.gitignore
LICENSE
README.md
__init__.py
atoms.py
calculated_bond_lengths.json
comp_output.py
component.py
config.ini
config.py
const.py
fileIO.py
finders.py
geometry.py
job_control.py
json_extension.py
new_fileIO.py
pathway.py
ring.py
setup.py
substituent.py
AaronTools.egg-info/PKG-INFO
AaronTools.egg-info/SOURCES.txt
AaronTools.egg-info/dependency_links.txt
AaronTools.egg-info/requires.txt
AaronTools.egg-info/top_level.txt
Ligands/ACN.xyz
Ligands/AcAc.xyz
Ligands/Ad-HC5C.xyz
Ligands/BDA.xyz
Ligands/BPE.xyz
Ligands/BPY.xyz
Ligands/BenQuin.xyz
Ligands/BiOX.xyz
Ligands/BiOx_Me.xyz
Ligands/CO.xyz
Ligands/COD.xyz
Ligands/Cp.xyz
Ligands/Cp_star.xyz
Ligands/DMBPY.xyz
Ligands/DMP.xyz
Ligands/DMPE.xyz
Ligands/DPEphos.xyz
Ligands/DPPE.xyz
Ligands/DPPF.xyz
Ligands/DPPP.xyz
Ligands/EDA.xyz
Ligands/IMes.xyz
Ligands/JoshPhos.xyz
Ligands/KASBAI.xyz
Ligands/Mes-NC5C.xyz
Ligands/Milstein.xyz
Ligands/NBD.xyz
Ligands/PHNNP.xyz
Ligands/PIN.xyz
Ligands/PPh3.xyz
Ligands/Paton_DL.xyz
Ligands/Paton_EL.xyz
Ligands/PhBP3.xyz
Ligands/PymdOx.xyz
Ligands/PyrOx.xyz
Ligands/R-BINAP.xyz
Ligands/R-Me-StackPhos.xyz
Ligands/R-Ph-BOX.xyz
Ligands/R-Ph-Mes-NC5C.xyz
Ligands/R-Quinox-AdtBu2.xyz
Ligands/R-Quinox-tBu3.xyz
Ligands/R-SEGPHOS.xyz
Ligands/R-StackPhos.xyz
Ligands/R-iPr-PyBOX.xyz
Ligands/R-pFPh-StackPhos.xyz
Ligands/R-tBu-BOX.xyz
Ligands/RR-BDPP.xyz
Ligands/RR-BPCp.xyz
Ligands/RR-Et-DuPhos.xyz
Ligands/RR-Me-BPE.xyz
Ligands/RR-Me-DuPhos.xyz
Ligands/RR-Me-TBF.xyz
Ligands/RR-Me-iPrPh-NC5C.xyz
Ligands/RR-QuinoxP.xyz
Ligands/RR-iPr-DuPhos.xyz
Ligands/RR-norphos.xyz
Ligands/RRSS-DuanPhos.xyz
Ligands/R_temp.xyz
Ligands/S-BINAP.xyz
Ligands/S-Me-StackPhos.xyz
Ligands/S-Ph-BOX.xyz
Ligands/S-Ph-Mes-NC5C.xyz
Ligands/S-Quinox-AdtBu2.xyz
Ligands/S-Quinox-tBu3.xyz
Ligands/S-SEGPHOS.xyz
Ligands/S-StackPhos.xyz
Ligands/S-iPr-PyBOX.xyz
Ligands/S-pFPh-StackPhos.xyz
Ligands/S-tBu-BOX.xyz
Ligands/SL-J212-1.xyz
Ligands/SL-J212-2.xyz
Ligands/SS-BDPP.xyz
Ligands/SS-BPCp.xyz
Ligands/SS-Et-DuPhos.xyz
Ligands/SS-Me-BPE.xyz
Ligands/SS-Me-DuPhos.xyz
Ligands/SS-Me-TBF.xyz
Ligands/SS-Me-iPrPh-NC5C.xyz
Ligands/SS-QuinoxP.xyz
Ligands/SS-iPr-DuPhos.xyz
Ligands/SS-norphos.xyz
Ligands/SSRR-DuanPhos.xyz
Ligands/TACN.xyz
Ligands/TACN_star.xyz
Ligands/Tp.xyz
Ligands/Xantphos.xyz
Ligands/Xphos.xyz
Ligands/achiral_ligands
Ligands/bi-isoquinoline-NN-dioxide.xyz
Ligands/chiral_ligands
Ligands/dithiolate-4F.xyz
Ligands/iPr-NC3C.xyz
Ligands/iPr-PNPEt.xyz
Ligands/iPrPh-BIP.xyz
Ligands/iPrPh-NC5C.xyz
Ligands/organocatalysts
Ligands/squaramide-iPr.xyz
Ligands/squaramide.xyz
Ligands/tBu-PCP.xyz
Ligands/tBu-PNPPyr.xyz
Rings/benzene.xyz
Rings/cyclohexane-chair.1.xyz
Rings/cyclohexane-chair.2.xyz
Rings/cyclohexane.xyz
Rings/cyclopentadiene.1.xyz
Rings/cyclopentadiene.2.xyz
Rings/cyclopentadiene.3.xyz
Rings/cyclopentadiene.5.xyz
Rings/cyclopentadiene.6.xyz
Rings/cyclopentadiene.7.xyz
Rings/cyclopentane.1.xyz
Rings/cyclopentane.2.xyz
Rings/cyclopentane.3.xyz
Rings/cyclopentane.4.xyz
Rings/cyclopentane.5.xyz
