├── .ase └── gui.py ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── conf.py ├── examples.rst ├── images │ ├── atropo.png │ ├── complex_embed_cd.png │ ├── embeds.svg │ ├── intro_embed.PNG │ ├── logo.jpg │ ├── orbitals.png │ ├── peptide.png │ ├── peptide_chemdraw.png │ ├── plot.svg │ ├── qz_tscode.gif │ └── trimolecular.png ├── index.rst ├── installation.rst ├── introduction.rst ├── license.rst ├── make.bat ├── modules.rst ├── operators_keywords.rst ├── requirements.txt ├── setup.rst ├── tscode.calculators.rst ├── tscode.rst └── usage.rst ├── icon.ico ├── setup.py └── tscode ├── __init__.py ├── __main__.py ├── algebra.py ├── ase_manipulations.py ├── atropisomer_module.py ├── automep.py ├── calculators ├── __init__.py ├── _gaussian.py ├── _mopac.py ├── _openbabel.py ├── _orca.py └── _xtb.py ├── concurrent_test.py ├── embedder.py ├── embedder_options.py ├── embeds.py ├── errors.py ├── graph_manipulations.py ├── hypermolecule_class.py ├── mep_relaxer.py ├── modify_settings.py ├── mprof.py ├── multiembed.py ├── nci.py ├── numba_functions.py ├── operators.py ├── optimization_methods.py ├── parameters.py ├── pka.py ├── profiler.py ├── pt.py ├── quotes.json ├── quotes.py ├── reactive_atoms_classes.py ├── references.py ├── rmsd_pruning.py ├── settings.py ├── solvents.py ├── tests.py ├── tests ├── C2F2H4.xyz ├── C2H4.xyz ├── CH3Cl.xyz ├── HCOOH.xyz ├── HCOOOH.xyz ├── chelotropic.txt ├── cyclical.txt ├── dihedral.txt ├── string.txt └── trimolecular.txt ├── torsion_module.py └── utils.py /.ase/gui.py: -------------------------------------------------------------------------------- 1 | gui_default_settings['show_bonds'] = True -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/examples.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/examples.rst -------------------------------------------------------------------------------- /docs/images/atropo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/atropo.png -------------------------------------------------------------------------------- /docs/images/complex_embed_cd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/complex_embed_cd.png -------------------------------------------------------------------------------- /docs/images/embeds.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/embeds.svg -------------------------------------------------------------------------------- /docs/images/intro_embed.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/intro_embed.PNG -------------------------------------------------------------------------------- /docs/images/logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/logo.jpg -------------------------------------------------------------------------------- /docs/images/orbitals.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/orbitals.png -------------------------------------------------------------------------------- /docs/images/peptide.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/peptide.png -------------------------------------------------------------------------------- /docs/images/peptide_chemdraw.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/peptide_chemdraw.png -------------------------------------------------------------------------------- /docs/images/plot.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/plot.svg -------------------------------------------------------------------------------- /docs/images/qz_tscode.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/qz_tscode.gif -------------------------------------------------------------------------------- /docs/images/trimolecular.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/images/trimolecular.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/introduction.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/introduction.rst -------------------------------------------------------------------------------- /docs/license.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/license.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/modules.rst -------------------------------------------------------------------------------- /docs/operators_keywords.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/operators_keywords.rst -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/setup.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/setup.rst -------------------------------------------------------------------------------- /docs/tscode.calculators.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/tscode.calculators.rst -------------------------------------------------------------------------------- /docs/tscode.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/tscode.rst -------------------------------------------------------------------------------- /docs/usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/docs/usage.rst -------------------------------------------------------------------------------- /icon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/icon.ico -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/setup.py -------------------------------------------------------------------------------- /tscode/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tscode/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/__main__.py -------------------------------------------------------------------------------- /tscode/algebra.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/algebra.py -------------------------------------------------------------------------------- /tscode/ase_manipulations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/ase_manipulations.py -------------------------------------------------------------------------------- /tscode/atropisomer_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/atropisomer_module.py -------------------------------------------------------------------------------- /tscode/automep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/automep.py -------------------------------------------------------------------------------- /tscode/calculators/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tscode/calculators/_gaussian.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/calculators/_gaussian.py -------------------------------------------------------------------------------- /tscode/calculators/_mopac.