├── .devcontainer └── devcontainer.json ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── docs ├── api │ ├── adapter.md │ ├── builder.md │ ├── core.md │ ├── index.md │ ├── io.md │ ├── op.md │ ├── pack.md │ ├── parser.md │ ├── potential.md │ ├── reacter.md │ └── typifier.md ├── assets │ ├── favicon.ico │ ├── javascripts │ │ └── mathjax.js │ ├── molpy.png │ ├── overrides │ │ └── home.html │ └── stylesheets │ │ └── extra.css ├── changelog │ ├── index.md │ └── releases.md ├── developer │ ├── coding-style.md │ ├── compute.py │ ├── contributing.md │ ├── development-setup.md │ ├── index.md │ ├── release-process.md │ └── testing.md ├── getting-started │ ├── core-concepts.ipynb │ ├── faq.md │ ├── installation.ipynb │ ├── output.pdb │ └── quickstart.ipynb ├── index.md ├── tutorials │ ├── box.ipynb │ ├── crystal-builder.ipynb │ ├── force-field.ipynb │ ├── frame-block.ipynb │ ├── index.md │ ├── molecular-graph-model.ipynb │ ├── selector.ipynb │ ├── topology.ipynb │ ├── trajectory.ipynb │ └── wrappers.ipynb └── user-guide │ ├── adapter.ipynb │ ├── builder.ipynb │ ├── compute.ipynb │ ├── index.md │ ├── io.ipynb │ ├── op.ipynb │ ├── pack.ipynb │ ├── parser.ipynb │ ├── potential.ipynb │ ├── reacter.ipynb │ ├── system.data │ └── typifier.ipynb ├── mkdocs.yml ├── pyproject.toml ├── src └── molpy │ ├── __init__.py │ ├── adapter │ ├── __init__.py │ └── rdkit_adapter.py │ ├── builder │ ├── __init__.py │ ├── crystal.py │ └── polymer │ │ ├── __init__.py │ │ ├── connectors.py │ │ ├── errors.py │ │ ├── linear.py │ │ └── placer.py │ ├── compute │ ├── __init__.py │ ├── base.py │ └── result.py │ ├── core │ ├── __init__.py │ ├── atomistic.py │ ├── box.py │ ├── cg.py │ ├── config.py │ ├── element.py │ ├── entity.py │ ├── forcefield.py │ ├── frame.py │ ├── logger.py │ ├── ops │ │ ├── __init__.py │ │ └── geometry.py │ ├── region.py │ ├── script.py │ ├── selector.py │ ├── topology.py │ ├── trajectory.py │ ├── units.py │ ├── utils.py │ └── wrappers │ │ ├── __init__.py │ │ ├── base.py │ │ ├── monomer.py │ │ └── polymer.py │ ├── data │ ├── README.md │ ├── __init__.py │ └── forcefield │ │ ├── __init__.py │ │ ├── oplsaa.xml │ │ └── tip3p.xml │ ├── engine │ ├── __init__.py │ ├── base.py │ ├── cp2k.py │ └── lammps.py │ ├── io │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── ac.py │ │ ├── amber.py │ │ ├── base.py │ │ ├── gro.py │ │ ├── lammps.py │ │ ├── lammps_molecule.py │ │ ├── mol2.py │ │ ├── pdb.py │ │ ├── top.py │ │ ├── xsf.py │ │ └── xyz.py │ ├── forcefield │ │ ├── __init__.py │ │ ├── amber.py │ │ ├── base.py │ │ ├── lammps.py │ │ ├── moltemplate.py │ │ ├── top.py │ │ └── xml.py │ ├── log │ │ └── lammps.py │ ├── readers.py │ ├── trajectory │ │ ├── __init__.py │ │ ├── base.py │ │ ├── lammps.py │ │ └── xyz.py │ ├── utils.py │ └── writers.py │ ├── op │ ├── __init__.py │ └── geometry.py │ ├── pack │ ├── __init__.py │ ├── constraint.py │ ├── molpack.py │ ├── optimizer │ │ └── __init__.py │ ├── packer │ │ ├── __init__.py │ │ ├── base.py │ │ └── packmol.py │ └── target.py │ ├── parser │ ├── __init__.py │ ├── base.py │ ├── grammar │ │ ├── smarts.lark │ │ └── smiles.lark │ ├── smarts.py │ └── smiles.py │ ├── potential │ ├── __init__.py │ ├── angle │ │ ├── __init__.py │ │ ├── base.py │ │ └── harmonic.py │ ├── base.py │ ├── bond │ │ ├── __init__.py │ │ ├── base.py │ │ └── harmonic.py │ ├── pair │ │ ├── __init__.py │ │ ├── base.py │ │ ├── coul.py │ │ └── lj.py │ └── utils.py │ ├── py.typed │ ├── reacter │ ├── __init__.py │ ├── base.py │ ├── connector.py │ ├── selectors.py │ ├── transformers.py │ └── utils.py │ ├── typifier │ ├── __init__.py │ ├── adapter.py │ ├── atomistic.py │ ├── base.py │ ├── dependency_analyzer.py │ ├── graph.py │ ├── layered_engine.py │ └── matcher.py │ └── version.py └── tests ├── conftest.py ├── test_adapter ├── __init__.py ├── test_bigsmiles.py └── test_rdkit_wrapper.py ├── test_builder └── test_crystal.py ├── test_core ├── __init__.py ├── test_atomistic.py ├── test_box.py ├── test_copy_behavior.py ├── test_element.py ├── test_entity_column_access.py ├── test_forcefield.py ├── test_frame.py ├── test_link.py ├── test_region.py ├── test_selection.py ├── test_topology.py └── test_trajectory.py ├── test_data └── test_data_access.py ├── test_engine ├── __init__.py └── test_base.py ├── test_io ├── test_data │ ├── test_amber.py │ ├── test_files │ │ ├── ethane.mol │ │ ├── water_tip3p.json │ │ └── water_tip3p.mol │ ├── test_gro.py │ ├── test_lammps_data.py │ ├── test_lammps_molecule.py │ ├── test_mol2.py │ ├── test_pdb.py │ ├── test_xsf.py │ └── test_xyz.py ├── test_forcefield │ ├── test_lammps_writer.py │ ├── test_top.py │ └── test_xml.py └── test_trajectory │ └── test_lammps_traj.py ├── test_pack ├── __init__.py └── test_molpack.py ├── test_parser ├── test_smarts.py └── test_smiles.py ├── test_reacter ├── test_base.py ├── test_basic.py ├── test_connector.py ├── test_selectors.py ├── test_transformers.py └── test_utils.py └── test_typifier ├── __init__.py ├── test_adapter.py ├── test_atomistic.py ├── test_base.py ├── test_dependency_analyzer.py ├── test_graph.py ├── test_layered_engine.py ├── test_matcher.py └── test_nylon66.py /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/README.md -------------------------------------------------------------------------------- /docs/api/adapter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/adapter.md -------------------------------------------------------------------------------- /docs/api/builder.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/builder.md -------------------------------------------------------------------------------- /docs/api/core.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/core.md -------------------------------------------------------------------------------- /docs/api/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/index.md -------------------------------------------------------------------------------- /docs/api/io.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/io.md -------------------------------------------------------------------------------- /docs/api/op.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/op.md -------------------------------------------------------------------------------- /docs/api/pack.