Updates fragment memory creation#32
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Jun 10, 2024
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- 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
alexfleury-sb
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Oct 20, 2024
Creates single memory fragment for pdb starting on a number different than 1. Updates seq_length_from_pdb to account for gaps in the sequence.
ftp changed to https for pdb_seqres.txt download
Adds parameters to fragment memory and contact term
Fixes burial term calculation for k_burial=0
Fixes the mapping of the residues for hydrogen bonding
…s refactored later--the most important change introduced here is that lambda and alpha parameters now depend on whether two residues are in the same chain or in different chains--this was always the case in the lammps code but was not translated correctly to openmm
… the hydrogen bond terms
…n for reporducing the LAMMPS hydrogen bond potential Message: openawsem is now agreeing with aram's lammps beta HB terms for simple short beta hairpin 2evq
…he hbond potential. original commit message below. helping steven check openawsem nfkb simulations (but really focusing on 1r69, which formed a beta sheet under different well widths) testing different well widths
…terchain pairs with |i-j|<18 unless both designated beta in ssweight. original commit message below: working for beta term 1 for 2evq and chain A of 2l8x
…erm, fixing minimum sequence separation hydrogen bond term, and fixing signs in the lambda functions original message: seems to be working for beta2 now
original message: refactoring in progress
refactored such that beta2 energies agree with energies computed in openawsem before the refactoring and with lammps, at least for the test case 2l8x; still need to check beta1 and beta3
found that beta1 wasn't working after my previous commit, so i fixed the guard conditionals and correct some energy terms strings by wrapping them in parentheses; beta2 now seems to be not quite right, so need to figure out why
…y commits advancing my hbond fixes
Fixes exclusion volume to be closer to original lammps implementation
…_by_distance to group_constraint_by_distance_protein
Merge to carlos constraints
…los-master getting latest updates
referencing oa.ca in the default argument leads to a name error upon importing
Change default group parameters for group_constraint_by_distance
added interface_q_term
remove ssweightFileName kwarg from pap_term_2
…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
Rho chain check
Revert "Rho chain check" until changes are finished
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