LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
molSimplify/__init__.py
molSimplify/__main__.py
molSimplify.egg-info/PKG-INFO
molSimplify.egg-info/SOURCES.txt
molSimplify.egg-info/dependency_links.txt
molSimplify.egg-info/entry_points.txt
molSimplify.egg-info/requires.txt
molSimplify.egg-info/top_level.txt
molSimplify/Bind/bicarbonate.mol
molSimplify/Bind/bind.dict
molSimplify/Bind/bisulfate.mol
molSimplify/Bind/bisulfite.mol
molSimplify/Bind/carbonmonoxide.mol
molSimplify/Bind/dihydrogenphosphate.mol
molSimplify/Bind/dihydrogenphosphite.mol
molSimplify/Bind/formate.mol
molSimplify/Bind/nitrate.mol
molSimplify/Bind/oxalate.mol
molSimplify/Bind/oxygen.mol
molSimplify/Bind/perchlorate.mol
molSimplify/Bind/test.smi.smi
molSimplify/Bind/water.mol
molSimplify/Classes/__init__.py
molSimplify/Classes/atom3D.py
molSimplify/Classes/dft_obs.py
molSimplify/Classes/globalvars.py
molSimplify/Classes/helpers.py
molSimplify/Classes/ligand.py
molSimplify/Classes/mGUI.py
molSimplify/Classes/mWidgets.py
molSimplify/Classes/miniGUI.py
molSimplify/Classes/mol3D.py
molSimplify/Classes/monomer3D.py
molSimplify/Classes/partialcharges.py
molSimplify/Classes/protein3D.py
molSimplify/Classes/rundiag.py
molSimplify/Cores/Coporphyrin.mol
molSimplify/Cores/Crporphyrin.mol
molSimplify/Cores/Cuporphyrin.mol
molSimplify/Cores/Fe2O2.xyz
molSimplify/Cores/Feporphyrin.mol
molSimplify/Cores/Mnporphyrin.mol
molSimplify/Cores/N2OTS.xyz
molSimplify/Cores/Niporphyrin.mol
molSimplify/Cores/Scporphyrin.mol
molSimplify/Cores/Tiporphyrin.mol
molSimplify/Cores/Vporphyrin.mol
molSimplify/Cores/Znporphyrin.mol
molSimplify/Cores/cores.dict
molSimplify/Cores/cr4nh3o.xyz
molSimplify/Cores/fen4py.xyz
molSimplify/Cores/fen4pyO.xyz
molSimplify/Cores/fenh3O.xyz
molSimplify/Cores/ferrcore.xyz
molSimplify/Cores/ferrocene.mol
molSimplify/Cores/mn3nh3o.xyz
molSimplify/Cores/mn5nh3o.xyz
molSimplify/Cores/zncat.xyz
molSimplify/Data/.tcdefinput.inp
molSimplify/Data/ML.dat
molSimplify/Data/MLS_FSR_for_inter.dat
molSimplify/Data/MLS_FSR_for_inter2.dat
molSimplify/Data/MLS_angle_for_click.dat
molSimplify/Data/MLS_angle_for_inter.dat
molSimplify/Data/MLS_angle_for_inter2.dat
molSimplify/Data/MLS_angle_for_intra.dat
molSimplify/Data/MLS_angle_for_intra2.dat
molSimplify/Data/MLS_angle_for_oa.dat
molSimplify/Data/ML_FSR_for_inter.dat
molSimplify/Data/ML_FSR_for_inter2.dat
molSimplify/Data/ML_bond_for_cat.dat
molSimplify/Data/ML_bond_for_click.dat
molSimplify/Data/ML_bond_for_inter.dat
molSimplify/Data/ML_bond_for_inter2.dat
molSimplify/Data/ML_bond_for_intra.dat
molSimplify/Data/ML_bond_for_intra2.dat
molSimplify/Data/ML_bond_for_oa.dat
molSimplify/Data/bp1.dat
molSimplify/Data/coordinations.dict
molSimplify/Data/li.dat
molSimplify/Data/no.dat
molSimplify/Data/oct.dat
molSimplify/Data/pbp.dat
molSimplify/Data/spy.dat
molSimplify/Data/sq.dat
molSimplify/Data/sqap.dat
molSimplify/Data/sqp.dat
molSimplify/Data/tbp.dat
molSimplify/Data/thd.dat
molSimplify/Data/tpl.dat
molSimplify/Data/tpr.dat
molSimplify/Informatics/.DS_Store
molSimplify/Informatics/FeatureSetVisualization.ipynb
molSimplify/Informatics/GeoFreeRAC.ipynb
molSimplify/Informatics/Mol2Parser.py
molSimplify/Informatics/RACassemble.py
molSimplify/Informatics/__init__.py
molSimplify/Informatics/autocorrelation.py
molSimplify/Informatics/bridge_functionalizer.py
molSimplify/Informatics/clean_autocorrelation.py
molSimplify/Informatics/coulomb_analyze.py
