├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── conda └── psikit │ └── meta.yaml ├── examples ├── CHARGE_COMPARISON │ ├── 1_default_results.out │ ├── charge_comparison.ipynb │ └── stdout.default.61628.intco ├── Rendering_Orbital │ ├── Psi_a_21_21-A.png │ └── Render_orbital.ipynb ├── Rendering_Orbital_in_PyMol │ ├── Visualize_MO_in_PyMol.ipynb │ ├── frontier.py │ ├── geom.xyz │ ├── sil_HOMO.png │ ├── sil_LUMO.png │ └── target.mol ├── Rendering_RESP_charge │ ├── RESP charge of the tetrazole.ipynb │ ├── cubefiles │ │ └── target.mol │ └── example.ipynb ├── Torsion_scan │ └── torsional_scan.ipynb ├── example_sapt │ ├── fisapt0.py │ ├── fsapt │ │ ├── Disp.pdb │ │ ├── Elst.pdb │ │ ├── Exch.pdb │ │ ├── IndAB.pdb │ │ ├── IndBA.pdb │ │ ├── README │ │ ├── Total.pdb │ │ ├── copy_pymol.py │ │ ├── copy_pymol2.py │ │ ├── fsapt.py │ │ ├── fsaptdiff.py │ │ ├── geom.xyz │ │ ├── pymol │ │ │ ├── Disp.pymol │ │ │ ├── Elst.pymol │ │ │ ├── Exch.pymol │ │ │ ├── IndAB.pymol │ │ │ ├── IndBA.pymol │ │ │ ├── Total.pymol │ │ │ ├── geom.pymol │ │ │ ├── orient.pymol │ │ │ ├── run.pymol │ │ │ └── vis.pymol │ │ └── pymol2 │ │ │ ├── DA.pymol │ │ │ ├── DB.pymol │ │ │ ├── DC.pymol │ │ │ ├── DFA.pymol │ │ │ ├── DFB.pymol │ │ │ ├── Geom.pymol │ │ │ ├── VA.pymol │ │ │ ├── VB.pymol │ │ │ ├── VC.pymol │ │ │ ├── dDA.pymol │ │ │ ├── dDB.pymol │ │ │ ├── orient.pymol │ │ │ ├── run.pymol │ │ │ └── vis.pymol │ ├── fsapt_ex.ipynb │ ├── phenol1.mol │ ├── phenol2.mol │ ├── sapt0.py │ ├── sapt_ex.ipynb │ ├── water1.mol │ └── water2.mol └── fchk │ └── ch4.fchk ├── images └── homo.png ├── psikit ├── __init__.py ├── fsapt_helper.py ├── helper_SAPT.py ├── psikit.py ├── pymol_helper.py ├── sapt.py └── util.py ├── setup.py └── tests ├── cocl2.mol ├── saptex ├── phenol1.mol ├── phenol2.mol ├── water1.mol └── water2.mol ├── test.mol ├── test_init.py ├── test_multiplicity.py └── test_sapt.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/README.md -------------------------------------------------------------------------------- /conda/psikit/meta.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/conda/psikit/meta.yaml -------------------------------------------------------------------------------- /examples/CHARGE_COMPARISON/1_default_results.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/CHARGE_COMPARISON/1_default_results.out -------------------------------------------------------------------------------- /examples/CHARGE_COMPARISON/charge_comparison.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/CHARGE_COMPARISON/charge_comparison.ipynb -------------------------------------------------------------------------------- /examples/CHARGE_COMPARISON/stdout.default.61628.intco: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/CHARGE_COMPARISON/stdout.default.61628.intco -------------------------------------------------------------------------------- /examples/Rendering_Orbital/Psi_a_21_21-A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital/Psi_a_21_21-A.png -------------------------------------------------------------------------------- /examples/Rendering_Orbital/Render_orbital.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital/Render_orbital.ipynb -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/Visualize_MO_in_PyMol.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/Visualize_MO_in_PyMol.ipynb -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/frontier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/frontier.py -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/geom.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/geom.xyz -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/sil_HOMO.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/sil_HOMO.png -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/sil_LUMO.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/sil_LUMO.png -------------------------------------------------------------------------------- /examples/Rendering_Orbital_in_PyMol/target.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_Orbital_in_PyMol/target.mol -------------------------------------------------------------------------------- /examples/Rendering_RESP_charge/RESP charge of the tetrazole.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_RESP_charge/RESP charge of the tetrazole.ipynb -------------------------------------------------------------------------------- /examples/Rendering_RESP_charge/cubefiles/target.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_RESP_charge/cubefiles/target.mol -------------------------------------------------------------------------------- /examples/Rendering_RESP_charge/example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Rendering_RESP_charge/example.ipynb -------------------------------------------------------------------------------- /examples/Torsion_scan/torsional_scan.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/Torsion_scan/torsional_scan.ipynb -------------------------------------------------------------------------------- /examples/example_sapt/fisapt0.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fisapt0.py -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/Disp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/Disp.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/Elst.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/Elst.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/Exch.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/Exch.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/IndAB.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/IndAB.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/IndBA.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/IndBA.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/README -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/Total.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/Total.pdb -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/copy_pymol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/copy_pymol.py -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/copy_pymol2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/copy_pymol2.py -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/fsapt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/fsapt.py -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/fsaptdiff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/fsaptdiff.py -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/geom.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/geom.xyz -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/Disp.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/Disp.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/Elst.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/Elst.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/Exch.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/Exch.