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/pack.md -------------------------------------------------------------------------------- /docs/api/parser.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/parser.md -------------------------------------------------------------------------------- /docs/api/potential.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/potential.md -------------------------------------------------------------------------------- /docs/api/reacter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/reacter.md -------------------------------------------------------------------------------- /docs/api/typifier.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/api/typifier.md -------------------------------------------------------------------------------- /docs/assets/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/assets/favicon.ico -------------------------------------------------------------------------------- /docs/assets/javascripts/mathjax.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/assets/javascripts/mathjax.js -------------------------------------------------------------------------------- /docs/assets/molpy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/assets/molpy.png -------------------------------------------------------------------------------- /docs/assets/overrides/home.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/assets/overrides/home.html -------------------------------------------------------------------------------- /docs/assets/stylesheets/extra.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/assets/stylesheets/extra.css -------------------------------------------------------------------------------- /docs/changelog/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/changelog/index.md -------------------------------------------------------------------------------- /docs/changelog/releases.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/changelog/releases.md -------------------------------------------------------------------------------- /docs/developer/coding-style.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/coding-style.md -------------------------------------------------------------------------------- /docs/developer/compute.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/compute.py -------------------------------------------------------------------------------- /docs/developer/contributing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/contributing.md -------------------------------------------------------------------------------- /docs/developer/development-setup.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/development-setup.md -------------------------------------------------------------------------------- /docs/developer/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/index.md -------------------------------------------------------------------------------- /docs/developer/release-process.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/release-process.md -------------------------------------------------------------------------------- /docs/developer/testing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/developer/testing.md -------------------------------------------------------------------------------- /docs/getting-started/core-concepts.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/getting-started/core-concepts.ipynb -------------------------------------------------------------------------------- /docs/getting-started/faq.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/getting-started/faq.md -------------------------------------------------------------------------------- /docs/getting-started/installation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/getting-started/installation.ipynb -------------------------------------------------------------------------------- /docs/getting-started/output.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/getting-started/output.pdb -------------------------------------------------------------------------------- /docs/getting-started/quickstart.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/getting-started/quickstart.ipynb -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/tutorials/box.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/box.ipynb -------------------------------------------------------------------------------- /docs/tutorials/crystal-builder.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/crystal-builder.ipynb -------------------------------------------------------------------------------- /docs/tutorials/force-field.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/force-field.ipynb -------------------------------------------------------------------------------- /docs/tutorials/frame-block.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/frame-block.ipynb -------------------------------------------------------------------------------- /docs/tutorials/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/index.md -------------------------------------------------------------------------------- /docs/tutorials/molecular-graph-model.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/molecular-graph-model.ipynb -------------------------------------------------------------------------------- /docs/tutorials/selector.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/selector.ipynb -------------------------------------------------------------------------------- /docs/tutorials/topology.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/topology.ipynb -------------------------------------------------------------------------------- /docs/tutorials/trajectory.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/trajectory.ipynb -------------------------------------------------------------------------------- /docs/tutorials/wrappers.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/tutorials/wrappers.ipynb -------------------------------------------------------------------------------- /docs/user-guide/adapter.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/adapter.ipynb -------------------------------------------------------------------------------- /docs/user-guide/builder.