Ecosyste.ms: Issues

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GitHub / charnley/rmsd issues and pull requests

#111 - fix the printed structure with selected atoms

Pull Request - State: open - Opened by takafumi-shiraogawa 9 days ago - 2 comments

#109 - Adding new Features to calculate_rmsd Code

Issue - State: open - Opened by yazdan12555 27 days ago

#107 - Calculating hungarian RMSD without alignment

Issue - State: closed - Opened by jgarcianafria 5 months ago - 3 comments

#106 - RMSD 95 Implementation

Issue - State: open - Opened by WhenMelancholy 9 months ago - 1 comment
Labels: enhancement

#105 - Strange RMSD values

Issue - State: open - Opened by livaschar 10 months ago - 5 comments

#104 - Change 'print' by 'return' in main

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

#103 - errors,Structures not same size

Issue - State: open - Opened by oyileo 11 months ago - 2 comments

#102 - How to use it

Issue - State: closed - Opened by oyileo 11 months ago - 2 comments

#101 - fix typo

Pull Request - State: closed - Opened by kamurani about 1 year ago

#100 - RMSD result using --reorder much higher than expected

Issue - State: closed - Opened by cassguff about 1 year ago - 5 comments

#99 - How to get full transformation in a script?

Issue - State: closed - Opened by Jellby over 1 year ago - 1 comment

#98 - Why these two pdbs can not calculate RMSD?

Issue - State: open - Opened by Qmi3 over 1 year ago - 4 comments
Labels: enhancement

#97 - Willing to add the rmsd value to title line?

Issue - State: open - Opened by rafaelpap almost 2 years ago

#96 - Fixing issue 95

Pull Request - State: closed - Opened by charnley almost 2 years ago

#95 - rmsd package requires typing_extensions but missing from setup.py

Issue - State: closed - Opened by epeisach almost 2 years ago - 1 comment
Labels: bug

#94 - Fixed issue 93

Pull Request - State: closed - Opened by charnley almost 2 years ago

#93 - reordering while preparing for output

Issue - State: closed - Opened by avocadit almost 2 years ago - 4 comments

#92 - error: Structures not same size

Issue - State: closed - Opened by mns-csharp about 2 years ago - 4 comments

#91 - Incorrect values for proteins

Issue - State: closed - Opened by KingisNitro over 2 years ago - 5 comments

#90 - Added testing to --print output (#78)

Pull Request - State: closed - Opened by charnley over 2 years ago

#89 - Added HETATM keyword for PDB reader

Pull Request - State: closed - Opened by charnley over 2 years ago

#88 - error: Structures not same size

Issue - State: closed - Opened by raji-pixel over 2 years ago - 3 comments
Labels: bug

#87 - --reorder-method qml --reorder-method none currently not available

Issue - State: closed - Opened by nbehrnd over 2 years ago - 4 comments

#81 - Adding mypy types

Pull Request - State: closed - Opened by charnley almost 3 years ago

#80 - Print contains reflection consistency (issue-78)

Pull Request - State: closed - Opened by charnley about 3 years ago

#79 - saving rotated coordinate?

Issue - State: closed - Opened by vaibhavadixit about 3 years ago - 2 comments

#78 - printed structure does not obey --use-reflections

Issue - State: closed - Opened by Jellby about 3 years ago - 3 comments
Labels: bug

#77 - Output rotation matrix

Issue - State: closed - Opened by Jellby over 3 years ago - 3 comments

#76 - be aware of reflection operation

Issue - State: closed - Opened by SingletC over 3 years ago - 3 comments

#75 - add research notice to readme

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

#74 - Pre-specify residuals?

Issue - State: closed - Opened by proteneer over 3 years ago - 4 comments

#73 - msg = f"error: Parsing atomtype for the following line:" f" \n{line}"

Issue - State: closed - Opened by brielletilson almost 4 years ago - 10 comments

#71 - How to align both position and orientation?

Issue - State: closed - Opened by marekyggdrasil almost 4 years ago - 5 comments

#70 - error: Structures not same size

Issue - State: closed - Opened by senjoro almost 4 years ago - 2 comments

#69 - How to calculate rotation matrix using rmsd?

Issue - State: closed - Opened by Z-Jeff about 4 years ago - 3 comments
Labels: question

#68 - Benjs suggested updates

Pull Request - State: closed - Opened by benjfitz about 4 years ago - 2 comments

#67 - Development merge

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

#66 - Bug fix, capitalization of elements in .xyz files

Pull Request - State: closed - Opened by nbehrnd over 4 years ago - 1 comment

#65 - Issue with capitalization of elements >1 letter

Issue - State: closed - Opened by andersx over 4 years ago - 3 comments
Labels: bug

#64 - add mass-weight to RMSD calculations

Issue - State: open - Opened by rsysadmin-com over 4 years ago
Labels: enhancement

#63 - reading .xyz files doesn't work when they contain scientific notation

Issue - State: closed - Opened by puckvg almost 5 years ago - 2 comments

#62 - Implemented principal axis alignment before reorder.

