mlmm-toolkit 0.3.3__tar.gz → 0.3.4__tar.gz

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/CHANGELOG.md

@@ -8,6 +8,15 @@ The format follows [Keep a Changelog](https://keepachangelog.com/).
 
 _No changes yet._
 
+## [0.3.4] — 2026-09-02
+
+### Added
+- Add full-system COMT and refined-path BezA Endpoint examples to the Colab GUI.
+
+### Changed
+- Improve the Colab workflow guidance, built-in example walkthroughs, and
+  linked setup and runtime help.
+
 ## [0.3.3] — 2026-08-29
 
 > Upgrade warning: unchanged inputs can produce different geometries, energies/barriers,

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/CITATION.cff

@@ -12,7 +12,7 @@ authors:
 license: GPL-3.0-or-later
 repository-code: "https://github.com/t-0hmura/mlmm_toolkit"
 url: "https://t-0hmura.github.io/mlmm_toolkit/"
-version: "0.3.3"
+version: "0.3.4"
 preferred-citation:
   type: article
   title: "ML/MM toolkit – Toward Accelerated Mechanistic Investigation of Enzymatic Reactions"

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlmm-toolkit
-Version: 0.3.3
+Version: 0.3.4
 Summary: mlmm - ML/MM toolkit for enzyme reaction analysis
 Author-email: Takuto Ohmura <ohmura.takuto@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -92,7 +92,7 @@ Test a reaction mechanism in a single command:
 mlmm all -i R.pdb P.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' --tsopt --thermo
 ```
 
-The source repository includes a full-system [BezA endpoint/scan mechanism](examples/beza/README.md), a methyltransferase walk-through, and a 122-atom ML/MM fixture; see [`examples/`](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples). Each stage is also exposed as an [individual subcommand](#cli-subcommands).
+The source repository includes full-system COMT and [BezA](examples/beza/README.md) endpoint mechanisms, a methyltransferase scan, and a 122-atom ML/MM fixture; see [`examples/`](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples). Each stage is also exposed as an [individual subcommand](#cli-subcommands).
 
 > **Prerequisites:** input PDB/mmCIF structures must already contain hydrogens; multiple reaction states must share the same atoms in the same order (only coordinates differ). `mlmm all` runs `mm-parm` automatically. Match `-l RES:CHARGE` to the H count actually present (e.g. SAM with 23 H = `SAM:1` cation, 22 H = `SAM:0` neutral) — full input-prep checklist in [docs/getting-started.md](docs/getting-started.md).
 
@@ -202,7 +202,7 @@ mlmm all -i R.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' \
 mlmm all -i TS_candidate_layered.pdb --parm complex.parm7 -q 1 --tsopt --opt-mode grad
 ```
 
-For Gaussian-ONIOM / ORCA-QM/MM input-deck export and import use [`oniom-export`](docs/oniom-export.md) / [`oniom-import`](docs/oniom-import.md). Per-stage walkthrough (`mm-parm` → `extract` → `define-layer` → `opt` → `path-search` → `tsopt` → `freq` → `irc` → `dft`): [docs/getting-started.md](docs/getting-started.md) and [docs/quickstart-all.md](docs/quickstart-all.md). Working scripts (BezA, methyltransferase, and toy system): [examples/](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples).
+For Gaussian-ONIOM / ORCA-QM/MM input-deck export and import use [`oniom-export`](docs/oniom-export.md) / [`oniom-import`](docs/oniom-import.md). Per-stage walkthrough (`mm-parm` → `extract` → `define-layer` → `opt` → `path-search` → `tsopt` → `freq` → `irc` → `dft`): [docs/getting-started.md](docs/getting-started.md) and [docs/quickstart-all.md](docs/quickstart-all.md). Working examples (COMT, BezA, methyltransferase, and toy system): [examples/](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples).
 