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/builder.ipynb -------------------------------------------------------------------------------- /docs/user-guide/compute.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/compute.ipynb -------------------------------------------------------------------------------- /docs/user-guide/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/index.md -------------------------------------------------------------------------------- /docs/user-guide/io.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/io.ipynb -------------------------------------------------------------------------------- /docs/user-guide/op.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/op.ipynb -------------------------------------------------------------------------------- /docs/user-guide/pack.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/pack.ipynb -------------------------------------------------------------------------------- /docs/user-guide/parser.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/parser.ipynb -------------------------------------------------------------------------------- /docs/user-guide/potential.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/potential.ipynb -------------------------------------------------------------------------------- /docs/user-guide/reacter.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/reacter.ipynb -------------------------------------------------------------------------------- /docs/user-guide/system.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/system.data -------------------------------------------------------------------------------- /docs/user-guide/typifier.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/docs/user-guide/typifier.ipynb -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/pyproject.toml -------------------------------------------------------------------------------- /src/molpy/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/__init__.py -------------------------------------------------------------------------------- /src/molpy/adapter/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/adapter/__init__.py -------------------------------------------------------------------------------- /src/molpy/adapter/rdkit_adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/adapter/rdkit_adapter.py -------------------------------------------------------------------------------- /src/molpy/builder/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/__init__.py -------------------------------------------------------------------------------- /src/molpy/builder/crystal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/crystal.py -------------------------------------------------------------------------------- /src/molpy/builder/polymer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/polymer/__init__.py -------------------------------------------------------------------------------- /src/molpy/builder/polymer/connectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/polymer/connectors.py -------------------------------------------------------------------------------- /src/molpy/builder/polymer/errors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/polymer/errors.py -------------------------------------------------------------------------------- /src/molpy/builder/polymer/linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/polymer/linear.py -------------------------------------------------------------------------------- /src/molpy/builder/polymer/placer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/builder/polymer/placer.py -------------------------------------------------------------------------------- /src/molpy/compute/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/compute/__init__.py -------------------------------------------------------------------------------- /src/molpy/compute/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/compute/base.py -------------------------------------------------------------------------------- /src/molpy/compute/result.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/compute/result.py -------------------------------------------------------------------------------- /src/molpy/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/__init__.py -------------------------------------------------------------------------------- /src/molpy/core/atomistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/atomistic.py -------------------------------------------------------------------------------- /src/molpy/core/box.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/box.py -------------------------------------------------------------------------------- /src/molpy/core/cg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/cg.py -------------------------------------------------------------------------------- /src/molpy/core/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/config.py -------------------------------------------------------------------------------- /src/molpy/core/element.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/element.py -------------------------------------------------------------------------------- /src/molpy/core/entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/entity.py -------------------------------------------------------------------------------- /src/molpy/core/forcefield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/forcefield.py -------------------------------------------------------------------------------- /src/molpy/core/frame.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/frame.py -------------------------------------------------------------------------------- /src/molpy/core/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/logger.py -------------------------------------------------------------------------------- /src/molpy/core/ops/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/molpy/core/ops/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/ops/geometry.py -------------------------------------------------------------------------------- /src/molpy/core/region.