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REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-05-14
ATOM 1 N GLY A 1 -20.176 -4.691 6.137 1.00 0.00 N
ATOM 2 CA GLY A 1 -18.772 -4.447 5.746 1.00 0.00 C
ATOM 3 C GLY A 1 -18.698 -3.139 4.942 1.00 0.00 C
ATOM 4 O GLY A 1 -19.720 -2.788 4.371 1.00 0.00 O
ATOM 5 H GLY A 1 -20.489 -3.984 6.798 1.00 0.00 H
ATOM 6 HA2 GLY A 1 -18.350 -5.210 5.212 1.00 0.00 H
ATOM 7 HA3 GLY A 1 -18.239 -4.243 6.657 1.00 0.00 H
ATOM 8 H2 GLY A 1 -20.222 -5.616 6.623 1.00 0.00 H
ATOM 9 H3 GLY A 1 -20.811 -4.695 5.382 1.00 0.00 H
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j-wags / 6hvi_prepared.pdb
Last active September 21, 2023 03:24
protein-loading-2023-ccpbiosim-workshop
REMARK 4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
TITLE 6HVI-deleted1-19 - final4FEP
MODEL 1
ATOM 1 CH3 ACE A 31 96.008 81.418 259.315 1.00 0.00 C
ATOM 2 C ACE A 31 96.374 80.044 259.866 1.00 0.00 C
ATOM 3 O ACE A 31 97.556 79.710 259.937 1.00 0.00 O
ATOM 4 1H ACE A 31 96.575 81.618 258.405 1.00 0.00 H
ATOM 5 2H ACE A 31 94.946 81.483 259.076 1.00 0.00 H
# Local conda environment
env*/
# Python and Jupyter stuff
__pycache__
.ipynb_checkpoints
# Notebook outputs
workflow-factory.yaml
bespoke-executor/
ligands.sdf
ligands.yml
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j-wags / biopolymer_rc_notebook.ipynb
Last active August 31, 2022 17:24
biopolymer_alpha_notebook.ipynb
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j-wags / slots.md
Created October 16, 2020 22:48
On slots

What are slots?

  • For the System object: A way to map between applied parameters in a System and the underlying graph molecule(s)
  • For ParameterHandlers: A way to look at a Topology and determine
    • how many parameters should be assigned
    • whether one SMIRKS parameter should clobber another, or both parameters should coexist
  • In formal math: An customizable language (algebra?) for describing how to take a graph where each node has a unique index and:
    • enumerate desired graph substructures
    • define an equivalence operator for graph substructures
@j-wags
j-wags / reSubForAWS.py
Created December 5, 2016 20:08
First shot at dict reformatting for AWS
import re
if __name__ == '__main__':
matching_pattern = ':"(?P<value>[A-Za-z0-9]+)"'
substitution_pattern = ':{"S":"\g<value>"}'
orig_text = '{"id":"1"}'
new_text = re.sub(matching_pattern,
substitution_pattern,
orig_text)
print new_text