Rings/cyclopentane.xyz
Substituents/26-F-Ph.xyz
Substituents/35-F-Ph.xyz
Substituents/Ad.xyz
Substituents/BF2.xyz
Substituents/Br.xyz
Substituents/CCH.xyz
Substituents/CF3.xyz
Substituents/CH2Cl.xyz
Substituents/CH2F.xyz
Substituents/CH2OH.xyz
Substituents/CH3.xyz
Substituents/CHCH2.xyz
Substituents/CHCl2.xyz
Substituents/CHF2.xyz
Substituents/CHO.xyz
Substituents/CN.xyz
Substituents/COCH3.xyz
Substituents/COOCH3.xyz
Substituents/COOH.xyz
Substituents/Cl.xyz
Substituents/Cy.xyz
Substituents/Et.xyz
Substituents/F.xyz
Substituents/H.xyz
Substituents/I.xyz
Substituents/Me.xyz
Substituents/Mes.xyz
Substituents/NCH3_2.xyz
Substituents/NH2.xyz
Substituents/NHCH3.xyz
Substituents/NHOH.xyz
Substituents/NO.xyz
Substituents/NO2.xyz
Substituents/O.xyz
Substituents/OCF3.xyz
Substituents/OH.xyz
Substituents/OMe.xyz
Substituents/Ph.xyz
Substituents/SCH3.xyz
Substituents/SH.xyz
Substituents/SiF3.xyz
Substituents/SiH3.xyz
Substituents/SuperMes.xyz
Substituents/iPr.xyz
Substituents/subs
Substituents/tBu.xyz
Substituents/triazole_C.xyz
Substituents/triazole_N.xyz
bin/PDFparse.py
bin/angle.py
bin/bond.py
bin/changeChirality.py
bin/changeElement.py
bin/closeRing.py
bin/dihedral.py
bin/fetchMolecule.py
bin/findAtoms.py
bin/follow.py
bin/grabStatus.py
bin/grabThermo.py
bin/interpolate.py
bin/jobSubmit.py
bin/libaddLigand.py
bin/libaddRing.py
bin/libaddSubstituent.py
bin/makeConf.py
bin/makeInput.py
bin/mapLigand.py
bin/percentVolumeBuried.py
bin/printFreq.py
bin/printFreqBild.py
bin/printInfo.py
bin/printXYZ.py
bin/rmsdAlign.py
bin/rotate.py
bin/substituentSterimol.py
bin/substitute.py
bin/translate.py
test/__init__.py
test/test_atoms.py
test/test_cls.py
test/test_comp_output.py
test/test_component.py
test/test_config.py
test/test_fetch.py
test/test_fileIO.py
test/test_finders.py
test/test_geometry.py
test/test_json_extension.py
test/test_pathway.py
test/test_substituent.py
test/test_utils.py
test/aaron_libs/config.ini
test/ref_files/atom.json
test/ref_files/benzene_dimer_ref.xyz
test/ref_files/cat.json
test/ref_files/chlorotoluene_180.xyz
test/ref_files/conf_spec.txt
test/ref_files/config_HOH_init.json
test/ref_files/config_blank_init.json
test/ref_files/detect_components.json
test/ref_files/file_io_died.xyz
test/ref_files/file_io_error.xyz
test/ref_files/file_io_normal.xyz
test/ref_files/freq.json
test/ref_files/geometry.json
test/ref_files/lig.json
test/ref_files/lig_map_1.xyz
test/ref_files/lig_map_2.xyz
test/ref_files/lig_map_3.xyz
test/ref_files/lig_map_4.xyz
test/ref_files/lig_map_5.xyz
test/ref_files/lig_map_6.xyz
test/ref_files/lig_map_7.xyz
test/ref_files/log.json
test/ref_files/make_conf_1.xyz
test/ref_files/make_conf_2.xyz
test/ref_files/minimize_torsion.xyz
test/ref_files/naphthalene.xyz
test/ref_files/orca_geom.xyz
test/ref_files/psi4_geom.xyz
test/ref_files/pyrene.xyz
test/ref_files/sub.json
test/ref_files/sub_rotate.xyz
test/ref_files/tetrahydronaphthalene.xyz
test/ref_files/torsion_interpolation.xyz
test/ref_files/vbur.xyz
