├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── docs ├── Makefile └── source │ ├── advanced_options.rst │ ├── conf.py │ ├── file_formats.rst │ ├── index.rst │ ├── introduction.rst │ ├── troubleshooting.rst │ └── tutorials │ ├── elastic_networks.rst │ ├── go_models.rst │ ├── index.rst │ ├── multiple_go.rst │ ├── non_protein.rst │ ├── protein_bead_sizes.rst │ └── secondary_structure.rst ├── examples ├── README.md ├── martini.itp ├── non_protein │ ├── README.md │ ├── input │ │ ├── generate_expected_files.sh │ │ ├── lipids.itp │ │ ├── martini_v2.0_ions.itp │ │ ├── mixed.gro │ │ ├── mol.itp │ │ └── system.top │ └── output │ │ ├── CL-_vis.itp │ │ ├── DOPC_vis.itp │ │ ├── DOPE_vis.itp │ │ ├── DOPG_vis.itp │ │ ├── MOTO_vis.itp │ │ ├── NA+_vis.itp │ │ ├── POPC_vis.itp │ │ ├── cg_bonds-v6.tcl │ │ ├── eigen.py │ │ ├── index.ndx │ │ ├── vis.gro │ │ ├── vis.top │ │ └── vis.vmd ├── protein_elastic_network │ ├── README.md │ ├── input │ │ └── generate_expected_files.sh │ └── output │ │ ├── 1UBQ_cg.pdb │ │ ├── cg_bonds-v6.tcl │ │ ├── eigen.py │ │ ├── en.top │ │ ├── index.ndx │ │ ├── molecule_0.itp │ │ ├── molecule_0_en.itp │ │ ├── molecule_0_surplus_en.txt │ │ ├── molecule_0_vis.itp │ │ ├── out.gro │ │ ├── topol.top │ │ ├── vis.top │ │ └── vis.vmd ├── protein_go_model │ ├── README.md │ ├── input │ │ ├── contact_map.out │ │ └── generate_expected_files.sh │ └── output │ │ ├── 1UBQ_cg.pdb │ │ ├── 1UBQ_clean.pdb │ │ ├── go.top │ │ ├── go_atomtypes.itp │ │ ├── go_nbparams.itp │ │ ├── molecule_0.itp │ │ ├── molecule_0_go.itp │ │ ├── molecule_0_vis.itp │ │ ├── out.gro │ │ ├── topol.top │ │ └── vis.top ├── protein_multiple_go │ ├── README.md │ ├── input │ │ ├── generate_expected_files.sh │ │ ├── prot0_clean.pdb │ │ ├── prot0_contact_map.out │ │ ├── prot1_clean.pdb │ │ ├── prot1_contact_map.out │ │ └── topol.top │ └── output │ │ ├── cg_bonds-v6.tcl │ │ ├── eigen.py │ │ ├── go.top │ │ ├── go_atomtypes.itp │ │ ├── go_nbparams.itp │ │ ├── index.ndx │ │ ├── prot0.itp │ │ ├── prot0_cg.pdb │ │ ├── prot0_go.itp │ │ ├── prot0_go_atomtypes.itp │ │ ├── prot0_go_nbparams.itp │ │ ├── prot0_topol.top │ │ ├── prot0_vis.itp │ │ ├── prot1.itp │ │ ├── prot1_cg.pdb │ │ ├── prot1_go.itp │ │ ├── prot1_go_atomtypes.itp │ │ ├── prot1_go_nbparams.itp │ │ ├── prot1_topol.top │ │ ├── prot1_vis.itp │ │ ├── vis.gro │ │ ├── vis.top │ │ └── vis.vmd ├── protein_secondary_structure │ ├── README.md │ ├── input │ │ └── generate_expected_files.sh │ └── output │ │ ├── 1UBQ_cg.pdb │ │ ├── 1UBQ_clean.pdb │ │ ├── cg_bonds-v6.tcl │ │ ├── eigen.py │ │ ├── index.ndx │ │ ├── martini.itp │ │ ├── molecule_0.itp │ │ ├── molecule_0_cgsecstruct.txt │ │ ├── molecule_0_vis.itp │ │ ├── out.gro │ │ ├── topol.top │ │ ├── vis.top │ │ └── vis.vmd └── protein_static_elastic_network │ ├── README.md │ ├── input │ └── generate_expected_files.sh │ └── output │ ├── 1UBQ_cg.pdb │ ├── 1UBQ_clean.pdb │ ├── 1ubq.pdb │ ├── cg_bonds-v6.tcl │ ├── eigen.py │ ├── en.top │ ├── index.ndx │ ├── molecule_0.itp │ ├── molecule_0_en.itp │ ├── molecule_0_surplus_en.txt │ ├── molecule_0_vis.itp │ ├── network_cylinders.tcl │ ├── out.gro │ ├── topol.top │ ├── vis.top │ └── vis.vmd ├── martiniglass ├── __init__.py ├── data │ ├── cg_bonds-v6.tcl │ ├── eigen.py │ ├── old_cg_bonds │ │ └── cg_bonds-v5.tcl │ ├── proteins.vmd │ └── vis.vmd ├── martiniglass.py └── src │ ├── __init__.py │ ├── cylinders_tcl.py │ ├── index_writer.py │ ├── molecule_editing.py │ ├── network_writer.py │ ├── output_file_append.py │ ├── system_reading.py │ └── topology.py ├── pyproject.toml └── requirements-docs.txt /.gitignore: -------------------------------------------------------------------------------- 1 | vis_tests 2 | *.idea 3 | /JOSS/ 4 | /dist/ 5 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Martini-Force-Field-Initiative/MartiniGlass/HEAD/.readthedocs.yaml 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