| protons/app/data/gaff.xml | |
|
|
| protons/app/data/gaff2-obc2.xml | |
|
|
| protons/app/data/gaff2.xml | |
|
|
| protons/app/data/hydrogens-amber10-constph.xml | |
|
|
| protons/app/data/ions_spce.xml | |
|
|
| protons/app/data/ions_tip3p.xml | |
|
|
| protons/app/data/ions_tip4pew.xml | |
|
|
| protons/app/data/readme.md | |
|
|
| protons/app/data/steps/forcefield_steps.py | 78 | A 0 mins |
|
| protons/app/driver.py | 3,977 | F 1 mo |
|
| protons/app/forcefield_generators.py | 513 | D 2 days |
|
| protons/app/generate_calibration_systems.py | 82 | A 35 mins |
|
| protons/app/integrators.py | 239 | C 1 day |
|
| protons/app/ions.py | 126 | A 3 hrs |
|
| protons/app/ligands.py | 2,255 | F 3 wks |
|
| protons/app/logger.py | 5 | A 0 mins |
|
| protons/app/metadatareporter.py | 132 | B 4 hrs |
|
| protons/app/modeller.py | 329 | F 5 days |
|
| protons/app/ncmcreporter.py | 208 | A 1 hr |
|
| protons/app/openeye.py | 493 | D 2 days |
|
| protons/app/pka.py | 159 | A 0 mins |
|
| protons/app/proposals.py | 641 | D 2 days |
|
| protons/app/saltswap_utils.py | 36 | A 0 mins |
|
| protons/app/samsreporter.py | 181 | A 1 hr |
|
| protons/app/schrodinger.py | 264 | C 7 hrs |
|
| protons/app/simulation.py | 230 | C 1 day |
|
| protons/app/template_patches.py | 88 | C 1 day |
|
| protons/app/titrationreporter.py | 191 | B 5 hrs |
|
| protons/app/topology.py | 15 | A 0 mins |
|
| protons/app/utils.py | 7 | A 0 mins |
|
| protons/scripts/__init__.py | 0 | A 0 mins |
|
| protons/scripts/cli.py | 78 | A 1 hr |
|
| protons/scripts/run_parametrize_ligand.py | 141 | B 5 hrs |
|
| protons/scripts/run_prep_ffxml.py | 336 | D 2 days |
|
| protons/scripts/run_simulation.py | 200 | C 7 hrs |
|
| protons/scripts/utilities.py | 138 | A 1 hr |
|
| readthedocs.yml | |
|
|
| references/J. Mol. Biol. 2007 Czodrowski.pdf | |
|
|
| references/J. Mol. Biol. 2007 Steuber.pdf | |
|
|
| references/PNAS-2011-Nilmeier-E1009-18.pdf | |
|
|
| references/mongan-case.pdf | |
|
|
| references/shirts-chodera-mbar.pdf | |
|
|
| references/stern.pdf | |
|
|
| setup.cfg | |
|
|
| setup.py | 67 | A 0 mins |
|
| versioneer.py | 1,326 | F 2 wks |
|