https://github.com/lilyminium/polymetrizer

https://github.com/lilyminium/polymetrizer

Last synced: 20 days ago
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• Host: GitHub
• URL: https://github.com/lilyminium/polymetrizer
• Owner: lilyminium
• License: mit
• Created: 2021-05-21T23:48:10.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2021-10-27T17:57:59.000Z (about 3 years ago)
• Last Synced: 2024-11-01T04:12:27.586Z (2 months ago)
• Language: Python
• Size: 221 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
polymetrizer

==============================

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Generate force fields for polymer-like molecules

```python

from polymetrizer import Polymetrizer

from polymetrizer.tests.smiles import ALA, SER, CYS, ACE, NME

from openff.toolkit.typing.engines.smirnoff import ForceField

# ALA = "[H][N]([C@]([H])([C](=[O])[*:2])[C]([H])([H])[H])[*:1]"

# SER = "[H][O][C]([H])([H])[C@@]([H])([C](=[O])[*:2])[N]([H])[*:1]"

# CYS = "[H][S][C]([H])([H])[C@@]([H])([C](=[O])[*:2])[N]([H])[*:1]"

# ACE = "CC(=O)-[*:6]"

# NME = "[*:7]NC"

# The linkage points go HN-R1, O=C-R2

# so we need to bond R1-R2 to get a peptide bond

# ACE is O=C-R6

# NME is CN-R7

met = Polymetrizer(monomers=dict(Ser=SER, Ala=ALA, Cys=CYS, Ace=ACE, Nme=NME),

                   caps=[ACE, NME],

                   r_linkages = {1: {2, 6}, 7: {2}})

original_ff = ForceField("openff_unconstrained-1.3.0.offxml")

new_ff = met.polymetrize(original_ff,

                         n_neighbor_monomers=1,  # builds tripeptides

                         n_overlapping_atoms=3,

                         prune_isomorphs=False,

                         # minimize before doing AM1BCC charges with MMFF

                         minimize_geometry=True,

                         # optimization too expensive, but if so....

                         optimize_geometry=False,

                         optimize_method="m06-2x/def2-TZVP",

                        )     

offsmi = met.oligomers[-1].to_smiles()

offmol = Molecule.from_smiles(offsmi, allow_undefined_stereo=True)

# or offmol = met.oligomers[-1].to_openff()

new_ff.create_openmm_system(offmol.to_topology())

```

You can inspect the force field by ID:

```python

>>> new_ff.get_parameter_handler("LibraryCharges").parameters[:3]

[,

 ,

 ]

 

 >>> [x for x in new_ff.get_parameter_handler("ProperTorsions").parameters

 ... if "CysNme" in x.id]

 [,

 ,

 ,

 ,

 ,

 ,

 ,

 ,

 ,

 ]

```

### Copyright

Copyright (c) 2021, Lily Wang

#### Acknowledgements

 

Project based on the 

[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.