Phase 10: conformer ensembles, transition structures in series, parallel channels by bobbypaton · Pull Request #13 · patonlab/Kinisot

bobbypaton · 2026-09-28T02:58:51Z

Implements Phase 10 of IMPLEMENTATION_PLAN.md with the recommended decisions: qRRHO weights by default, nargs="+" per flag, exact equivalent-position averaging, degeneracies supplied by the user, and a JSON job file for series and channels. It also adds the Gaussian inputs for the Wittig case.

Conformer ensembles (`kinisot/ensemble.py`)

Input. A species given as several files (kinisot --rct gs_1.out gs_2.out --ts ts_*.out), or in Python as a nested list or Conformers(files, free_energies=None, degeneracy=None), is a set of conformers of one species.
Formula. KIE = Σ x_i ρ_i / Σ y_j ρ‡_j, weighted by the light isotopologue, which is exact. A transition structure's weight is its share of the rate and includes its own tunnelling factor. EQEs work the same way.
--weights: qrrho (default; Grimme's entropy interpolation through GoodVibes' functions), rrho, user, lowest or equal. --energies TABLE supplies free energies and degeneracies.
Result (EnsembleIsotopeEffect):
- the conformer table (free energy, share, each conformer's own KIE);
- the KIE of the lowest conformers alone;
- the effective number of transition structures, 1/Σy²;
- the range when each free energy moves by ±0.5 kcal/mol (--weight-uncertainty).
Checks. Conformers of a species must have the same atoms in the same order, otherwise it is an error. Different bonding, duplicate structures and mixed levels of theory are warnings.
Unchanged cases. One conformer per species returns the ordinary IsotopeEffect with unchanged numbers.
equivalent_positions() gives the exact average for positions made equivalent by fast motion.

Benchmark runner: exact averaging (separate commit)

iso_average and reference_average now average the isotope ratios over the placements of the label on each side, instead of taking a geometric mean of the KIEs.
Two reported values move by 1 × 10⁻⁴:
- Diels–Alder H3: 0.9904 → 0.9905;
- nitroarene TS1B: 1.0305 → 1.0304.
The overall mean absolute deviation stays 0.0058 over 34 positions.

Series and channels (`kinisot/pathways.py`)

Series. compute_kie(rct, ts=Series([...]), iso=...) gives KIE = Σ w_n KIE_n with w_n ∝ exp(+G_n/RT)/κ_L,n.
- The weights come from a commitment factor (two steps), the steps' free energies, or computed free energies.
- A step may be a set of conformers.
- commitment_for(value) returns the C_f that reproduces a measured KIE.
Channels. channels([dict(rct=..., ts=..., iso=...), ...]) gives 1/KIE = Σ y_c/KIE_c.
- The shares are given directly (a measured selectivity), built from barriers, or computed.
- amounts covers reactants that do not interconvert.
- selectivity_for(value) inverts the relation for two channels.
Formula functions. series_kie() and channel_kie() combine KIEs obtained elsewhere.
kinisot --job job.json runs series, channels and several isotopologues from one file (docs/job_files.md).

Worked example (`examples/conformers`)

Structures. Eight GFN2-xTB conformers of allyl vinyl ether plus the chair and boat Claisen transition structures.
- scripts/make_conformer_example.py generates them in about two minutes and reproduces the committed Hessians to 1e-11.
- Each saddle point is checked to connect allyl vinyl ether with 4-pentenal.
Results.
- ¹³C and ¹⁷O KIEs change by 2 × 10⁻⁴ or less between the lowest pair and the ensemble.
- The C4-d₂ KIE ranges from 0.926 to 0.984 across conformers; the ensemble (0.968) differs from the lowest pair by 0.010.
- The boat carries 0.04 % of the rate.

Documentation

docs/theory.md: new section 7 (ensembles, 7a series, 7b channels); the constants move to section 8.
docs/job_files.md (new), plus updates to the README, FAQ, CHANGELOG and IMPLEMENTATION_PLAN.md (decisions recorded, status).