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/calculators/_mopac.py -------------------------------------------------------------------------------- /tscode/calculators/_openbabel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/calculators/_openbabel.py -------------------------------------------------------------------------------- /tscode/calculators/_orca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/calculators/_orca.py -------------------------------------------------------------------------------- /tscode/calculators/_xtb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/calculators/_xtb.py -------------------------------------------------------------------------------- /tscode/concurrent_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/concurrent_test.py -------------------------------------------------------------------------------- /tscode/embedder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/embedder.py -------------------------------------------------------------------------------- /tscode/embedder_options.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/embedder_options.py -------------------------------------------------------------------------------- /tscode/embeds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/embeds.py -------------------------------------------------------------------------------- /tscode/errors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/errors.py -------------------------------------------------------------------------------- /tscode/graph_manipulations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/graph_manipulations.py -------------------------------------------------------------------------------- /tscode/hypermolecule_class.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/hypermolecule_class.py -------------------------------------------------------------------------------- /tscode/mep_relaxer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/mep_relaxer.py -------------------------------------------------------------------------------- /tscode/modify_settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/modify_settings.py -------------------------------------------------------------------------------- /tscode/mprof.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/mprof.py -------------------------------------------------------------------------------- /tscode/multiembed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/multiembed.py -------------------------------------------------------------------------------- /tscode/nci.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/nci.py -------------------------------------------------------------------------------- /tscode/numba_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/numba_functions.py -------------------------------------------------------------------------------- /tscode/operators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/operators.py -------------------------------------------------------------------------------- /tscode/optimization_methods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/optimization_methods.py -------------------------------------------------------------------------------- /tscode/parameters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/parameters.py -------------------------------------------------------------------------------- /tscode/pka.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/pka.py -------------------------------------------------------------------------------- /tscode/profiler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/profiler.py -------------------------------------------------------------------------------- /tscode/pt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/pt.py -------------------------------------------------------------------------------- /tscode/quotes.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/quotes.json -------------------------------------------------------------------------------- /tscode/quotes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/quotes.py -------------------------------------------------------------------------------- /tscode/reactive_atoms_classes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/reactive_atoms_classes.py -------------------------------------------------------------------------------- /tscode/references.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/references.py -------------------------------------------------------------------------------- /tscode/rmsd_pruning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/rmsd_pruning.py -------------------------------------------------------------------------------- /tscode/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/settings.py -------------------------------------------------------------------------------- /tscode/solvents.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/solvents.py -------------------------------------------------------------------------------- /tscode/tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests.py -------------------------------------------------------------------------------- /tscode/tests/C2F2H4.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/C2F2H4.xyz -------------------------------------------------------------------------------- /tscode/tests/C2H4.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/C2H4.xyz -------------------------------------------------------------------------------- /tscode/tests/CH3Cl.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/CH3Cl.xyz -------------------------------------------------------------------------------- /tscode/tests/HCOOH.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/HCOOH.xyz -------------------------------------------------------------------------------- /tscode/tests/HCOOOH.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/HCOOOH.xyz -------------------------------------------------------------------------------- /tscode/tests/chelotropic.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/chelotropic.txt -------------------------------------------------------------------------------- /tscode/tests/cyclical.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/cyclical.txt -------------------------------------------------------------------------------- /tscode/tests/dihedral.txt: -------------------------------------------------------------------------------- 1 | KCAL=0 2 | scan> C2F2H4.xyz 3 0 1 5 -------------------------------------------------------------------------------- /tscode/tests/string.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/string.txt -------------------------------------------------------------------------------- /tscode/tests/trimolecular.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/tests/trimolecular.txt -------------------------------------------------------------------------------- /tscode/torsion_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/torsion_module.py -------------------------------------------------------------------------------- /tscode/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ntampellini/TSCoDe/HEAD/tscode/utils.py --------------------------------------------------------------------------------