molSimplify/Informatics/decoration_manager.py
molSimplify/Informatics/frag_functionalizer.py
molSimplify/Informatics/fragment_classes.py
molSimplify/Informatics/geo_analyze.py
molSimplify/Informatics/geometrics.py
molSimplify/Informatics/geometrics_csd.json
molSimplify/Informatics/graph_analyze.py
molSimplify/Informatics/jupyter_vis.py
molSimplify/Informatics/lacRACAssemble.py
molSimplify/Informatics/lacRACAssemble_bisdithiolenes.py
molSimplify/Informatics/macrocycle_synthesis.py
molSimplify/Informatics/misc_descriptors.py
molSimplify/Informatics/organic_fingerprints.py
molSimplify/Informatics/partialcharges.py
molSimplify/Informatics/py3Dmol_visualization.ipynb
molSimplify/Informatics/rac155_geo.py
molSimplify/Informatics/HFXsensitivity/__init__.py
molSimplify/Informatics/HFXsensitivity/measure_HFX_sensitivity_oxo_hat_reb_rel.py
molSimplify/Informatics/HFXsensitivity/measure_HFX_stable.py
molSimplify/Informatics/MOF/Linker_rotation.py
molSimplify/Informatics/MOF/MOF_descriptors.py
molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional_2.py
molSimplify/Informatics/MOF/MOF_functionalizer.py
molSimplify/Informatics/MOF/PBC_functions.py
molSimplify/Informatics/MOF/__init__.py
molSimplify/Informatics/MOF/atomic.py
molSimplify/Informatics/MOF/cluster_extraction.py
molSimplify/Informatics/MOF/fragment_MOFs_for_pormake.py
molSimplify/Ligands/(1_methylbenzimidazol_2_yl)pyridine.xyz
molSimplify/Ligands/.DS_Store
molSimplify/Ligands/.gitignore
molSimplify/Ligands/1-4-dimethyl-1-2-3-triazole.xyz
molSimplify/Ligands/12crown4.mol
molSimplify/Ligands/5fad5a0b35c34d073da2cde5.xyz
molSimplify/Ligands/Antipyrine.mol
molSimplify/Ligands/BPAbipy.mol
molSimplify/Ligands/Hpyrrole.mol
molSimplify/Ligands/N-quinolinylbutyramidate.xyz
molSimplify/Ligands/N-quinolinylmethylmethinylacetamidate.xyz
molSimplify/Ligands/NMe2_-1.xyz
molSimplify/Ligands/PCy3.mol
molSimplify/Ligands/PMe3.xyz
molSimplify/Ligands/PPh3.mol
molSimplify/Ligands/Propyphenazone.mol
molSimplify/Ligands/README
molSimplify/Ligands/acac.mol
molSimplify/Ligands/acacen.mol
molSimplify/Ligands/acetate.smi
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molSimplify/Ligands/benzenedithiol.mol
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molSimplify/Ligands/bihydrooxazine.mol
molSimplify/Ligands/bihydrooxazole.mol
molSimplify/Ligands/bihydrothiazine.mol
molSimplify/Ligands/bihydrothiazole.mol
molSimplify/Ligands/biimidazole.mol
molSimplify/Ligands/bioxazole.mol
molSimplify/Ligands/bipy.mol
molSimplify/Ligands/bipyrazine.xyz
molSimplify/Ligands/bipyrimidine.mol
molSimplify/Ligands/bipyrrole.mol
molSimplify/Ligands/bisnapthyridylpyridine.mol
molSimplify/Ligands/bithiazole.mol
molSimplify/Ligands/bromide.mol
molSimplify/Ligands/bromide.smi
molSimplify/Ligands/c2.mol
molSimplify/Ligands/caprolactone.mol
molSimplify/Ligands/carbonyl.mol
molSimplify/Ligands/carboxyl.mol
molSimplify/Ligands/cat.mol
molSimplify/Ligands/chloride.mol
molSimplify/Ligands/chloride.smi
molSimplify/Ligands/chloropyridine.mol
molSimplify/Ligands/co2.mol
molSimplify/Ligands/corrolazine.mol
molSimplify/Ligands/cs.mol
molSimplify/Ligands/cyanate.xyz
molSimplify/Ligands/cyanide.mol
molSimplify/Ligands/cyanoaceticporphyrin.mol
molSimplify/Ligands/cyanopyridine.mol
molSimplify/Ligands/cyclam.mol
molSimplify/Ligands/cyclen.mol
molSimplify/Ligands/cyclopentadienyl.mol
molSimplify/Ligands/cysteine.mol
molSimplify/Ligands/dF(CF3)ppy.xyz
