute (#181)

e3e7121

new regions feature to detect interactions between protein regions (e…

d50e3ed

….g., domains)

improved --regions argument parsing for tuples with only one entry.

062d7c5

Add pyproject.toml, courtesy Nikitas Rontsis, nrontsis@gmail.com

d18a355

Drop requirements.txt

9bdf35d

Update pyproject.toml, adjust build system to use setup.py

871ef56

hardocde verion, since ./plip is not available while building module

6d5f718

Update Dockerfile, drop python3-distutils Debian package

86cccd5

Merge branch 'development' into feature/domains

67d5d5d

citation information update to latest PLIP publication.

864551f

Merge pull request #188 from snbolz/feature/domains

9132b5c

Regions Feature

Merge branch 'development' into bug/ter_lines

df921f8

mestia and others added 12 commits October 16, 2025 16:45

Merge pull request #172 from snbolz/bug/ter_lines

6744681

Fix handling of TER entries without numbering

Merge branch 'development' into chore/update-citation

0f0f651

Merge pull request #191 from snbolz/chore/update-citation

7573f04

citation information update to latest PLIP publication.

More control about report filename parsing, new default report naming…

e422d72

…, new option to gzip-compress the report files, and proper filenaming for batch processing.

Merge pull request #192 from snbolz/feature/report-filename

7ee10a8

Report filenaming and compression

Merge branch 'development' into module_packaging

87a7e6d

Merge pull request #193 from mestia/module_packaging

35a06d9

Update module packaging

update CHANGES.txt

ee5a096

Merge pull request #194 from snbolz/chore/update-changelog

b49cc44

Update CHANGES.txt

Version 3.0.0

39f0484

Update version in plip/basic/config.py

Version 3.0.0

017a4e3

Update version in setup.py

Merge branch 'master' into development

3327e8a

mestia merged commit 947eba6 into master Oct 27, 2025
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Release 3.0.0#195

Release 3.0.0#195
mestia merged 42 commits into
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mestia commented Oct 27, 2025

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mestia commented Oct 27, 2025

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