loos

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

2

**Describe the bug** When loos can't open a file, it emits an error. For the last several months, it has emitted errors with unicode that don't print properly to terminal....

lgsmith

2DRMSD

1

2drmsd.py script to calculate 2D RMSD after aligning with a different selection.

aneesmkp

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

3

**Describe the bug** The tool `contact_distance.py`, while having apparently correct usage of the description and fullhelp strings used to initialize loos options, is unable to print the fullhelp. Instead, it...

lgsmith

integration with PLUMED

6

**Is your feature request related to a problem? Please describe.** Not so much a problem as an expansion. Right now PLUMED often is used to perform analysis, and often it...

lgsmith

lipid_unwrap.py

2

Hi Alan, I placed the lipid_unwrap.py code that I have been working on in loos/Pacakges/Pyloos. Let me know anything that you need me to do and thank you again for...

krb0073

loos package is not available in conda-forge repository

2

**Describe the bug** INSTALL file states the package is avaible in conda-forge when it is not. **To Reproduce** $ conda install -c conda-forge loos **Expected behavior** Installation of package and...

RubenRam

Installation fails on MacOS Monterey, Apple M1 Pro MBP

14

**Describe the bug** When I attempt to install loos, the build fails partway through. **To Reproduce** Steps to reproduce the behavior: - On an appropriate machine: git clone https://github.com/GrossfieldLab/loos.git -...

ayanb73

File open error on list creation with hundreds of 'Trajectory' objects (needed for VirtualTrajectory init)

7

## Describe the bug When I splat a list of PDBs into `pyloos.VirtualTrajectory`'s init method, I get a `loos.loos.FileOpenError: Error while opening some_random_pdb.pdb` file open error on a particular structure,...

lgsmith

Update our use of Accelerate framework to avoid clapack deprecation issues for macos 13.3+

tromo

## Is your feature request related to a problem? LOOS has a bunch of clustering tools, but they all use things like k-means. It would be nice to have density-based...

agrossfield