Comments (3)
chrisjonesBSU
commented on September 24, 2024
I just thought about this while helping Marjan with something. Does GRiTS and smiles string matching work on united atom trajectories?
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JimmyRushing
commented on September 24, 2024
Is this helpful? This finegrains xml.
https://bitbucket.org/cmelab/morphct/src/master/morphct/code/fine_grainer.py
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jennyfothergill
commented on September 24, 2024
Grits can add hydrogens to a trajectory for coarse-graining https://grits.readthedocs.io/en/latest/grits.html#grits.coarsegrain.CG_Compound
but it's not implemented very well for fine graining purposes yet.
Does GRiTS and smiles string matching work on united atom trajectories?
yes, just use the add_hydrogens kwarg
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Related Issues (14)
- Add CI/tests
- mappings to ring structures should not always share atoms
- Add a mapping save and load from mapping functions HOT 1
- Simulation example HOT 1
- speed up and scale up! HOT 2
- clean up repo HOT 1
- Add bead mass
- Fix visualize method
- Idea: non chemistry based grammar
- CG_System not completely populating bonding informaiton in snapshots HOT 3
- switch from openbabel to rdkit HOT 2
- SMILES matching on UA need a better warning or different functionality
- Improve the mapping operator HOT 1
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