.gitignore
LICENSE
README.md
mkdocs.yml
pyproject.toml
.github/workflows/ci.yml
.github/workflows/docs.yml
.github/workflows/publish.yml
.vscode/launch.json
docs/api.md
docs/getting-started.md
docs/index.md
docs/performance.md
docs/references.md
docs/tutorial.md
examples/ethane/GS.fchk
examples/ethane/GS.log
examples/ethane/GS.mol2
examples/ethane/README.md
examples/ethane/TS.fchk
examples/ethane/TS.log
examples/ethane/TS.mol2
examples/rh-enamide/README.md
examples/rh-enamide/atom.typ
examples/rh-enamide/freq_runner.sh
examples/rh-enamide/mm3.fld
examples/rh-enamide/rh-hydrogenation-enamide-template.mae
examples/rh-enamide/rh_hyd_enamide_seminario.fld
examples/rh-enamide/rh_hyd_enamide_start.fld
examples/rh-enamide/ff/rh-hydrogenation-enamide-final.fld
examples/rh-enamide/ff/rh_hyd_enamide_final.fld
examples/rh-enamide/ff/rh_hyd_enamide_start.fld
examples/rh-enamide/rh_enamide_training_set/rh_enamide_training_set.mae
examples/rh-enamide/rh_enamide_training_set/rh_enamide_training_set.mmo
examples/rh-enamide/rh_enamide_training_set/rh_enamide_training_set.mol2
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/1ZDMPfromJCTCSI_loner1.01.in
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/1ZDMPfromJCTCSI_loner1.out
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/2DMPEConformation1fromJCTCSI_isomer1.01.in
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/2DMPEConformation1fromJCTCSI_isomer1.out
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examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/3DMPEConformation2fromJCTCSI_isomer2.out
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examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/4RR-Me-DuPHOSpro-RfromJCTCSI_isomer3.out
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examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/6RR-Me-BPEpro-RConformation1fromJCTCSI_isomer5.out
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examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/7RR-Me-BPEpro-RConformation2fromJCTCSI_isomer6.out
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/8RR-Me-BPEpro-SConformation1fromJCTCSI_isomer7.01.in
examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/8RR-Me-BPEpro-SConformation1fromJCTCSI_isomer7.out
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examples/rh-enamide/rh_enamide_training_set/jaguar_spe_freq_in_out/9RR-Me-BPEpro-SConformation2fromJCTCSI_isomer8.out
examples/rh-enamide/rh_enamide_training_set/mae/1_ZDMP_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/2_DMPE_Conformation_1_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/3_DMPE_Conformation_2_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/4__R_R_-Me-DuPHOS_pro-R_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/5__R_R_-Me-DuPHOS_pro-S_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/6__R_R_-Me-BPE_pro-R_Conformation_1_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/7__R_R_-Me-BPE_pro-R_Conformation_2_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/8__R_R_-Me-BPE_pro-S_Conformation_1_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mae/9__R_R_-Me-BPE_pro-S_Conformation_2_from_JCTC_SI.mae
examples/rh-enamide/rh_enamide_training_set/mol2/1_ZDMP_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/1_zdmp.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/2_DMPE_Conformation_1_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/2_dmpe_conf_1.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/3_DMPE_Conformation_2_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/3_dmpe_conf_2.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/4__R_R_-Me-DuPHOS_pro-R_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/4_duphos_r.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/5__R_R_-Me-DuPHOS_pro-S_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/5_duphos_s.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/6__R_R_-Me-BPE_pro-R_Conformation_1_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/6_bpe_r_conf_1.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/7__R_R_-Me-BPE_pro-R_Conformation_2_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/7_bpe_r_conf_2.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/8__R_R_-Me-BPE_pro-S_Conformation_1_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/8_bpe_s_conf_2.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/9__R_R_-Me-BPE_pro-S_Conformation_2_from_JCTC_SI.mol2