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/IndAB.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/IndAB.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/IndBA.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/IndBA.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/Total.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/Total.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/geom.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/geom.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/orient.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/orient.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/run.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/run.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol/vis.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol/vis.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/DA.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/DA.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/DB.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/DB.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/DC.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/DC.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/DFA.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/DFA.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/DFB.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/DFB.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/Geom.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/Geom.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/VA.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/VA.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/VB.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/VB.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/VC.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/VC.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/dDA.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/dDA.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/dDB.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/dDB.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/orient.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/orient.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/run.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/run.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt/pymol2/vis.pymol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt/pymol2/vis.pymol -------------------------------------------------------------------------------- /examples/example_sapt/fsapt_ex.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/fsapt_ex.ipynb -------------------------------------------------------------------------------- /examples/example_sapt/phenol1.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/phenol1.mol -------------------------------------------------------------------------------- /examples/example_sapt/phenol2.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/phenol2.mol -------------------------------------------------------------------------------- /examples/example_sapt/sapt0.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/sapt0.py -------------------------------------------------------------------------------- /examples/example_sapt/sapt_ex.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/sapt_ex.ipynb -------------------------------------------------------------------------------- /examples/example_sapt/water1.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/water1.mol -------------------------------------------------------------------------------- /examples/example_sapt/water2.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/example_sapt/water2.mol -------------------------------------------------------------------------------- /examples/fchk/ch4.fchk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/examples/fchk/ch4.fchk -------------------------------------------------------------------------------- /images/homo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/images/homo.png -------------------------------------------------------------------------------- /psikit/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/__init__.py -------------------------------------------------------------------------------- /psikit/fsapt_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/fsapt_helper.py -------------------------------------------------------------------------------- /psikit/helper_SAPT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/helper_SAPT.py -------------------------------------------------------------------------------- /psikit/psikit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/psikit.py -------------------------------------------------------------------------------- /psikit/pymol_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/pymol_helper.py -------------------------------------------------------------------------------- /psikit/sapt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/sapt.py -------------------------------------------------------------------------------- /psikit/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/psikit/util.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/setup.py -------------------------------------------------------------------------------- /tests/cocl2.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/cocl2.mol -------------------------------------------------------------------------------- /tests/saptex/phenol1.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/saptex/phenol1.mol -------------------------------------------------------------------------------- /tests/saptex/phenol2.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/saptex/phenol2.mol -------------------------------------------------------------------------------- /tests/saptex/water1.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/saptex/water1.mol -------------------------------------------------------------------------------- /tests/saptex/water2.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/saptex/water2.mol -------------------------------------------------------------------------------- /tests/test.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/test.mol -------------------------------------------------------------------------------- /tests/test_init.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/test_init.py -------------------------------------------------------------------------------- /tests/test_multiplicity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/test_multiplicity.py -------------------------------------------------------------------------------- /tests/test_sapt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Mishima-syk/psikit/HEAD/tests/test_sapt.py --------------------------------------------------------------------------------