Validation

Shi epoxidation (all 18 transition structures). compute_kie reproduces the earlier prototype ensemble to 2 × 10⁻⁶ at every site. Kinisot's relative qRRHO free energies agree with GoodVibes' to 0.006 kcal/mol.
Published combinations.
- Wittig (Chen et al. 2014): 1.0280/1.0070 from the free energies and 1.0326/1.0116 from the trajectories.
- DyKAT (van Dijk et al. 2021): Fig. 3d with s = 3.3.
Exact kinetics. The series formula matches the slowest eigenvalue of a three-step rate matrix to 7 × 10⁻⁸.
Internal consistency.
- Channels that share one reactant, with computed shares, equal the conformer ensemble of their transition structures to 10⁻¹³.
- Methyl rotamers built by renumbering atoms reproduce the equivalent-position average to 10⁻¹².
Tests and lint. New tests: test_ensemble.py, test_pathways.py, test_jobs.py, plus additions to test_shi_ensemble.py, test_nitroarene.py and test_examples.py. pytest: 222 passed, 1 skipped. ruff check and ruff format --check are clean, and the new modules parse as Python 3.9.

Not included

The Wittig and DyKAT benchmark cases still need their Gaussian jobs. Once the logs are in, they will be computed with Series and channels and compared with experiment.

Summary by CodeRabbit

New Features
- Added conformer-ensemble calculations with configurable weighting and per-conformer results.
- Added calculations for transition structures in series and comparisons of parallel reaction channels.
- Added JSON job files for configuring calculations and producing text, JSON, or CSV results.
- Added a worked Claisen rearrangement example.
Improvements
- Equivalent-position benchmark averages now use arithmetic or harmonic isotope-ratio averages, as applicable. Some reported KIE values change slightly; the stated mean absolute deviation remains 0.0058.

Frequency inputs for anisaldehyde 1, the ylide Ph3P=CHCOMe 2 and the two transition structures 4 (C-C bond formation) and 6 (P-O bond formation), from the SI of Chen, Nieves-Quinones, Waas and Singleton (JACS 2014) at M06-2X/6-31+G**/PCM(THF) with default radii and FineGrid (Gaussian 09's default). Title lines carry the SI energies and zero-point energies; the README lists SI Table S4's predictions that the jobs should reproduce. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

A species given as a list of files, or as Conformers(...), is a conformer ensemble: KIE = sum_i x_i rho_i / sum_j y_j rho'_j, with light-isotopologue weights (for a transition structure, y_j proportional to kappa_L,j exp(-G_j/RT)). Weights are qRRHO free energies by default (Grimme's entropy interpolation, via GoodVibes' functions), or rrho, user-supplied free energies, the lowest conformer, or equal. Degeneracies cover conformers whose mirror images are not listed. The result, EnsembleIsotopeEffect, carries the conformer table (populations, each conformer's KIE), the lowest-conformer KIE, the effective number of transition-structure conformers and the range when each free energy moves by +/- 0.5 kcal/mol. Conformers are checked for the same atoms in the same order (error), matching bonds and duplicates (warnings). One conformer per species gives the ordinary IsotopeEffect, unchanged. equivalent_positions() averages rho over the placements of a label on positions made equivalent by fast motion, which is exact; for a difference on one side it is the harmonic mean of the separate KIEs. compute_kie reproduces the Shi epoxidation prototype over all 18 transition structures (every site to 2e-6). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

iso_average and reference_average now average the isotope ratios over the placements of the label on each side (kinisot.equivalent_positions) instead of taking the geometric mean of the separate KIEs. The placements are conformers of equal weight, so this is exact; for a difference on one side it is the harmonic mean. Two reported values move by 1e-4: Diels-Alder H3 (0.9904 to 0.9905) and the singly labelled TS1B nitroarene KIE (1.0305 to 1.0304, 1.0321 to 1.0319 with Bell). The overall mean absolute deviation stays 0.0058. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

