- 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
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name: 2024-smirnoff-workshop | |
channels: | |
- conda-forge | |
dependencies: | |
- openff-qcsubmit | |
- qcportal=0.53 | |
- nglview | |
- ipywidgets=7.6.0 | |
- plotly |
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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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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 |
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# 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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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 |