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/region.py -------------------------------------------------------------------------------- /src/molpy/core/script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/script.py -------------------------------------------------------------------------------- /src/molpy/core/selector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/selector.py -------------------------------------------------------------------------------- /src/molpy/core/topology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/topology.py -------------------------------------------------------------------------------- /src/molpy/core/trajectory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/trajectory.py -------------------------------------------------------------------------------- /src/molpy/core/units.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/units.py -------------------------------------------------------------------------------- /src/molpy/core/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/utils.py -------------------------------------------------------------------------------- /src/molpy/core/wrappers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/wrappers/__init__.py -------------------------------------------------------------------------------- /src/molpy/core/wrappers/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/wrappers/base.py -------------------------------------------------------------------------------- /src/molpy/core/wrappers/monomer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/wrappers/monomer.py -------------------------------------------------------------------------------- /src/molpy/core/wrappers/polymer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/core/wrappers/polymer.py -------------------------------------------------------------------------------- /src/molpy/data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/data/README.md -------------------------------------------------------------------------------- /src/molpy/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/data/__init__.py -------------------------------------------------------------------------------- /src/molpy/data/forcefield/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/data/forcefield/__init__.py -------------------------------------------------------------------------------- /src/molpy/data/forcefield/oplsaa.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/data/forcefield/oplsaa.xml -------------------------------------------------------------------------------- /src/molpy/data/forcefield/tip3p.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/data/forcefield/tip3p.xml -------------------------------------------------------------------------------- /src/molpy/engine/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/engine/__init__.py -------------------------------------------------------------------------------- /src/molpy/engine/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/engine/base.py -------------------------------------------------------------------------------- /src/molpy/engine/cp2k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/engine/cp2k.py -------------------------------------------------------------------------------- /src/molpy/engine/lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/engine/lammps.py -------------------------------------------------------------------------------- /src/molpy/io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/__init__.py -------------------------------------------------------------------------------- /src/molpy/io/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/__init__.py -------------------------------------------------------------------------------- /src/molpy/io/data/ac.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/ac.py -------------------------------------------------------------------------------- /src/molpy/io/data/amber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/amber.py -------------------------------------------------------------------------------- /src/molpy/io/data/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/base.py -------------------------------------------------------------------------------- /src/molpy/io/data/gro.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/gro.py -------------------------------------------------------------------------------- /src/molpy/io/data/lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/lammps.py -------------------------------------------------------------------------------- /src/molpy/io/data/lammps_molecule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/lammps_molecule.py -------------------------------------------------------------------------------- /src/molpy/io/data/mol2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/mol2.py -------------------------------------------------------------------------------- /src/molpy/io/data/pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/pdb.py -------------------------------------------------------------------------------- /src/molpy/io/data/top.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/top.py -------------------------------------------------------------------------------- /src/molpy/io/data/xsf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/xsf.py -------------------------------------------------------------------------------- /src/molpy/io/data/xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/data/xyz.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/__init__.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/amber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/amber.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/base.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/lammps.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/moltemplate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/moltemplate.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/top.