--rct, --ts and --prd take several files each: the files after one flag are conformers of one species, so --rct a.out --rct b.out still means two species. New options --weights, --energies (a table of file, free energy and optional degeneracy; --energy-unit) and --weight-uncertainty. The text output prints the conformer table (free energy, degeneracy, share, the conformer's own KIE) and "KIE (ensemble) @ T" lines with the lowest- conformer KIE, the sensitivity range and the effective number of transition structures; --json and --csv carry the same. Benchmark cases may list conformers per species. docs/theory.md gains section 7 (conformer ensembles; the constants move to section 8). README, FAQ, CHANGELOG and IMPLEMENTATION_PLAN.md (Phase 10 decisions confirmed with the recommended options, status) are updated. Tests cover rotamers made by renumbering a methyl group (they reproduce the equivalent-position average), a conformer 10 kcal/mol higher, temperature scans, an EQE ensemble and the command line. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

compute_kie(rct, ts=Series([ts_1, ts_2, ...]), iso=...) combines steps that none alone commits the substrate: KIE = sum_n w_n KIE_n with w_n proportional to exp(+G_n/RT)/kappa_L,n, so the highest transition structure counts most. The weights come from a commitment factor (two steps, C_f = k_2/k_-1, e.g. from trajectories), the steps' free energies, or qRRHO free energies Kinisot computes when every step has the same atoms. A step may be a conformer ensemble. The result gives each step's KIE and share, C_f, the range when each step moves by +/- 0.5 kcal/mol, kie_at(C_f) and commitment_for(measured value). channels([dict(rct=..., ts=..., iso=...), ...]) combines parallel routes with their own reactants, transition structures or labels: 1/KIE = sum_c y_c/KIE_c. The shares are given (a measured selectivity), built from barriers, or computed; amounts cover reactants that do not interconvert. selectivity_for(value) inverts two channels (eq S111 of Dale et al.). A channel may be a series or an ensemble. series_kie() and channel_kie() apply the formulas to KIEs from anywhere. They reproduce Chen et al.'s Wittig predictions (1.0280/1.0070 from the free energies, 1.0326/1.0116 from the trajectories) and van Dijk et al.'s Figure 3d (s = 3.3). The series formula matches the slowest eigenvalue of a three-step rate matrix to 7e-8; channels computed from one reactant reproduce the conformer ensemble of their transition structures to 1e-13. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

…ologues A job file holds the structures (reactants plus a transition_structure, product, series or channels), the labels (iso/reference, or a list of isotopologues) and the settings; the command line then gives only the outputs. File names are relative to the job file; unknown keys and settings given on the command line as well are usage errors. The results file prints, per isotopologue, the steps of a series (effective free energy, share, KIE of each) or the channels (share, KIE of each), then one "KIE (series)" or "KIE (channels)" line per temperature with the sensitivity range and C_f or s. --json and --csv carry an isotopologue key. Docs: docs/job_files.md; theory.md sections 7a (series) and 7b (channels); README, CHANGELOG and IMPLEMENTATION_PLAN.md (Phase 10 implemented; the worked example and the Wittig/DyKAT validations remain). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

examples/conformers holds GFN2-xTB Hessians of eight allyl vinyl ether conformers (within 3 kcal/mol) and the chair and boat Claisen transition structures, all with one atom numbering, plus degeneracies.txt and a job file for every measured position. scripts/make_conformer_example.py makes them in about two minutes and reproduces the committed Hessians to 1e-11: every combination of the three rotatable dihedrals minimized, duplicates and mirror images recognized up to renumbered hydrogens, degeneracy 2 for chiral structures, the boat built from the chair by reflecting the allyl fragment and refined with Sella. Each saddle point is checked to connect allyl vinyl ether with 4-pentenal (the boat is asynchronous at this level, so the stricter mode test of make_claisen_structures.py does not apply to it). The README shows that 13C and 17O KIEs change by 2e-4 or less between the lowest pair and the ensemble, while the C4-d2 KIE runs from 0.926 to 0.984 over the conformers and the ensemble (0.968) differs from the lowest pair by 0.010; the boat carries 0.04% of the rate. run_examples.sh and tests/test_examples.py include the three runs (the result regex now also matches "KIE (ensemble) @" lines). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

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kinisot/cli.py
kinisot/ensemble.py
kinisot/jobs.py
kinisot/pathways.py
tests/test_ensemble.py
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tests/test_pathways.py

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📝 Walkthrough

Walkthrough

The package adds conformer-ensemble KIE and EQE calculations, series and parallel-channel calculations, and JSON job-file execution. The CLI and Python APIs expose these workflows. The pull request adds a worked Claisen conformer example and updates benchmark averaging and reference data.