molSimplify/Ligands/diaminomethyl.mol
molSimplify/Ligands/diazine.mol
molSimplify/Ligands/diazole.mol
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molSimplify/Ligands/dmap.xyz
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molSimplify/Ligands/dtbpy.xyz
molSimplify/Ligands/edta.mol
molSimplify/Ligands/en.mol
molSimplify/Ligands/ethanethiol.mol
molSimplify/Ligands/ethanolamine.mol
molSimplify/Ligands/ethbipy.mol
molSimplify/Ligands/ethyl.mol
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molSimplify/Ligands/ethylene.mol
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molSimplify/Ligands/fluoride.mol
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molSimplify/Ligands/gitignore
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molSimplify/Ligands/histidine.mol
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molSimplify/Ligands/hs-.mol
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molSimplify/Ligands/hydrocarboxyacetylide.xyz
molSimplify/Ligands/hydrocyanide.mol
molSimplify/Ligands/hydrodiazine.mol
molSimplify/Ligands/hydrodiazole.mol
molSimplify/Ligands/hydrogensulfide.mol
molSimplify/Ligands/hydroisocyanide.mol
molSimplify/Ligands/hydrooxazine.mol
molSimplify/Ligands/hydrooxazole.mol
molSimplify/Ligands/hydrothiazine.mol
molSimplify/Ligands/hydrothiazole.mol
molSimplify/Ligands/hydroxyl.mol
molSimplify/Ligands/imidazole.mol
molSimplify/Ligands/imidazolidinone.mol
molSimplify/Ligands/imine.mol
molSimplify/Ligands/iminodiacetic.mol
molSimplify/Ligands/iodide.mol
molSimplify/Ligands/iodobenzene.xyz
molSimplify/Ligands/isoleucine.mol
molSimplify/Ligands/isothiocyanate.mol
molSimplify/Ligands/leucine.mol
molSimplify/Ligands/ligands.dict
molSimplify/Ligands/lysine.mol
molSimplify/Ligands/mebenzenedithiol.mol
molSimplify/Ligands/mebim_py.xyz
molSimplify/Ligands/mebim_pz.xyz
molSimplify/Ligands/mebipy.mol
molSimplify/Ligands/mecat.mol
molSimplify/Ligands/methanal.mol
molSimplify/Ligands/methanethiol.mol
molSimplify/Ligands/methanol.mol
molSimplify/Ligands/methionine.mol
molSimplify/Ligands/methyl.mol
molSimplify/Ligands/methylacetylide.xyz
molSimplify/Ligands/methylamine.mol
molSimplify/Ligands/methylazide.xyz
molSimplify/Ligands/methylisocy.mol
molSimplify/Ligands/methylpyridine.mol
molSimplify/Ligands/n2.mol
molSimplify/Ligands/n4py.xyz
molSimplify/Ligands/nch.mol
molSimplify/Ligands/nco-.mol
molSimplify/Ligands/nethanolamine.mol
molSimplify/Ligands/nitrate.mol
molSimplify/Ligands/nitrite.mol
molSimplify/Ligands/nitro.mol
molSimplify/Ligands/nitrobipy.mol
molSimplify/Ligands/nitroso.mol
molSimplify/Ligands/nme3.mol
molSimplify/Ligands/no-.mol
molSimplify/Ligands/no2-.mol
molSimplify/Ligands/noxygen.mol
molSimplify/Ligands/ns-.mol
molSimplify/Ligands/o-pyridylbenzene.xyz
molSimplify/Ligands/o-pyridylphenylanion.xyz
molSimplify/Ligands/o2-.mol
molSimplify/Ligands/o2.xyz
molSimplify/Ligands/och2.mol
molSimplify/Ligands/oethanolamine.mol
molSimplify/Ligands/ome2.mol
molSimplify/Ligands/ooh.xyz
molSimplify/Ligands/oxalate.mol
molSimplify/Ligands/oxalate.smi
molSimplify/Ligands/oxygen.mol
molSimplify/Ligands/pentacyanocyclopentadienide.mol
molSimplify/Ligands/ph2-.mol
molSimplify/Ligands/ph3.mol
molSimplify/Ligands/phen.mol
molSimplify/Ligands/phenacac.mol
molSimplify/Ligands/phenalalanine.mol
molSimplify/Ligands/phendione.mol
molSimplify/Ligands/phenphen.mol
molSimplify/Ligands/phenylbenzoxazole.mol
molSimplify/Ligands/phenylcyc.mol
