j-wags

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

j-wags

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  

j-wags

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  

j-wags

# Local conda environment
env*/
# Python and Jupyter stuff
__pycache__
.ipynb_checkpoints
# Notebook outputs
workflow-factory.yaml
bespoke-executor/
ligands.sdf
ligands.yml

j-wags

j-wags

j-wags

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

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