abmptools 1.15.0__tar.gz

abmptools-1.15.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Koji Okuwaki
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

abmptools-1.15.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: abmptools
+Version: 1.15.0
+Summary: Pre/post-processing and analysis toolkit for ABINIT-MP Fragment Molecular Orbital calculations
+Author-email: Koji Okuwaki <koujioku81@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/kojioku/abmptools
+Project-URL: Repository, https://github.com/kojioku/abmptools
+Project-URL: Documentation, https://github.com/kojioku/abmptools/blob/main/docs/ABMPTools-user-manual.md
+Project-URL: Changelog, https://github.com/kojioku/abmptools/blob/main/CHANGELOG.md
+Keywords: FMO,ABINIT-MP,IFIE,PIEDA,fragment molecular orbital,computational chemistry
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Provides-Extra: amorphous
+Requires-Dist: openff-toolkit>=0.14.0; extra == "amorphous"
+Requires-Dist: openff-interchange>=0.3.0; extra == "amorphous"
+Requires-Dist: openmm>=8.0; extra == "amorphous"
+Provides-Extra: geomopt
+Requires-Dist: pyscf; extra == "geomopt"
+Requires-Dist: ase; extra == "geomopt"
+Provides-Extra: mace
+Requires-Dist: ase; extra == "mace"
+Requires-Dist: mace-torch; extra == "mace"
+Requires-Dist: torch; extra == "mace"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# ABMPTools (ABINIT-MP Tools)
+
+A Python toolkit for pre-processing, post-processing, and analysis of Fragment Molecular Orbital (FMO) calculations with [ABINIT-MP](https://fmodd.jp/member_contents/manual_ABINIT-MP/).
+
+## Features
+
+### IFIE/PIEDA Analysis (`getifiepieda`, `anlfmo`, `cpf2ifielist`, `getcharge`)
+
+- Distance-filtered IFIE tables for target fragments or molecules
+- Fragment–fragment interaction matrices (1:1, 1:N, N:1, N:N)
+- Time-series IFIE from MD-FMO trajectory snapshots
+- SVD-based interaction decomposition
+- Charge extraction from ABINIT-MP logs
+
+### CPF Management (`cpfmanager`, `convertcpf`, `generate_difie`, `log2cpf`)
+
+- Parse and write CPF files (versions 4.201, 7.0 MIZUHO, 10, 23)
+- Version conversion between CPF formats
+- Residue-based CPF extraction
+- Dynamic IFIE (DIFIE) averaging across MD snapshots with mean/σ statistics
+- Generate CPF from ABINIT-MP log files
+
+### FMO Input Generation (`generateajf`, `pdb2fmo`, `udf2fmo`, `setfmo`, `addsolvfrag`)
+
+- Auto-generate AJF input files from PDB structures
+- Fragment assignment for proteins and molecular assemblies
+- Solvation fragment addition
+- Support for sp2 fragmentation and various basis sets
+
+### File Format Conversion
+
+- CIF → PDB/XYZ (`readcif`) with symmetry operations
+- ABINIT-MP log → fragment config (`log2config`, `ajf2config`)
+- PDB editing and serial AJF generation (`pdbmodify`, `ajfserial`)
+
+### GROMACS ↔ OCTA COGNAC Conversion
