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rocklinc's Introduction

RocklinC

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A python module for performing Rocklin Correction.

Installing from source

from source. Clone the source from GitHub with::

git clone https://github.com/xiki-tempula/rocklinc.git

then do::

cd rocklinc
pip install .

Uasge

To compute Rocklin correction. The following data is required.

  • u: MDAnalysis.Universe object that contains positions, charges, radii and dimensions.
  • box: The dimension (Å) of the simulation box in the form of a list (e.g. [100, 100, 100]).
  • lig_netq: The total charge of the ligand.
  • protein_netq: The total charge of the rest of the system excluding ligand.
  • temp: The temperature of the simulation (K).
  • water: The water model being used. Only rocklinc.waters.TIP3P and rocklinc.waters.TIP4P are supported for now.
  • lig_selection: The MDAnalysis selection string for the ligand.
  • apbs_exe: The executable path of the APBS software.

A full automatic calculation of Rocklin correction could be performed with:

    import rocklinc
    correction = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp)
    correction.make_APBS_input(u, lig_selection)
    correction.run_APBS(apbs_exe=apbs_exe)
    correction.read_APBS()
    result = correction.compute()
    correction.write('correction.txt')

result is the correction energy, while the details are written in 'correction.txt'.

Please see the full documentation from RTD. https://rocklinc.readthedocs.io/

Copyright

Copyright (c) 2020, Zhiyi Wu

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.3.

rocklinc's People

Contributors

xiki-tempula avatar

Stargazers

Kevin avatar avatar Chris Lockhart avatar Oliver Beckstein avatar

Watchers

James Cloos avatar avatar

Forkers

eduardo359 bigginlab ywu-roivant

rocklinc's Issues

running a mda.Universe through make_APS_input zeros ligand charges

Because of the zero-ing on line 159, the charges for the ligand in the Universe get zeroed, modifying in-place the universe being parsed

rocklinc/rocklinc/rocklin_correction.py

Lines 153 to 161 in 14e6378

# Charge only the ligand
universe.select_atoms('not {}'.format(ligand_selection)).charges = 0
self.apbs_qL = np.sum(universe.atoms.charges) * pq.e
universe.select_atoms('not {}'.format(solvent_selection)).write(in_lig_in_prot)
# Charge only the Rest of the system
universe.atoms.charges = charges
universe.select_atoms('{}'.format(ligand_selection)).charges = 0
self.apbs_qP = np.sum(universe.atoms.charges) * pq.e
universe.select_atoms('not {}'.format(solvent_selection)).write(in_prot_only)

I guess the simplest solution here is just to feed the charges back (i.e. akin to line 158) after line 161, or just operate on a copy of the Universe?

Travis CI Security Breach Notice

MolSSI is reaching out to every repository created from the MolSSI Cookiecutter-CMS with a .travis.yml file present to alert them to a potential security breach in using the Travis-CI service.

Between September 3 and September 10 2021, the Secure Environment Variables Travis-CI uses were leaked for ALL projects and injected into the publicly available runtime logs. See more details here. All Travis-CI users should cycle any secure variables/files, and associated objects as soon as possible. We are reaching out to our users in the name of good stewards of the third-party products we recommended and might still be in use and provide a duty-to-warn to our end-users given the potential severity of the breach.

We at MolSSI recommend moving away from Travis-CI to another CI provider as soon as possible. The nature of this breach and the way the response was mis-handled by Travis-CI, MolSSI cannot recommend the Travis-CI platform for any reason at this time. We suggest either GitHub Actions (as is used from v1.5 of the Cookiecutter-CMS) or some other service offered on GitHub.

If you have already addressed this security concern or it does not apply to you, feel free to close this issue.

This issue was created programmatically to reach as many potential end-users as possible. We do apologize if this was sent in error.

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