Changes

KIE calculation extensions

Layer / File(s)	Summary
Conformer ensembles and isotope-position averaging `kinisot/ensemble.py`, `kinisot/api.py`, `kinisot/thermo.py`, `kinisot/__init__.py`, `docs/theory.md`, `docs/faq.md`, `README.md`, `tests/test_ensemble.py`, `tests/test_shi_ensemble.py`, `CHANGELOG.md`	Adds conformer inputs, weighting modes, ensemble KIE and EQE results, diagnostics, and equivalent-position isotope-ratio averaging. The API dispatches ensemble inputs and adds tests and documentation for these calculations.
Series and parallel-channel calculations `kinisot/pathways.py`, `kinisot/api.py`, `kinisot/__init__.py`, `docs/theory.md`, `README.md`, `tests/test_pathways.py`, `CHANGELOG.md`	Adds series and channel KIE combination methods, weighting and share options, result types, and related API examples and tests.
CLI and JSON job workflows `kinisot/cli.py`, `kinisot/jobs.py`, `docs/job_files.md`, `README.md`, `IMPLEMENTATION_PLAN.md`, `CHANGELOG.md`, `tests/test_jobs.py`	The CLI accepts grouped conformer files, weighting options, and JSON jobs. Job files support structures, series, channels, and named isotopologues; output supports text, JSON, and CSV.
Conformer example and generated structures `scripts/make_conformer_example.py`, `examples/conformers/*`, `examples/README.md`, `examples/run_examples.sh`, `tests/test_examples.py`	Adds a generator and Claisen example inputs for reactant conformers and chair and boat transition structures. Example commands and output checks include ensemble runs.

Benchmark updates

Layer / File(s)	Summary
Benchmark averaging and reference data `benchmarks/run.py`, `benchmarks/README.md`, `benchmarks/REPORT.md`, `benchmarks//case.json`, `benchmarks/nitroarene_phosphetane/README.md`, `benchmarks/wittig_anisaldehyde/`, `tests/test_nitroarene.py`, `IMPLEMENTATION_PLAN.md`	The benchmark runner combines results across equivalent isotope positions and supports grouped conformer paths. Benchmark descriptions and selected values change to match isotope-ratio averaging. Wittig benchmark files add Gaussian inputs and SI-based reference details.

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Sequence Diagram(s)

sequenceDiagram
  participant CLI
  participant load_job
  participant run_job
  participant compute_kie
  participant channels
  participant ResultWriter
  CLI->>load_job: Load and validate JSON job
  CLI->>run_job: Run job at each temperature
  run_job->>compute_kie: Calculate non-channel isotopologue result
  run_job->>channels: Calculate channel result
  compute_kie-->>run_job: Return calculation result
  channels-->>run_job: Return channel result
  run_job-->>CLI: Return named isotopologue results
  CLI->>ResultWriter: Write results by result type

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On Windows runners the checkout (D:) and pytest's temporary directory (C:) are on different drives, where os.path.relpath raises ValueError. The job tests now fall back to absolute file names there, and a new test copies two small Hessians next to its job file so that relative names are still exercised on every platform. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

…ree energies Channels and series with computed shares subtract absolute free energies of about 1e4 kcal/mol, so they agree with the conformer-ensemble route only to round-off. On Python 3.9 / Windows the channel and ensemble KIEs differed by 1.02e-13 against a tolerance of 1e-13. Those cross-route comparisons now use 1e-11; comparisons that follow the same arithmetic keep their tight tolerances. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

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Inline comments:
Review comments at @kinisot/ensemble.py:
- Around line 651-652: Update the `kie_lowest` and `kie_tunnel_lowest`
calculations so `scheme == "equal"` does not use the zeroed ensemble energies to
select conformers: rank by computed qRRHO free energies when electronic energies
are available, and report `None` when they are not. Preserve the existing
`_ensemble_value` behavior for other weighting schemes.

