Ecosyste.ms: Issues

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GitHub / GrossfieldLab/loos issues and pull requests

#110 - improve error messages with file names when possible

Issue - State: open - Opened by lgsmith over 1 year ago - 5 comments

#108 - Implement Mdtraj-hdf5 format

Pull Request - State: closed - Opened by agrossfield over 1 year ago - 3 comments
Labels: enhancement

#106 - svd vs big-svd, core dumping over atomic indices

Issue - State: open - Opened by mmfarrugia over 1 year ago - 12 comments

#105 - Create selectors for 'altloc' and the other various AG fields

Issue - State: open - Opened by lgsmith almost 2 years ago - 6 comments

#104 - Handle general periodic boxes

Issue - State: open - Opened by agrossfield almost 2 years ago - 1 comment
Labels: enhancement, help wanted

#103 - AlignedVirtualTrajectory doesn't work the right way when operating with a reference.

Issue - State: closed - Opened by lgsmith almost 2 years ago - 21 comments

#102 - Remove np.float, etc for compatibility with newest Numpy (> 1.24, I think)

Issue - State: closed - Opened by agrossfield about 2 years ago - 2 comments
Labels: bug, help wanted

#101 - added molecular order parameter to AtomicGroup

Pull Request - State: closed - Opened by agrossfield about 2 years ago

#100 - pyloos doesn't always update when it should

Issue - State: closed - Opened by agrossfield about 2 years ago - 2 comments
Labels: bug

#99 - relax boost version on conda-forge distribution

Issue - State: open - Opened by lgsmith about 2 years ago - 26 comments

#98 - cmake doesn't detect BLAS libraries

Issue - State: open - Opened by blakemertz about 2 years ago - 11 comments

#94 - binaries in sub-directories of packages not installed

Issue - State: closed - Opened by lgsmith about 2 years ago

#93 - ramachandran only does FW formatting for certain segments of output

Issue - State: closed - Opened by lgsmith about 2 years ago - 1 comment

#92 - make netcdf support mandatory, fix #91

Pull Request - State: closed - Opened by agrossfield about 2 years ago
Labels: bug

#91 - Conda-forge package 4.0.2 doesn't have netcdf support

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

#90 - loos package is not available in conda-forge repository

Issue - State: closed - Opened by RubenRam about 2 years ago - 5 comments

#89 - Added subsection about env upgrade to 4.0

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

#88 - Installation fails on MacOS Monterey, Apple M1 Pro MBP

Issue - State: closed - Opened by ayanb73 about 2 years ago - 25 comments

#82 - PDB ensembles instead of repeated calls to `createSystem`

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

#81 - included switch to cast int64 to slice type for numpy compatibility

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

#80 - `np.int64` not recognized as index for AtomicGroupVector

Issue - State: closed - Opened by lgsmith over 2 years ago

#79 - in python, loos.fileopenerror prints unicode garbage instead of file-path.

Issue - State: closed - Opened by lgsmith over 2 years ago - 3 comments

#78 - Hydrogen selector fails when the system uses hydrogen mass repartitioning

Issue - State: closed - Opened by agrossfield almost 3 years ago
Labels: bug

#77 - Long bond finder and python uplift

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

#76 - Fix LoosOptions pre-made command line options

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

#73 - integration with PLUMED

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

#72 - LoosOptions can't print fullhelp and exit if there are required arguments

Issue - State: open - Opened by lgsmith almost 3 years ago - 3 comments

#70 - Merge changes from main into release candidate

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

#69 - correctly export AtomicGroup.splitByName to python

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

#68 - SplitByName usage in python script

Issue - State: closed - Opened by agrossfield about 3 years ago - 1 comment

#65 - Rama residues

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

#64 - Added rare event detection tool

Pull Request - State: closed - Opened by gracejulien about 3 years ago - 1 comment

#63 - Fixed command line args issue with all_contacts.py

Pull Request - State: closed - Opened by gracejulien over 3 years ago - 1 comment

#62 - lipid_unwrap.py

Pull Request - State: open - Opened by krb0073 over 3 years ago - 2 comments

#57 - Stacking

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

#56 - 2DRMSD

Pull Request - State: open - Opened by aneesmkp over 3 years ago - 1 comment

#49 - Python options

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

#46 - Bonds for Martini protein residues not applying correctly

Issue - State: closed - Opened by robincorey over 3 years ago - 6 comments

#44 - Fix tinker

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

#41 - smoothed sharper edges of cluster-kgs

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

#40 - Trouble using subsetter with OpenMM trajectories

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

#39 - OCF tool

Pull Request - State: closed - Opened by lgsmith about 4 years ago - 13 comments

#37 - Gitignore upgrade

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

#36 - Make gitignore cleaner and more maintainable

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

#35 - merge-traj --regex and --scanf options should imply --sort

Issue - State: closed - Opened by agrossfield about 4 years ago - 1 comment

#33 - Weights default

Pull Request - State: closed - Opened by lgsmith about 4 years ago - 5 comments

#32 - Ocf tool

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

#31 - OMG/NAMD.py class not imposing constraints

Issue - State: closed - Opened by krb0073 about 4 years ago - 5 comments

#30 - Hard contacts

Pull Request - State: closed - Opened by Poruthoor about 4 years ago - 3 comments

#29 - Conda install

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

#28 - ESP mesh tool

Pull Request - State: closed - Opened by chapincavender over 4 years ago - 6 comments

#27 - PyLoos: import loos won't release the GIL

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

#26 - python import doesn't work right in OSX

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

#25 - Rgyr upgrade

Pull Request - State: closed - Opened by lgsmith almost 5 years ago - 2 comments

#24 - Dihedral

Pull Request - State: closed - Opened by lgsmith almost 5 years ago - 3 comments

#23 - OMG TM-helix LOOS Secondary structure

Issue - State: closed - Opened by krb0073 about 5 years ago - 3 comments

#22 - Conda only build

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

#21 - Conda only build

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

#20 - issues with cylindrical-density

Issue - State: closed - Opened by VBurns about 5 years ago - 5 comments

#19 - cluster_structures.py should write mediods instead of centroids

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

#18 - Clustering

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

#17 - Problems running any of the rdf tools

Issue - State: closed - Opened by krb0073 over 5 years ago - 7 comments

#16 - Handling internal waters in omg.py

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

#15 - Fullhelper

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

#14 - Fullhelper

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

#13 - Clustering

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

#12 - Quick question : windows subsystem?

Issue - State: closed - Opened by krb0073 over 5 years ago - 3 comments

#11 - precision tool option for RMSD tools

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

#10 - Added optional rotation of the protein in solvate.py and PSFGen.py

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

#9 - Added atom names to salt segment in solvate.py

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

#8 - Implement NMRCLUST

Issue - State: closed - Opened by agrossfield almost 6 years ago - 2 comments
Labels: enhancement

#7 - Compiling issue with scons

Issue - State: closed - Opened by Alan-Rusty24 over 6 years ago - 12 comments

#6 - Erroneous results from threaded tools with Fedora and openblas

Issue - State: closed - Opened by tromo over 6 years ago - 2 comments

#5 - cleaned up some unignored binaries.

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

#4 - Rms overlap

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

#3 - Fullhelper

Pull Request - State: closed - Opened by lgsmith over 6 years ago - 2 comments

#2 - Added version 1.0 of native-hbs.py

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

#1 - Broken link in HTML docs

Issue - State: closed - Opened by jhenin almost 8 years ago - 2 comments