+
+- **udf2gro**: Convert OCTA UDF files to GROMACS format (`.gro`, `.top`, `.mdp`, `.itp`)
+- **gro2udf**: Convert GROMACS files to OCTA UDF format (supports `--from-top` mode)
+
+### Geometry Optimization (`geomopt`)
+
+- **MacePdbOptimizer**: MACE/ASE-based PDB structure optimization
+- **OpenFFOpenMMMinimizer**: OpenFF force-field minimization via OpenMM
+- **QMOptimizerPySCF**: Quantum chemistry optimization with PySCF
+
+### Amorphous Structure Building (`amorphous`)
+
+- Multi-component amorphous system construction using Packmol and OpenMM
+
+## Supported ABINIT-MP Versions
+
+- ABINIT-MP v1: Rev.10–23
+- ABINIT-MP v2: Rev.4–8
+
+## Installation
+
+```bash
+pip install --user .
+```
+
+This runs `make` during install to compile the optional Fortran shared library for accelerated IFIE/PIEDA reading. If `gfortran` is not available, the install still succeeds without Fortran acceleration.
+
+### Requirements
+
+- **Required**: Python 3.8+, numpy, pandas
+- **Optional**: UDFManager (OCTA COGNAC), gfortran, OpenBabel, PySCF, ASE, OpenMM, Packmol
+
+## Quick Start
+
+```bash
+# Extract IFIE for fragment 10, within 8 Å
+python -m abmptools.getifiepieda --frag 10 -d 8.0 -i calculation.log
+
+# Generate AJF input from PDB
+python -m abmptools.generateajf -i protein.pdb -basis 6-31G* --method MP2
+
+# Convert log to CPF
+python -m abmptools.log2cpf -i calculation.log -o output.cpf
+
+# Create DIFIE-averaged CPF from trajectory
+python -m abmptools.generate_difie -i traj-xxx.cpf -t 1 10 1 -f 1-100 -np 4
+
+# Convert UDF to GROMACS
+python -m abmptools.udf2gro.cli -i system.udf -o output
+
+# Convert GROMACS to UDF
+python -m abmptools.gro2udf.cli -i system.gro -t system.top -o output.udf
+```
+
+Use `-h` with any module for full option details.
+
+## Documentation
+
+- **[User Manual](docs/ABMPTools-user-manual.md)** — CLI options, output formats, and workflow examples
+- **[Architecture](docs/architecture.md)** — Class hierarchy and design overview
+- **[Developer Quickstart](docs/dev_quickstart.md)** — Setup and code conventions
+- **[I/O Spec](docs/io_spec.md)** — File format specifications
+- **[gro2udf](docs/gro2udf.md)** / **[udf2gro](docs/udf2gro.md)** — GROMACS ↔ OCTA conversion
+- **[geomopt](docs/geomopt.md)** / **[amorphous](docs/amorphous.md)** — Optimization and structure building
+
+## Testing
+
+```bash
+pytest tests/ -v         # 658 tests
+pytest tests/ -v -k molcalc  # specific module
+```
+
+See [tests/TEST_COVERAGE.md](tests/TEST_COVERAGE.md) for details.
+
+## Samples
+
+Each `sample/` subdirectory contains input data and a `run.sh` script:
+
+```bash
+cd sample/generateajf && bash run.sh
+cd sample/log2cpf && bash run.sh
+cd sample/generate_difie/TrpCage && bash run.sh
+cd sample/convertcpf && bash run.sh
+```
+
+## Author
+
+[Koji Okuwaki](mailto:koujioku81@gmail.com)