Review comments at @kinisot/jobs.py:
- Around line 151-155: Update the isotopologue input handling in load_job to
validate that isotopologues is a non-empty list when provided, raising
KinisotInputError for empty lists and non-list values. Only build the
single-entry fallback from iso when isotopologues is absent.

Review comments at @kinisot/pathways.py:
- Around line 138-148: Update _members to accept the species object, use its
files for conformer inputs, and preserve its first degeneracy for non-ensemble
results, defaulting to 1 when unset. Update both _members call sites to pass the
species rather than species.files.

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CHANGELOG.md
IMPLEMENTATION_PLAN.md
README.md
benchmarks/README.md
benchmarks/REPORT.md
benchmarks/diels_alder/case.json
benchmarks/nitroarene_phosphetane/README.md
benchmarks/nitroarene_phosphetane_ts1b/case.json
benchmarks/run.py
benchmarks/shi_epoxidation/case.json
benchmarks/wittig_anisaldehyde/README.md
benchmarks/wittig_anisaldehyde/anisaldehyde_1.gjf
benchmarks/wittig_anisaldehyde/case.json
benchmarks/wittig_anisaldehyde/ts_4.gjf
benchmarks/wittig_anisaldehyde/ts_6.gjf
benchmarks/wittig_anisaldehyde/ylide_2.gjf
docs/faq.md
docs/job_files.md
docs/theory.md
examples/README.md
examples/conformers/README.md
examples/conformers/degeneracies.txt
examples/conformers/ensemble.json
examples/conformers/gs_1.hessian.json
examples/conformers/gs_1.xyz
examples/conformers/gs_2.hessian.json
examples/conformers/gs_2.xyz
examples/conformers/gs_3.hessian.json
examples/conformers/gs_3.xyz
examples/conformers/gs_4.hessian.json
examples/conformers/gs_4.xyz
examples/conformers/gs_5.hessian.json
examples/conformers/gs_5.xyz
examples/conformers/gs_6.hessian.json
examples/conformers/gs_6.xyz
examples/conformers/gs_7.hessian.json
examples/conformers/gs_7.xyz
examples/conformers/gs_8.hessian.json
examples/conformers/gs_8.xyz
examples/conformers/ts_boat.hessian.json
examples/conformers/ts_boat.xyz
examples/conformers/ts_chair.hessian.json
examples/conformers/ts_chair.xyz
examples/run_examples.sh
kinisot/__init__.py
kinisot/api.py
kinisot/cli.py
kinisot/ensemble.py
kinisot/jobs.py
kinisot/pathways.py
kinisot/thermo.py
scripts/make_conformer_example.py
tests/test_ensemble.py
tests/test_examples.py
tests/test_jobs.py
tests/test_nitroarene.py
tests/test_pathways.py
tests/test_shi_ensemble.py

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…equal-weight lowest - Series weights and channel shares dropped the degeneracy of a species given as one file (Conformers([ts], degeneracy=[2]), a job-file species with "degeneracy", an --energies row): it reached compute_kie as a plain file and _members used g = 1. _members now reads the degeneracy from the loaded species, so such a channel's share doubles and such a step's 1/k weight halves, as they should. - A job file with "isotopologues": [] (or a non-list) raised KeyError; it is now a KinisotInputError. - With weights="equal" every free energy is zero, so the "lowest" diagnostic reported the first file of each species. It now ranks the conformers by given free energies, else by computed qRRHO ones, and is None (printed "-") when neither is available. Each has a regression test that fails without its fix. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K49r16vaYeUsGCHD26vmM2

claude added 7 commits September 28, 2026 02:01

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bobbypaton merged commit d955059 into master Sep 28, 2026
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Phase 10: conformer ensembles, transition structures in series, parallel channels - #13

Phase 10: conformer ensembles, transition structures in series, parallel channels#13
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Conformer ensembles (kinisot/ensemble.py)

Benchmark runner: exact averaging (separate commit)

Series and channels (kinisot/pathways.py)

Worked example (examples/conformers)

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Conformer ensembles (`kinisot/ensemble.py`)

Series and channels (`kinisot/pathways.py`)

Worked example (`examples/conformers`)

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