Pull Request - State: closed - Opened by hmcezar about 5 years ago - 2 comments

#61 - Reorder with Hungarian and distance gives larger RMSD

Issue - State: closed - Opened by hmcezar about 5 years ago - 6 comments
Labels: enhancement

#60 - support of *.xyz.gz and *.pdb.gz

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

#59 - Modify W instead of V

Issue - State: closed - Opened by Koushikphy over 5 years ago - 1 comment

#58 - Babel issue, pull request

Pull Request - State: closed - Opened by nbehrnd over 5 years ago - 2 comments

#57 - pdb coordinate reader: error: Parsing coordinates for the following line

Issue - State: open - Opened by tccyl over 5 years ago - 8 comments
Labels: bug

#56 - .pdb coordinate reader can be improved

Issue - State: open - Opened by nabraham47 over 5 years ago - 2 comments
Labels: bug

#55 - cite

Issue - State: closed - Opened by SherlockQiu over 5 years ago

#54 - attempt exporting both *.xyz and (reflection based) RMSD

Pull Request - State: closed - Opened by nbehrnd over 5 years ago - 3 comments

#53 - Enhancement of Kabsch-based routines to work with weighted data

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

#52 - feature suggest: output of *.xyz .AND. RMSD

Issue - State: closed - Opened by nbehrnd over 5 years ago - 2 comments

#51 - multiprocessing with calculate_rmsd.py

Issue - State: closed - Opened by nbehrnd over 5 years ago - 2 comments

#50 - Reordering two differently sized but similar molecules

Issue - State: closed - Opened by JonKragskow almost 6 years ago - 3 comments

#48 - Fails to read XYZ files written by ASE

Issue - State: closed - Opened by yurivict almost 6 years ago - 4 comments

#47 - accounting for dissent help output / xyz-structure output

Pull Request - State: closed - Opened by nbehrnd almost 6 years ago

#46 - partially defunct structure export.

Issue - State: closed - Opened by nbehrnd almost 6 years ago - 2 comments
Labels: bug

#45 - error: cannot reorder atoms and print result with a view

Issue - State: closed - Opened by emiliecauet almost 6 years ago - 15 comments

#44 - Problems with check_reflections function

Issue - State: closed - Opened by share1992 almost 6 years ago - 3 comments

#43 - A new option which keeps stereochemistry.

Pull Request - State: closed - Opened by xg590 almost 6 years ago - 10 comments

#42 - mirroring / inversion of relative alignments; increment version counter.

Issue - State: closed - Opened by nbehrnd about 6 years ago - 1 comment

#41 - Function docstrings are a bit confusing about whether centroids are subtracted or not

Issue - State: closed - Opened by smheidrich about 6 years ago - 2 comments
Labels: enhancement

#40 - infer the two coordinate sets for 3D data

Issue - State: closed - Opened by ahorvath about 6 years ago - 7 comments

#39 - Issue with Importing RMSD in Python

Issue - State: closed - Opened by yahtree about 6 years ago - 3 comments

#38 - Citing charnley/rmsd (with a DOI)

Issue - State: closed - Opened by bertrand-caron about 6 years ago - 2 comments
Labels: enhancement, question

#37 - Dev

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

#36 - Atom re-ordering

Pull Request - State: closed - Opened by benjfitz over 6 years ago - 1 comment

#35 - Align N molecules to M other molecules

Issue - State: closed - Opened by larsbratholm over 6 years ago - 3 comments
Labels: enhancement

#34 - moved __version__ to setup file

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

#32 - Kabsch not zero for same file

Issue - State: closed - Opened by polyluxus almost 7 years ago - 3 comments

#31 - Pip version has slight error

Issue - State: closed - Opened by smcolby almost 7 years ago - 1 comment

#30 - RMSD operation in a numpy array of moelcules

Issue - State: closed - Opened by Megaterium almost 7 years ago - 5 comments

#29 - MAINT: Docstring change + some PEP8 compatibility

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

#28 - Added travis CI tests

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

#27 - Added new unittest for all the methods currently in rmsd.

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

#26 - Autofixes for PEP8 compliance.

Pull Request - State: closed - Opened by KPLauritzen over 7 years ago - 1 comment

#25 - Redundant matrix calculation in quaternion method

Issue - State: closed - Opened by JensVK over 7 years ago

#24 - python3 compatibility for example.py

Pull Request - State: closed - Opened by andersx over 7 years ago - 2 comments

#23 - Restructured for pip support and following python standard

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

#21 - What does --normal, --kabsch and --quater do?

Issue - State: closed - Opened by KPLauritzen over 7 years ago - 2 comments

#20 - Added example for usage in python scripts

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

#19 - Can't install with pip

Issue - State: closed - Opened by KPLauritzen over 7 years ago - 2 comments

#18 - Citations and license are outputted to terminal with the help message

Issue - State: closed - Opened by KPLauritzen over 7 years ago - 3 comments

#17 - Allow imports into other python scripts

Pull Request - State: closed - Opened by KPLauritzen over 7 years ago - 4 comments

#16 - Python2/3 compatible, PEP8 formatting, first test

Pull Request - State: closed - Opened by Ashafix over 7 years ago - 2 comments

#15 - Fixed typo in P matrix storage that caused the 'add-idx' option not t…

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

#14 - Fixed small bug and added features

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

#13 - quaternion

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

#12 - Added artwork

Pull Request - State: closed - Opened by ddemapan over 8 years ago - 2 comments

#11 - Wrong result for Kabsch RMSD

Issue - State: closed - Opened by cossio over 8 years ago - 4 comments

#10 - Import argparse iff running rmsd directly

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

#9 - add support for xyz files with scientific notation

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

#8 - Option to calculate RMSD without hydrogen atoms

Issue - State: closed - Opened by charnley about 9 years ago - 1 comment
Labels: enhancement

#7 - Adds DOI URL in README

Pull Request - State: closed - Opened by cstein almost 10 years ago

#6 - rmsd now Conforms to PEP8

Pull Request - State: closed - Opened by cstein almost 10 years ago

#5 - Wrote some python to align molecules, allowing output of the aligned poses.

Pull Request - State: closed - Opened by ryancoleman almost 11 years ago - 1 comment