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/top.py -------------------------------------------------------------------------------- /src/molpy/io/forcefield/xml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/forcefield/xml.py -------------------------------------------------------------------------------- /src/molpy/io/log/lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/log/lammps.py -------------------------------------------------------------------------------- /src/molpy/io/readers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/readers.py -------------------------------------------------------------------------------- /src/molpy/io/trajectory/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/trajectory/__init__.py -------------------------------------------------------------------------------- /src/molpy/io/trajectory/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/trajectory/base.py -------------------------------------------------------------------------------- /src/molpy/io/trajectory/lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/trajectory/lammps.py -------------------------------------------------------------------------------- /src/molpy/io/trajectory/xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/trajectory/xyz.py -------------------------------------------------------------------------------- /src/molpy/io/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/utils.py -------------------------------------------------------------------------------- /src/molpy/io/writers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/io/writers.py -------------------------------------------------------------------------------- /src/molpy/op/__init__.py: -------------------------------------------------------------------------------- 1 | from .geometry import * 2 | -------------------------------------------------------------------------------- /src/molpy/op/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/op/geometry.py -------------------------------------------------------------------------------- /src/molpy/pack/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/__init__.py -------------------------------------------------------------------------------- /src/molpy/pack/constraint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/constraint.py -------------------------------------------------------------------------------- /src/molpy/pack/molpack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/molpack.py -------------------------------------------------------------------------------- /src/molpy/pack/optimizer/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/molpy/pack/packer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/packer/__init__.py -------------------------------------------------------------------------------- /src/molpy/pack/packer/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/packer/base.py -------------------------------------------------------------------------------- /src/molpy/pack/packer/packmol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/packer/packmol.py -------------------------------------------------------------------------------- /src/molpy/pack/target.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/pack/target.py -------------------------------------------------------------------------------- /src/molpy/parser/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/__init__.py -------------------------------------------------------------------------------- /src/molpy/parser/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/base.py -------------------------------------------------------------------------------- /src/molpy/parser/grammar/smarts.lark: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/grammar/smarts.lark -------------------------------------------------------------------------------- /src/molpy/parser/grammar/smiles.lark: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/grammar/smiles.lark -------------------------------------------------------------------------------- /src/molpy/parser/smarts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/smarts.py -------------------------------------------------------------------------------- /src/molpy/parser/smiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/parser/smiles.py -------------------------------------------------------------------------------- /src/molpy/potential/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/__init__.py -------------------------------------------------------------------------------- /src/molpy/potential/angle/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/angle/__init__.py -------------------------------------------------------------------------------- /src/molpy/potential/angle/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/angle/base.py -------------------------------------------------------------------------------- /src/molpy/potential/angle/harmonic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/angle/harmonic.py -------------------------------------------------------------------------------- /src/molpy/potential/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/base.py -------------------------------------------------------------------------------- /src/molpy/potential/bond/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/bond/__init__.py -------------------------------------------------------------------------------- /src/molpy/potential/bond/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/bond/base.py -------------------------------------------------------------------------------- /src/molpy/potential/bond/harmonic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/bond/harmonic.py -------------------------------------------------------------------------------- /src/molpy/potential/pair/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/pair/__init__.py -------------------------------------------------------------------------------- /src/molpy/potential/pair/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/pair/base.py -------------------------------------------------------------------------------- /src/molpy/potential/pair/coul.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/pair/coul.py -------------------------------------------------------------------------------- /src/molpy/potential/pair/lj.