Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / rosettacommons/tools issues and pull requests

#109 - Tweak tools for RosettaQM

Pull Request - State: open - Opened by vmullig 7 months ago
Labels: enhancement

#108 - Update Tools repo to use `main` instead of `master`

Pull Request - State: closed - Opened by roccomoretti 10 months ago

#107 - Bring python_pdb_reader to Python3

Pull Request - State: closed - Opened by aleaverfay 12 months ago

#106 - Update beautifier.py to look in PyTorch/Tensorflow blocks

Pull Request - State: open - Opened by roccomoretti about 1 year ago
Labels: ready for review

#105 - Updating documentation update script to auto-generate documentation for ensemble metrics.

Pull Request - State: open - Opened by vmullig almost 3 years ago
Labels: enhancement

#104 - Adjustments to the beautifier to make it run on the Foldit branch

Pull Request - State: closed - Opened by roccomoretti almost 3 years ago - 2 comments
Labels: ready for review

#103 - fixing psipred download path

Pull Request - State: closed - Opened by decarboxy over 3 years ago
Labels: Cyrus, industry

#102 - Add support for raw strings to the Beautifier.

Pull Request - State: closed - Opened by roccomoretti over 3 years ago - 4 comments

#100 - Fix beautify_changed_files_in_branch.py with respect to moved files.

Pull Request - State: closed - Opened by roccomoretti over 3 years ago - 2 comments
Labels: ready for review

#99 - Script to find large files in the Rosetta repo.

Pull Request - State: closed - Opened by roccomoretti over 3 years ago

#98 - redundant line

Pull Request - State: closed - Opened by danielzaidman almost 4 years ago - 3 comments

#97 - Python2 to python3 syntax changes

Pull Request - State: closed - Opened by danielzaidman almost 4 years ago - 1 comment

#96 - Modifies SequenceProfile.py allow functionality for multiple chains w…

Pull Request - State: open - Opened by nzrandol almost 4 years ago

#95 - Smlewis/update commons master oct20

Pull Request - State: closed - Opened by smlewis about 4 years ago - 1 comment

#94 - Scripts to do header removal with Include What You Use

Pull Request - State: closed - Opened by roccomoretti about 4 years ago

#93 - Samuel schmitz/favor direct info

Pull Request - State: closed - Opened by MoritzErtelt over 4 years ago
Labels: ready for review

#92 - Fix the convert_pdb_to_antibody_numbering_scheme.py script

Pull Request - State: closed - Opened by roccomoretti over 4 years ago

#91 - inclusion removal to python3

Pull Request - State: closed - Opened by aleaverfay over 4 years ago

#90 - updating release scripts

Pull Request - State: closed - Opened by lyskov over 4 years ago - 2 comments

#89 - Update tools repo for boost submod changes.

Pull Request - State: closed - Opened by roccomoretti almost 5 years ago

#88 - Add boost_submod to tool directory scripts.

Pull Request - State: closed - Opened by roccomoretti almost 5 years ago - 1 comment
Labels: ready for review

#87 - Adding a Python script to compute PNear

Pull Request - State: closed - Opened by vmullig about 5 years ago - 1 comment
Labels: enhancement

#86 - Add diff5.py, a tool for helping deduce merge conflicts.

Pull Request - State: closed - Opened by roccomoretti about 5 years ago - 1 comment

#85 - aleaverfay/beautifier to python3

Pull Request - State: closed - Opened by aleaverfay about 5 years ago

#84 - Add a line that should scope `alignment` properly

Pull Request - State: closed - Opened by everyday847 over 5 years ago

#83 - Update mhc_energy_tools for generation of IEDB-based databases

Pull Request - State: closed - Opened by BYachnin over 5 years ago

#82 - make install deps copy files not folders (when using localnrcopy)

Pull Request - State: closed - Opened by danpf over 5 years ago

#81 - Add an option to simply copy an NR database in fragment db making

Pull Request - State: closed - Opened by danpf over 5 years ago

#80 - Danpf/fix install deps

Pull Request - State: closed - Opened by danpf over 5 years ago

#79 - add extract_top_model.py script for rescoring

Pull Request - State: closed - Opened by Alisa-Kh over 5 years ago

#78 - fixing bugs in fragment processing

Pull Request - State: closed - Opened by Alisa-Kh over 5 years ago

#77 - Scripts to run PIPER-FPD protocol

Pull Request - State: closed - Opened by Alisa-Kh over 5 years ago

#76 - Auto-updating antibody database

Pull Request - State: closed - Opened by lqtza over 5 years ago - 1 comment

#75 - Add submodule updates to the release script.