molSimplify/Ligands/phenylenediamine.mol
molSimplify/Ligands/phenylisocy.mol
molSimplify/Ligands/phosacidbipy.mol
molSimplify/Ligands/phosphine.mol
molSimplify/Ligands/phosphorine.mol
molSimplify/Ligands/phosphorustrifluoride.mol
molSimplify/Ligands/phthalocyanine.mol
molSimplify/Ligands/pme3o.mol
molSimplify/Ligands/porphyrin.mol
molSimplify/Ligands/pph3o.mol
molSimplify/Ligands/proline.mol
molSimplify/Ligands/propdiol.mol
molSimplify/Ligands/propylene.mol
molSimplify/Ligands/pyridine.mol
molSimplify/Ligands/pyrimidone.mol
molSimplify/Ligands/pyrrole.mol
molSimplify/Ligands/quinoxalinedithiol.mol
molSimplify/Ligands/s2-.mol
molSimplify/Ligands/salen.mol
molSimplify/Ligands/salphen.mol
molSimplify/Ligands/serine.mol
molSimplify/Ligands/simple_ligands.dict
molSimplify/Ligands/sulfacidbipy.mol
molSimplify/Ligands/tbucat.mol
molSimplify/Ligands/tbuphisocy.mol
molSimplify/Ligands/tbutylcyclen.mol
molSimplify/Ligands/tbutylisocy.mol
molSimplify/Ligands/tbutylthiol.mol
molSimplify/Ligands/tcnoet.mol
molSimplify/Ligands/tcnoetOH.mol
molSimplify/Ligands/terpy.mol
molSimplify/Ligands/tetrahydrofuran.mol
molSimplify/Ligands/thiane.mol
molSimplify/Ligands/thiazole.mol
molSimplify/Ligands/thiocyanate.mol
molSimplify/Ligands/thiol.mol
molSimplify/Ligands/thiophene.mol
molSimplify/Ligands/thiopyridine.mol
molSimplify/Ligands/threonine.mol
molSimplify/Ligands/tpp.mol
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molSimplify/Ligands/tryptophan.mol
molSimplify/Ligands/tyrosine.mol
molSimplify/Ligands/uthiol.mol
molSimplify/Ligands/uthiolme2.mol
molSimplify/Ligands/valine.mol
molSimplify/Ligands/water.mol
molSimplify/Ligands/x.mol
molSimplify/Scripts/__init__.py
molSimplify/Scripts/addtodb.py
molSimplify/Scripts/cellbuilder.py
molSimplify/Scripts/cellbuilder_tools.py
molSimplify/Scripts/chains.py
molSimplify/Scripts/convert_2to3.py
molSimplify/Scripts/dbinteract.py
molSimplify/Scripts/distgeom.py
molSimplify/Scripts/findcorrelations.py
molSimplify/Scripts/generator.py
molSimplify/Scripts/geometry.py
molSimplify/Scripts/grabguivars.py
molSimplify/Scripts/in_b3lyp_usetc.py
molSimplify/Scripts/inparse.py
molSimplify/Scripts/io.py
molSimplify/Scripts/isomers.py
molSimplify/Scripts/jobgen.py
molSimplify/Scripts/krr_prep.py
molSimplify/Scripts/molSimplify_io.py
molSimplify/Scripts/molden2psi4wfn.py
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molSimplify/Scripts/oct_check_mols.py
molSimplify/Scripts/periodic_QE.py
molSimplify/Scripts/postmold.py
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molSimplify/Substrates/propyne.xyz
molSimplify/Substrates/substrates.dict
molSimplify/Substrates/tert-butane.xyz
molSimplify/Substrates/toluene.xyz
molSimplify/Substrates/trunc.xyz
molSimplify/Substrates/xanthene.xyz
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molSimplify/job_manager/__init__.py
molSimplify/job_manager/classes.py
molSimplify/job_manager/manager_io.py
molSimplify/job_manager/moltools.py
molSimplify/job_manager/populate_jobs.py
molSimplify/job_manager/recovery.py
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molSimplify/molscontrol/__init__.py
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molSimplify/molscontrol/clf_tools.py
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molSimplify/molscontrol/molscontrol.py
molSimplify/molscontrol/data/README.md
molSimplify/molscontrol/data/look_and_say.dat
molSimplify/molscontrol/terachem/jobscript_control.sh