abmptools-1.15.0/README.md

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+# ABMPTools (ABINIT-MP Tools)
+
+A Python toolkit for pre-processing, post-processing, and analysis of Fragment Molecular Orbital (FMO) calculations with [ABINIT-MP](https://fmodd.jp/member_contents/manual_ABINIT-MP/).
+
+## Features
+
+### IFIE/PIEDA Analysis (`getifiepieda`, `anlfmo`, `cpf2ifielist`, `getcharge`)
+
+- Distance-filtered IFIE tables for target fragments or molecules
+- Fragment–fragment interaction matrices (1:1, 1:N, N:1, N:N)
+- Time-series IFIE from MD-FMO trajectory snapshots
+- SVD-based interaction decomposition
+- Charge extraction from ABINIT-MP logs
+
+### CPF Management (`cpfmanager`, `convertcpf`, `generate_difie`, `log2cpf`)
+
+- Parse and write CPF files (versions 4.201, 7.0 MIZUHO, 10, 23)
+- Version conversion between CPF formats
+- Residue-based CPF extraction
+- Dynamic IFIE (DIFIE) averaging across MD snapshots with mean/σ statistics
+- Generate CPF from ABINIT-MP log files
+
+### FMO Input Generation (`generateajf`, `pdb2fmo`, `udf2fmo`, `setfmo`, `addsolvfrag`)
+
+- Auto-generate AJF input files from PDB structures
+- Fragment assignment for proteins and molecular assemblies
+- Solvation fragment addition
+- Support for sp2 fragmentation and various basis sets
+
+### File Format Conversion
+
+- CIF → PDB/XYZ (`readcif`) with symmetry operations
+- ABINIT-MP log → fragment config (`log2config`, `ajf2config`)
+- PDB editing and serial AJF generation (`pdbmodify`, `ajfserial`)
+
+### GROMACS ↔ OCTA COGNAC Conversion
+
+- **udf2gro**: Convert OCTA UDF files to GROMACS format (`.gro`, `.top`, `.mdp`, `.itp`)
+- **gro2udf**: Convert GROMACS files to OCTA UDF format (supports `--from-top` mode)
+
+### Geometry Optimization (`geomopt`)
+
+- **MacePdbOptimizer**: MACE/ASE-based PDB structure optimization
+- **OpenFFOpenMMMinimizer**: OpenFF force-field minimization via OpenMM
+- **QMOptimizerPySCF**: Quantum chemistry optimization with PySCF
+
+### Amorphous Structure Building (`amorphous`)
+
+- Multi-component amorphous system construction using Packmol and OpenMM
+
+## Supported ABINIT-MP Versions
+
+- ABINIT-MP v1: Rev.10–23
+- ABINIT-MP v2: Rev.4–8
+
+## Installation
+
+```bash
+pip install --user .
+```
+
+This runs `make` during install to compile the optional Fortran shared library for accelerated IFIE/PIEDA reading. If `gfortran` is not available, the install still succeeds without Fortran acceleration.
+
+### Requirements
+
+- **Required**: Python 3.8+, numpy, pandas
+- **Optional**: UDFManager (OCTA COGNAC), gfortran, OpenBabel, PySCF, ASE, OpenMM, Packmol
+
+## Quick Start
+
+```bash
+# Extract IFIE for fragment 10, within 8 Å
+python -m abmptools.getifiepieda --frag 10 -d 8.0 -i calculation.log
+
+# Generate AJF input from PDB
+python -m abmptools.generateajf -i protein.pdb -basis 6-31G* --method MP2
+
+# Convert log to CPF
+python -m abmptools.log2cpf -i calculation.log -o output.cpf
+
+# Create DIFIE-averaged CPF from trajectory
+python -m abmptools.generate_difie -i traj-xxx.cpf -t 1 10 1 -f 1-100 -np 4
+
+# Convert UDF to GROMACS
+python -m abmptools.udf2gro.cli -i system.udf -o output
+
+# Convert GROMACS to UDF
+python -m abmptools.gro2udf.cli -i system.gro -t system.top -o output.udf
+```
+
+Use `-h` with any module for full option details.
+
+## Documentation
+
+- **[User Manual](docs/ABMPTools-user-manual.md)** — CLI options, output formats, and workflow examples
+- **[Architecture](docs/architecture.md)** — Class hierarchy and design overview
+- **[Developer Quickstart](docs/dev_quickstart.md)** — Setup and code conventions
+- **[I/O Spec](docs/io_spec.md)** — File format specifications
+- **[gro2udf](docs/gro2udf.md)** / **[udf2gro](docs/udf2gro.md)** — GROMACS ↔ OCTA conversion
+- **[geomopt](docs/geomopt.md)** / **[amorphous](docs/amorphous.md)** — Optimization and structure building
+
+## Testing
+
+```bash
+pytest tests/ -v         # 658 tests
+pytest tests/ -v -k molcalc  # specific module
+```
+
+See [tests/TEST_COVERAGE.md](tests/TEST_COVERAGE.md) for details.
+
+## Samples
+
+Each `sample/` subdirectory contains input data and a `run.sh` script:
+
+```bash
+cd sample/generateajf && bash run.sh
+cd sample/log2cpf && bash run.sh
+cd sample/generate_difie/TrpCage && bash run.sh
+cd sample/convertcpf && bash run.sh
+```
+
+## Author
+
+[Koji Okuwaki](mailto:koujioku81@gmail.com)

abmptools-1.15.0/abmptools/__init__.py

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+from .pdb_io import pdb_io
+from .abinit_io import abinit_io
+from .setfmo import setfmo
+from .mol_io import mol_io
+from .molcalc import molcalc
+from .udfrm_io import udfrm_io
+from .udf_io import udf_io
+from .udfcreate import udfcreate
+from .anlfmo import anlfmo
+from .cpfmanager import CPFManager
+from .logmanager import LOGManager
+# udf2gro and gro2udf are imported lazily because they require UDFManager (optional dep)
+try:
+    from .udf2gro import Exporter as Udf2groExporter
+except ImportError:
+    pass
+try:
+    from .gro2udf import Exporter as Gro2udfExporter
+except ImportError:
+    pass
+try:
+    from .amorphous import AmorphousBuilder
+except ImportError:
+    pass