Pull Request - State: closed - Opened by roccomoretti about 6 years ago - 5 comments
Labels: ready for review

#74 - Davela/share anarci2rosetta

Pull Request - State: closed - Opened by d8vela about 6 years ago - 5 comments

#73 - Add the nanobody 4w6w to the outlier_list

Pull Request - State: closed - Opened by d8vela about 6 years ago - 3 comments

#72 - blast: ncbi -> artifactory

Pull Request - State: closed - Opened by danpf about 6 years ago - 1 comment

#71 - mhc_db_tools, for creating external mhc databases

Pull Request - State: closed - Opened by BYachnin about 6 years ago - 3 comments

#70 - Beautifier compatibility

Pull Request - State: closed - Opened by everyday847 over 6 years ago

#69 - RECCES new wrapper scripts

Pull Request - State: closed - Opened by rhiju over 6 years ago

#68 - Beautifier can't parse C++11 raw strings

Issue - State: open - Opened by bcov77 over 6 years ago

#67 - More updates for python3 compatibility

Pull Request - State: closed - Opened by everyday847 over 6 years ago

#66 - Some more python3 compatibility within rna tools

Pull Request - State: closed - Opened by everyday847 over 6 years ago

#64 - Add simple metric type for xsd doc generation.

Pull Request - State: closed - Opened by jadolfbr over 6 years ago

#64 - Add simple metric type for xsd doc generation.

Pull Request - State: closed - Opened by jadolfbr over 6 years ago

#63 - allow configuration of make_fragments.pl via environment variables

Pull Request - State: closed - Opened by decarboxy over 6 years ago - 1 comment
Labels: Cyrus

#62 - fixing install_dependencies.pl BLAST path

Pull Request - State: closed - Opened by decarboxy over 6 years ago - 1 comment
Labels: Cyrus

#61 - Update XSD documentation generator

Pull Request - State: closed - Opened by roccomoretti over 6 years ago

#60 - Updating colorcdrs to be python 2/3 compatible.

Pull Request - State: closed - Opened by weitzner almost 7 years ago

#59 - Two RNA fixes

Pull Request - State: closed - Opened by everyday847 about 7 years ago

#58 - Address release system issues

Pull Request - State: closed - Opened by roccomoretti over 7 years ago

#57 - parse_tag can't handle negative seqpos

Issue - State: open - Opened by everyday847 over 7 years ago

#56 - Rhiju/swa revival into master

Pull Request - State: closed - Opened by rhiju almost 8 years ago

#55 - Enhance Color CDRs script

Pull Request - State: closed - Opened by jadolfbr almost 8 years ago

#54 - Some rewrite_rosetta_script.py usability improvements

Pull Request - State: closed - Opened by roccomoretti almost 8 years ago - 1 comment

#53 - XSD to md script

Pull Request - State: closed - Opened by roccomoretti almost 8 years ago

#52 - No need for ERRASER in tools now that it's in main

Pull Request - State: closed - Opened by everyday847 about 8 years ago

#51 - Cyrus tools PR: options_writer

Pull Request - State: closed - Opened by smlewis about 8 years ago - 2 comments

#50 - I accidentally messed up a conflict resolution, breaking a script.

Pull Request - State: closed - Opened by everyday847 about 8 years ago

#49 - Handle LINK records a little better in ERRASER

Pull Request - State: closed - Opened by everyday847 about 8 years ago

#47 - Rhiju/devel

Pull Request - State: closed - Opened by rhiju over 8 years ago

#46 - ERRASER updates from the tools/python level side

Pull Request - State: closed - Opened by everyday847 over 8 years ago

#45 - Generalize around $ROSETTA_TOOLS

Pull Request - State: closed - Opened by everyday847 over 8 years ago

#44 - Add csbuild-based fragment picking.