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molSimplify/python_nn/.gitignore
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molSimplify/python_nn/ms_ls_w3.csv
molSimplify/python_nn/ms_slope_b1.csv
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molSimplify/python_nn/ms_slope_b3.csv
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molSimplify/python_nn/ms_slope_w3.csv
molSimplify/python_nn/ms_split_b1.csv
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molSimplify/python_nn/ms_split_b3.csv
molSimplify/python_nn/ms_split_w1.csv
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molSimplify/python_nn/ms_split_w3.csv
molSimplify/python_nn/slope_center.csv
molSimplify/python_nn/slope_scale.csv
molSimplify/python_nn/split_center.csv
molSimplify/python_nn/split_scale.csv
molSimplify/python_nn/tf_ANN.py
molSimplify/python_nn/train_data.csv
molSimplify/tf_nn/__init__.py
molSimplify/tf_nn/geo_static_clf/geo_static_clf_model.h5
molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_name.csv
molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_x.csv
molSimplify/tf_nn/geo_static_clf/geo_static_clf_train_y.csv
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molSimplify/tf_nn/geos/hs_ii_bl_x.csv
molSimplify/tf_nn/geos/hs_ii_bl_y.csv
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tests/refs/bidentate_new/fe_oct_2_smi6_3_s_1_conf_1.molinp
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tests/refs/bidentate_new/fe_oct_2_smi9_3_s_1_conf_1.xyz
tests/refs/bidentate_new/jobscript
tests/refs/bidentate_new/terachem_input
tests/refs/bidentate_v3/fe_oct_2_smi10_3_s_1_conf_1.molinp
tests/refs/bidentate_v3/fe_oct_2_smi10_3_s_1_conf_1.report
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tests/refs/bidentate_v3/fe_oct_2_smi9_3_s_1_conf_1.xyz
tests/refs/bidentate_v3/jobscript
tests/refs/bidentate_v3/terachem_input
tests/refs/old_ref_cp/example_1.report
tests/refs/old_ref_cp/example_1.xyz
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tests/refs/old_ref_cp/molcas_caspt2.qcin
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tests/refs/old_ref_cp/orca_dft.qcin
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tests/refs/racs/co_acac_en_water_hydrogensulfide.xyz
tests/refs/racs/cr_acac_acac_bipy.xyz
tests/refs/racs/fe_bipy_2_bifuran.xyz
tests/refs/racs/fe_bipy_3.xyz
tests/refs/racs/fe_carbonyl_6.xyz
tests/refs/racs/fe_pyr_4_furan_2.xyz
tests/refs/racs/fe_pyr_6.xyz
tests/refs/racs/generate_references.py
tests/refs/racs/mn_furan_water_ammonia_furan_water_ammonia.xyz
tests/refs/racs/racs_Co_acac_en_water_hydrogensulfide.pickle
tests/refs/racs/racs_Cr_acac_acac_bipy.pickle
tests/refs/racs/racs_Fe_carbonyl_6.pickle
tests/refs/racs/racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle
tests/refs/ref_new/example_1.report
tests/refs/ref_new/example_1.xyz
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tests/refs/ref_new/example_7.xyz
tests/refs/ref_new/example_8.report
tests/refs/ref_new/example_8.xyz
tests/refs/ref_new/molcas_caspt2.qcin
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tests/refs/ref_new/molcas_casscf.qcin
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tests/refs/ref_new/orca_ccsdt.qcin
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tests/refs/ref_new/orca_ccsdt.xyz
tests/refs/ref_new/orca_dft.qcin
tests/refs/ref_new/orca_dft.report
tests/refs/ref_new/orca_dft.xyz