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/pair/lj.py -------------------------------------------------------------------------------- /src/molpy/potential/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/potential/utils.py -------------------------------------------------------------------------------- /src/molpy/py.typed: -------------------------------------------------------------------------------- 1 | # Marker file for PEP 561 2 | -------------------------------------------------------------------------------- /src/molpy/reacter/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/__init__.py -------------------------------------------------------------------------------- /src/molpy/reacter/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/base.py -------------------------------------------------------------------------------- /src/molpy/reacter/connector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/connector.py -------------------------------------------------------------------------------- /src/molpy/reacter/selectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/selectors.py -------------------------------------------------------------------------------- /src/molpy/reacter/transformers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/transformers.py -------------------------------------------------------------------------------- /src/molpy/reacter/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/reacter/utils.py -------------------------------------------------------------------------------- /src/molpy/typifier/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/__init__.py -------------------------------------------------------------------------------- /src/molpy/typifier/adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/adapter.py -------------------------------------------------------------------------------- /src/molpy/typifier/atomistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/atomistic.py -------------------------------------------------------------------------------- /src/molpy/typifier/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/base.py -------------------------------------------------------------------------------- /src/molpy/typifier/dependency_analyzer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/dependency_analyzer.py -------------------------------------------------------------------------------- /src/molpy/typifier/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/graph.py -------------------------------------------------------------------------------- /src/molpy/typifier/layered_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/layered_engine.py -------------------------------------------------------------------------------- /src/molpy/typifier/matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/typifier/matcher.py -------------------------------------------------------------------------------- /src/molpy/version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/src/molpy/version.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/test_adapter/__init__.py: -------------------------------------------------------------------------------- 1 | """Test adapter module.""" 2 | -------------------------------------------------------------------------------- /tests/test_adapter/test_bigsmiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_adapter/test_bigsmiles.py -------------------------------------------------------------------------------- /tests/test_adapter/test_rdkit_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_adapter/test_rdkit_wrapper.py -------------------------------------------------------------------------------- /tests/test_builder/test_crystal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_builder/test_crystal.py -------------------------------------------------------------------------------- /tests/test_core/__init__.py: -------------------------------------------------------------------------------- 1 | """Core functionality tests.""" 2 | -------------------------------------------------------------------------------- /tests/test_core/test_atomistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_atomistic.py -------------------------------------------------------------------------------- /tests/test_core/test_box.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_box.py -------------------------------------------------------------------------------- /tests/test_core/test_copy_behavior.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_copy_behavior.py -------------------------------------------------------------------------------- /tests/test_core/test_element.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_element.py -------------------------------------------------------------------------------- /tests/test_core/test_entity_column_access.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_entity_column_access.py -------------------------------------------------------------------------------- /tests/test_core/test_forcefield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_forcefield.py -------------------------------------------------------------------------------- /tests/test_core/test_frame.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_frame.py -------------------------------------------------------------------------------- /tests/test_core/test_link.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_link.py -------------------------------------------------------------------------------- /tests/test_core/test_region.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_region.py -------------------------------------------------------------------------------- /tests/test_core/test_selection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_selection.py -------------------------------------------------------------------------------- /tests/test_core/test_topology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_topology.py -------------------------------------------------------------------------------- /tests/test_core/test_trajectory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_core/test_trajectory.py -------------------------------------------------------------------------------- /tests/test_data/test_data_access.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_data/test_data_access.py -------------------------------------------------------------------------------- /tests/test_engine/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Tests for engine module. 