Pull Request - State: closed - Opened by asford over 8 years ago

#43 - Add csbuild-based fragment picking to make_fragment.pl

Pull Request - State: closed - Opened by asford over 8 years ago

#42 - Smlewis/jd0

Pull Request - State: closed - Opened by smlewis over 8 years ago

#41 - ERRASER script converting python versions results in spurious diffs

Issue - State: open - Opened by everyday847 over 8 years ago - 1 comment

#40 - ERRASER Bug Fix

Pull Request - State: closed - Opened by calebgeniesse over 8 years ago

#39 - Rhiju/auto queue

Pull Request - State: closed - Opened by rhiju almost 9 years ago

#38 - ERRASER Bug Fix

Pull Request - State: closed - Opened by calebgeniesse almost 9 years ago

#37 - Calebgeniesse/pp jobsub bug fix

Pull Request - State: closed - Opened by calebgeniesse almost 9 years ago - 1 comment

#36 - Adding more GLYCAM codes to carbohydrate_code_generator.py

Pull Request - State: closed - Opened by JWLabonte about 9 years ago
Labels: enhancement, carbohydrates

#35 - PEP8/Style Tweaks to carbohydrate_code_generator.py

Pull Request - State: closed - Opened by JWLabonte about 9 years ago
Labels: style/clean-up, carbohydrates

#34 - submit jobs to 'biochem' partition on sherlock (we are owners now!)

Pull Request - State: closed - Opened by calebgeniesse about 9 years ago - 4 comments

#33 - ERRASER Performance Restoration

Pull Request - State: closed - Opened by calebgeniesse about 9 years ago

#31 - Added comments (docstrings) to antibody.py

Pull Request - State: closed - Opened by smoe about 9 years ago - 2 comments
Labels: enhancement

#30 - Calebgeniesse/cluster setup comet

Pull Request - State: closed - Opened by calebgeniesse over 9 years ago

#29 - antibody.py: submission of heavy chain alone

Pull Request - State: closed - Opened by smoe over 9 years ago - 1 comment
Labels: enhancement

#28 - antibody.py: default H1_end

Pull Request - State: open - Opened by smoe over 9 years ago
Labels: bug, enhancement

#27 - Introducing randomness for template selection

Pull Request - State: open - Opened by smoe over 9 years ago - 5 comments
Labels: enhancement

#26 - Update ERRASER for compatibility with latest Phenix releases

Pull Request - State: closed - Opened by calebgeniesse over 9 years ago

#25 - update parallel python job submission tools to work on sherlock

Pull Request - State: closed - Opened by calebgeniesse over 9 years ago

#24 - antibody.py separating command line activity/checks from rosetta semantics

Pull Request - State: closed - Opened by smoe over 9 years ago - 3 comments
Labels: enhancement, question

#23 - trivial eye candy in antibody.py

Pull Request - State: closed - Opened by smoe over 9 years ago - 1 comment
Labels: enhancement

#22 - Reworked separation into first and second half

Pull Request - State: closed - Opened by smoe over 9 years ago - 3 comments
Labels: enhancement, question

#21 - Adding multi-template grafting functionality to antibody.py.

Pull Request - State: closed - Opened by nmarze over 9 years ago - 2 comments

#20 - antibody/convert_pdb_to_antibody_numbering_scheme.py BioPython ref

Pull Request - State: closed - Opened by smoe over 9 years ago
Labels: enhancement

#19 - adding structure profile scripts

Pull Request - State: closed - Opened by tjbrunette over 9 years ago

#18 - antibody/chothia_renumber_v2.pl: refactoring - use strict, simplifications, indenting, undef vals

Pull Request - State: closed - Opened by smoe over 9 years ago
Labels: enhancement

#17 - antibody/chothia_mapping_v2.pl now "use(s) strict;"

Pull Request - State: closed - Opened by smoe over 9 years ago
Labels: enhancement

#16 - H3 now always terminated with 101,102

Pull Request - State: closed - Opened by smoe over 9 years ago
Labels: bug

#15 - antibody.py: simplifying split H/L chains first second

Pull Request - State: closed - Opened by smoe over 9 years ago - 2 comments
Labels: enhancement

#14 - antibody.py: printing L123 H123 sequence positions

Pull Request - State: closed - Opened by smoe over 9 years ago - 2 comments
Labels: enhancement

#13 - antibody.py: cut of second half of light chain was too early

Pull Request - State: closed - Opened by smoe over 9 years ago - 1 comment
Labels: bug

#12 - Adjusting tests to 5b21d22b8c1b393fa2bdd002cb0

Pull Request - State: closed - Opened by smoe over 9 years ago - 1 comment
Labels: bug