Polymer class revamp #851
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Polymer class revamp #851
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This pull request introduces 3 alerts when merging a06bc72 into 29e4699 - view on LGTM.com new alerts:
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This pull request introduces 3 alerts when merging 0e36cd0 into a185759 - view on LGTM.com new alerts:
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jennyfothergill
approved these changes
May 13, 2021
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| first_part = this_part | ||
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first_part is never used. I think we can simplify this logic to:
Suggested change
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This pull request introduces 1 alert when merging 883f25f into a185759 - view on LGTM.com new alerts:
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This pull request introduces 1 alert when merging ed10425 into a185759 - view on LGTM.com new alerts:
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This pull request introduces 1 alert when merging 2608b9d into ba793dd - view on LGTM.com new alerts:
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FYI, for anyone that still wants/needs to review this, I made a PR in the mbuild-examples repo that goes over the various ways to build polymers. |
justinGilmer
approved these changes
May 20, 2021
bc118
requested changes
May 20, 2021
bc118
approved these changes
May 20, 2021
umesh-timalsina
referenced
this pull request
in GOMC-WSU/MoSDeF-GOMC
Mar 22, 2022
* added a couple new functions, moved existing code into build function * added some doc strings * added a default value to the port labels * reworked the _add_port function * saving my progress with the add_end_groups function * made progress with end group funcitonality * removing a couple print statements * added 2 new attributes to port class * removed changes from port.py, commented out orientation and separation lines * changed method of removing hydrogens, added n_monomers var for finding last monomer * adding to the doc strings * added update_separation function * update orientation func; separation property func * added the up subports to the rotations * fixed the change_orientation function * fix handling when their is no anchor particle * fix typo * docstring: separation is None when port has no anchor * added 3 unit tests * remove the port updating stuff I was trying to use * updating port separations for end groups * fix the way clone is being called * added some doc strings and comments * updated doc strings * including jupyter notebook example and walk through * example notebook ready * added to recipe examples * expanded end_group options * update alkane recipe to make tests pass * cleaned up if statements when updating head/tail ports * remove trailing whitespace * allow use of compound with existing ports to be specified in init whitespace/formatting * update alkane to new schema * update tests * blacked, changed how head/tail port work * remove debug print * update notebook * update notebook * clear nb * add back add_hydrogens * add add_hydrogens=False * add_hydrogens=False, all tests pass * changed orientation of down port to face opposite direction of up port * Few more examples added to show new functionality * adding a few unit tests * removing the example notebook from the PR * test for errors, and manually passing in end group compounds * expanded doc strings with more detailed explanations, and some examples * fix a conflict that was sticking around in the port doc strings * fix formatting in the doc strings * Doc strings to explain implementation of sequence in the build function * add unit test for value of n < 1 * 2 new tests to test for errors * remove unused imports * oops, typo Co-authored-by: chrisjonesBSU <[email protected]> Co-authored-by: Jenny <[email protected]> Co-authored-by: Jenny Fothergill <[email protected]>
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PR Summary:
For some background, I'm currently working on a project where we need to easily initialize polydisperse polymer systems, so I spent quite a bit of time playing around with
polymer.py. ThePolymerclass worked great at building up polymers from monomers, but in order to automate the process it required some work "preparing" the monomers before usingPolymer()then some steps to "finish" the polymer compounds (basically putting back any missing hydrogens).So, I thought it might be worth a shot to implement these "pre" and "post" polymer steps into the
Polymerclass itself while making it functional for just about any monomer compound that's initialized from either a SMILES string or a file.I included a jupyter notebook that shows an example of how to go through the process and describing what is happening. It's currently located at
mbuild/mbuild-polymer-example.ipynb. I wasn't sure if there was a better way to attach or include an interactive notebook, so I just included it in the PR. If this gets merged, I'll make sure to remove the notebook and make a separate PR to the tutorials repo.Also, I merged in the changes from #839 to this PR as I needed to use some of the functionality from it.
I'm interested in any feedback, I imagine this is more in the rough draft stages than near completion, but hopefully it's a start to making it easier to build-up polymers.
PR Checklist