Open
Conversation
Collaborator
cabb99
commented
Jun 10, 2024
cabb99
commented
- Updates Readme
- Calculate Qc by defaul
- Introduces awsem command
- Adds device binding for Aries
- Changes default fragment length to 10 to solve issue Propose Using 10 instead of 9 for Segment Length in Fragment Memory #31
- Adds support for lowercase chain names
- Parallelizes fragment memory creation
- Updates pdb database
- Adds function to create fragment alignment
- Adds logging
Adds parallel fragment memory creation and AWSEM commandline interface
Development mw
Merges from master
Allows calculating Qc by default
Changes default memory length to 10
… q value with additional bias force in biasTerms.py
…hydrogen bonds present in structure
testing differences between my github repo ftclark3 master and my local repo master.
allow user to change min contact distance
… of support for FTP
changed FTP to HTTPS in pdb_seqres.txt download due to RCSB/wwPDB end…
…10. This does not affect any behavior when the script is used as intended because this function parameter is overridden by the --frag_fragmentLength command line argument (or its default value of 10). However, the change may prevent future developer confusion
stop writing PDB trajectory by default
append statedatareporters if continuing from checkpoint
fixing typo
automatically remove excess fragment memories
Parallelize hb init
HB docs update
clean up user_guide.rst
Update user_guide.rst
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.