examples/rh-enamide/rh_enamide_training_set/mol2/9_bpe_s_conf_2.mol2
examples/rh-enamide/rh_enamide_training_set/raw_xyz/1_zdmp.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/2_dmpe_conf_1.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/3_dmpe_conf_2.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/4_duphos_r.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/5_duphos_s.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/6_bpe_r_conf_1.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/7_bpe_r_conf_2.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/8_bpe_s_conf_2.xyz
examples/rh-enamide/rh_enamide_training_set/raw_xyz/9_bpe_s_conf_2.xyz
examples/sn2-test/README.md
examples/sn2-test/compare_direct.py
examples/sn2-test/compare_implementations.py
examples/sn2-test/compare_rh_enamide.py
examples/sn2-test/compute_barrier.py
examples/sn2-test/generate_mm_data.py
examples/sn2-test/generate_qm_data.py
examples/sn2-test/run_tsff_pipeline.py
examples/sn2-test/sn2-ts-guess.xyz
examples/sn2-test/test_backends.py
examples/sn2-test/test_pipeline.py
examples/sn2-test/mm-reference/analyze-energy.txt
examples/sn2-test/mm-reference/mm-frequencies.txt
examples/sn2-test/mm-reference/sn2-ts.001
examples/sn2-test/mm-reference/sn2-ts.002
examples/sn2-test/mm-reference/sn2-ts.003
examples/sn2-test/mm-reference/sn2-ts.004
examples/sn2-test/mm-reference/sn2-ts.005
examples/sn2-test/mm-reference/sn2-ts.006
examples/sn2-test/mm-reference/sn2-ts.007
examples/sn2-test/mm-reference/sn2-ts.008
examples/sn2-test/mm-reference/sn2-ts.009
examples/sn2-test/mm-reference/sn2-ts.010
examples/sn2-test/mm-reference/sn2-ts.011
examples/sn2-test/mm-reference/sn2-ts.012
examples/sn2-test/mm-reference/sn2-ts.013
examples/sn2-test/mm-reference/sn2-ts.014
examples/sn2-test/mm-reference/sn2-ts.015
examples/sn2-test/mm-reference/sn2-ts.016
examples/sn2-test/mm-reference/sn2-ts.017
examples/sn2-test/mm-reference/sn2-ts.018
examples/sn2-test/mm-reference/sn2-ts.xyz
examples/sn2-test/mm-reference/vibrate-output.txt
examples/sn2-test/qm-reference/ch3f-energy.txt
examples/sn2-test/qm-reference/ch3f-frequencies.txt
examples/sn2-test/qm-reference/ch3f-hessian.npy
examples/sn2-test/qm-reference/ch3f-optimized.xyz
examples/sn2-test/qm-reference/complex-optimized.xyz
examples/sn2-test/qm-reference/sn2-ts-energy.txt
examples/sn2-test/qm-reference/sn2-ts-frequencies.txt
examples/sn2-test/qm-reference/sn2-ts-hessian.npy
examples/sn2-test/qm-reference/sn2-ts-optimized.xyz
examples/sn2-test/qm-reference/summary.txt
hooks/pre-commit
q2mm/__init__.py
q2mm/constants.py
q2mm/linear_algebra.py
q2mm/utilities.py
q2mm.egg-info/PKG-INFO
q2mm.egg-info/SOURCES.txt
q2mm.egg-info/dependency_links.txt
q2mm.egg-info/requires.txt
q2mm.egg-info/top_level.txt
q2mm/backends/__init__.py
q2mm/backends/base.py
q2mm/backends/mm/__init__.py
q2mm/backends/mm/openmm.py
q2mm/backends/mm/tinker.py
q2mm/backends/qm/__init__.py
q2mm/backends/qm/psi4.py
q2mm/forcefields/__init__.py
q2mm/io/__init__.py
q2mm/models/__init__.py
q2mm/models/datum.py
q2mm/models/ff_io.py
q2mm/models/forcefield.py
q2mm/models/hessian.py
q2mm/models/identifiers.py
q2mm/models/molecule.py
q2mm/models/param.py
q2mm/models/seminario.py
q2mm/optimizers/__init__.py
q2mm/optimizers/defaults.py
q2mm/optimizers/objective.py
q2mm/optimizers/scipy_opt.py
q2mm/optimizers/scoring.py
q2mm/parsers/__init__.py
q2mm/parsers/_patterns.py
q2mm/parsers/amber_ff.py
q2mm/parsers/base.py
q2mm/parsers/gaussian.py
q2mm/parsers/jaguar.py
q2mm/parsers/macromodel.py
q2mm/parsers/mm3.py
q2mm/parsers/mol2.py
q2mm/parsers/structures.py
q2mm/parsers/tinker_ff.py
scripts/generate_benchmarks.py
scripts/generate_optimization_fixtures.py
scripts/regenerate_parity_fixtures.py
scripts/setup_upstream_worktree.ps1
scripts/setup_upstream_worktree.sh
scripts/validate_against_upstream.ps1
scripts/validate_against_upstream.py
test/__init__.py
test/test_datatypes.py
test/test_ffs.py
test/test_linear_algebra.py
test/test_models.py
test/test_seminario.py
test/test_utilities.py
test/fixtures/optimization_golden.json
test/fixtures/seminario_parity/rh_enamide_reference.json
test/fixtures/seminario_parity/sn2_reference.json
test/integration/__init__.py
test/integration/test_openmm_backend.py
test/integration/test_optimization_validation.py
test/integration/test_pipeline.py
test/integration/test_psi4_backend.py
test/integration/test_scipy_optimizer.py
test/integration/test_seminario_parity.py
test/integration/test_tinker_backend.py