test/ref_files/vbur2.xyz
test/ref_files/change_chirality_cls/diastereomer-1.xyz
test/ref_files/change_chirality_cls/diastereomer-2.xyz
test/ref_files/change_chirality_cls/diastereomer-3.xyz
test/ref_files/change_chirality_cls/diastereomer-4.xyz
test/ref_files/make_conf_cls/conformer-1.xyz
test/ref_files/make_conf_cls/conformer-2.xyz
test/ref_files/make_conf_cls/conformer-3.xyz
test/ref_files/make_conf_cls/conformer-4.xyz
test/ref_files/make_conf_cls/conformer-5.xyz
test/ref_files/make_conf_cls/conformer-6.xyz
test/ref_files/make_conf_cls/conformer-7.xyz
test/ref_files/make_conf_cls/conformer-8.xyz
test/test_files/5a-sub1.R.ts1.Cf1.3.com
test/test_files/6a2e5am1hex.xyz
test/test_files/COCH3.xyz
test/test_files/Et_1-NO2.xyz
test/test_files/NO2.xyz
test/test_files/R-Quinox-tBu3.xyz
test/test_files/benzene.xyz
test/test_files/benzene_1-NO2_4-Cl.can.xyz
test/test_files/benzene_1-NO2_4-Cl.txt
test/test_files/benzene_1-NO2_4-Cl.xyz
test/test_files/benzene_1-OH_4-Cl.xyz
test/test_files/benzene_1-Ph_4-Cl.xyz
test/test_files/benzene_4-Cl.xyz
test/test_files/benzene_dimer.xyz
test/test_files/change_dihedral_0.xyz
test/test_files/chiral_centers_1.xyz
test/test_files/chiral_centers_2.xyz
test/test_files/chiral_centers_3.xyz
test/test_files/chiral_centers_4.xyz
test/test_files/chiral_ring.xyz
test/test_files/chlorotoluene.xyz
test/test_files/config_HOH.ini
test/test_files/config_blank.ini
test/test_files/died.log
test/test_files/error.log
test/test_files/lig_1.xyz
test/test_files/lig_2.xyz
test/test_files/normal.log
test/test_files/opt_constraint.log
test/test_files/opt_normal.log
test/test_files/opt_running.log
test/test_files/orca_geom.out
test/test_files/pentane.xyz
test/test_files/psi4-test.out
test/test_files/ptco4.xyz
test/test_files/pyridine.xyz
test/test_files/step3.log
test/test_files/test-route-2.com
test/test_files/test-route.com
test/test_files/test_rmsd_sort1.xyz
test/test_files/test_rmsd_sort2.xyz
test/test_files/torsion-60.xyz
test/test_files/torsion-90.xyz
test/test_files/catalysts/org_1.xyz
test/test_files/catalysts/org_tri.xyz
test/test_files/catalysts/tm_multi-lig.xyz
test/test_files/catalysts/tm_single-lig.xyz
test/test_files/ligands/ACN.xyz
test/test_files/ligands/R-Quinox-tBu3.xyz
test/test_files/ligands/S-tBu-BOX.xyz
test/test_files/ligands/squaramide.xyz
theory/__init__.py
theory/basis.py
theory/emp_dispersion.py
theory/grid.py
theory/implicit_solvent.py
theory/job_types.py
theory/method.py
theory/theory.py
utils/__init__.py
utils/prime_numbers.py
utils/utils.py
utils/quad_grids/Leb110.grid
utils/quad_grids/Leb1454.grid
utils/quad_grids/Leb194.grid
utils/quad_grids/Leb2030.grid
utils/quad_grids/Leb2702.grid
utils/quad_grids/Leb302.grid
utils/quad_grids/Leb5810.grid
utils/quad_grids/Leb590.grid
utils/quad_grids/Leb974.grid
utils/quad_grids/Leg127.grid
utils/quad_grids/Leg20.grid
utils/quad_grids/Leg32.grid
utils/quad_grids/Leg64.grid
utils/quad_grids/Leg75.grid
utils/quad_grids/Leg99.grid
utils/quad_grids/NOTES