3 | """ 4 | -------------------------------------------------------------------------------- /tests/test_engine/test_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_engine/test_base.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_amber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_amber.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_files/ethane.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_files/ethane.mol -------------------------------------------------------------------------------- /tests/test_io/test_data/test_files/water_tip3p.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_files/water_tip3p.json -------------------------------------------------------------------------------- /tests/test_io/test_data/test_files/water_tip3p.mol: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_files/water_tip3p.mol -------------------------------------------------------------------------------- /tests/test_io/test_data/test_gro.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_gro.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_lammps_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_lammps_data.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_lammps_molecule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_lammps_molecule.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_mol2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_mol2.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_pdb.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_xsf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_xsf.py -------------------------------------------------------------------------------- /tests/test_io/test_data/test_xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_data/test_xyz.py -------------------------------------------------------------------------------- /tests/test_io/test_forcefield/test_lammps_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_forcefield/test_lammps_writer.py -------------------------------------------------------------------------------- /tests/test_io/test_forcefield/test_top.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_forcefield/test_top.py -------------------------------------------------------------------------------- /tests/test_io/test_forcefield/test_xml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_forcefield/test_xml.py -------------------------------------------------------------------------------- /tests/test_io/test_trajectory/test_lammps_traj.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_io/test_trajectory/test_lammps_traj.py -------------------------------------------------------------------------------- /tests/test_pack/__init__.py: -------------------------------------------------------------------------------- 1 | """Tests for molpy.pack module.""" 2 | -------------------------------------------------------------------------------- /tests/test_pack/test_molpack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_pack/test_molpack.py -------------------------------------------------------------------------------- /tests/test_parser/test_smarts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_parser/test_smarts.py -------------------------------------------------------------------------------- /tests/test_parser/test_smiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_parser/test_smiles.py -------------------------------------------------------------------------------- /tests/test_reacter/test_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_base.py -------------------------------------------------------------------------------- /tests/test_reacter/test_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_basic.py -------------------------------------------------------------------------------- /tests/test_reacter/test_connector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_connector.py -------------------------------------------------------------------------------- /tests/test_reacter/test_selectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_selectors.py -------------------------------------------------------------------------------- /tests/test_reacter/test_transformers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_transformers.py -------------------------------------------------------------------------------- /tests/test_reacter/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_reacter/test_utils.py -------------------------------------------------------------------------------- /tests/test_typifier/__init__.py: -------------------------------------------------------------------------------- 1 | """Tests for the typifier module.""" 2 | -------------------------------------------------------------------------------- /tests/test_typifier/test_adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_adapter.py -------------------------------------------------------------------------------- /tests/test_typifier/test_atomistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_atomistic.py -------------------------------------------------------------------------------- /tests/test_typifier/test_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_base.py -------------------------------------------------------------------------------- /tests/test_typifier/test_dependency_analyzer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_dependency_analyzer.py -------------------------------------------------------------------------------- /tests/test_typifier/test_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_graph.py -------------------------------------------------------------------------------- /tests/test_typifier/test_layered_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_layered_engine.py -------------------------------------------------------------------------------- /tests/test_typifier/test_matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_matcher.py -------------------------------------------------------------------------------- /tests/test_typifier/test_nylon66.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MolCrafts/molpy/HEAD/tests/test_typifier/test_nylon66.py --------------------------------------------------------------------------------