 ## Output
 

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/README.md

@@ -15,7 +15,7 @@ Test a reaction mechanism in a single command:
 mlmm all -i R.pdb P.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' --tsopt --thermo
 ```
 
-The source repository includes a full-system [BezA endpoint/scan mechanism](examples/beza/README.md), a methyltransferase walk-through, and a 122-atom ML/MM fixture; see [`examples/`](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples). Each stage is also exposed as an [individual subcommand](#cli-subcommands).
+The source repository includes full-system COMT and [BezA](examples/beza/README.md) endpoint mechanisms, a methyltransferase scan, and a 122-atom ML/MM fixture; see [`examples/`](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples). Each stage is also exposed as an [individual subcommand](#cli-subcommands).
 
 > **Prerequisites:** input PDB/mmCIF structures must already contain hydrogens; multiple reaction states must share the same atoms in the same order (only coordinates differ). `mlmm all` runs `mm-parm` automatically. Match `-l RES:CHARGE` to the H count actually present (e.g. SAM with 23 H = `SAM:1` cation, 22 H = `SAM:0` neutral) — full input-prep checklist in [docs/getting-started.md](docs/getting-started.md).
 
@@ -125,7 +125,7 @@ mlmm all -i R.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' \
 mlmm all -i TS_candidate_layered.pdb --parm complex.parm7 -q 1 --tsopt --opt-mode grad
 ```
 
-For Gaussian-ONIOM / ORCA-QM/MM input-deck export and import use [`oniom-export`](docs/oniom-export.md) / [`oniom-import`](docs/oniom-import.md). Per-stage walkthrough (`mm-parm` → `extract` → `define-layer` → `opt` → `path-search` → `tsopt` → `freq` → `irc` → `dft`): [docs/getting-started.md](docs/getting-started.md) and [docs/quickstart-all.md](docs/quickstart-all.md). Working scripts (BezA, methyltransferase, and toy system): [examples/](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples).
+For Gaussian-ONIOM / ORCA-QM/MM input-deck export and import use [`oniom-export`](docs/oniom-export.md) / [`oniom-import`](docs/oniom-import.md). Per-stage walkthrough (`mm-parm` → `extract` → `define-layer` → `opt` → `path-search` → `tsopt` → `freq` → `irc` → `dft`): [docs/getting-started.md](docs/getting-started.md) and [docs/quickstart-all.md](docs/quickstart-all.md). Working examples (COMT, BezA, methyltransferase, and toy system): [examples/](https://github.com/t-0hmura/mlmm_toolkit/tree/main/examples).
 
 ## Output
 

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/examples/beza/README.md

@@ -20,8 +20,11 @@ bash examples/beza/run.sh /path/to/mlmm_beza_output
 ```
 
 The script uses `mlmm all`, which builds the Amber topology and ML/MM layers
-from the input structures. AmberTools is required; a backend-compatible GPU
-environment and scheduled execution are strongly recommended for this
-full-system example. `2.IM.pdb` is included as the known intermediate for
-inspection or an explicitly guided multi-structure run; the default endpoint
-workflow searches from `1.R.pdb` to `3.P.pdb`.
+from the input structures. Its endpoint workflow enables `--refine-path`, so
+the MEP is recursively divided where bonding changes and the methyl-transfer
+and proton-abstraction steps are reported separately. AmberTools is required;
+a backend-compatible GPU environment and scheduled execution are strongly
+recommended for this full-system example. `2.IM.pdb` is included as the known
+intermediate for inspection or an explicitly guided multi-structure run; the
+default endpoint workflow searches from `1.R.pdb` to `3.P.pdb` without using
+the intermediate as an input.

{mlmm_toolkit-0.3.3 → mlmm_toolkit-0.3.4}/examples/beza/run.sh

@@ -10,7 +10,7 @@ cd -- "$work_dir"
 
 mlmm all -i "$script_dir/1.R.pdb" "$script_dir/3.P.pdb" \
   -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \
-  --tsopt --thermo --out-dir result_mep > mep.log 2>&1
+  --refine-path --tsopt --thermo --out-dir result_mep > mep.log 2>&1
 
 mlmm all -i "$script_dir/1.R.pdb" \
   -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \