├── .coveragerc ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile └── sphinx-src │ ├── _themes │ └── sphinx_rtd_theme │ │ ├── __init__.py │ │ ├── breadcrumbs.html │ │ ├── footer.html │ │ ├── layout.html │ │ ├── layout_old.html │ │ ├── search.html │ │ ├── searchbox.html │ │ ├── static │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── badge_only.css.map │ │ │ ├── theme.css │ │ │ └── theme.css.map │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ └── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── theme.conf │ │ └── versions.html │ ├── conf.py │ ├── documentation │ ├── apl.rst │ ├── common.rst │ ├── images │ │ ├── apl_lipids.png │ │ ├── apl_protein.png │ │ ├── bilayer_chol_nobox.png │ │ ├── bilayer_kalp.png │ │ ├── bilayer_peptide_thickness.png │ │ ├── bilayer_prot_apl.png │ │ ├── bilayer_prot_apl2.png │ │ ├── bilayer_prot_nowater.png │ │ ├── dppc_vesicle.png │ │ ├── lipid_simplification.png │ │ ├── membrane-identification_examples.png │ │ ├── model_vesicle.png │ │ ├── normal-calculation.png │ │ ├── src │ │ │ ├── 00_raw_system_side.png │ │ │ ├── 01_simplification_both_side.png │ │ │ ├── 01_simplification_full_side.png │ │ │ ├── 01_simplification_simplified_side.png │ │ │ ├── 02_simplified_system_side.png │ │ │ ├── 03_NS_all_side.png │ │ │ ├── 03_NS_all_top.png │ │ │ ├── 03_NS_no_lower_side.png │ │ │ ├── 03_NS_no_lower_top.png │ │ │ ├── 03_NS_nocutoff_side.png │ │ │ ├── 03_NS_nocutoff_top.png │ │ │ ├── 03_NS_normal_side.png │ │ │ ├── 03_NS_normal_top.png │ │ │ ├── 03_NS_only_neighbors_normal_side.png │ │ │ ├── 03_NS_only_neighbors_normal_top.png │ │ │ ├── 03_NS_only_neighbors_side.png │ │ │ ├── 03_NS_only_neighbors_top.png │ │ │ ├── 04_Normals_side.png │ │ │ ├── 05_Leaflets_positions_side.png │ │ │ ├── 05_Leaflets_positions_top.png │ │ │ ├── 05_Leaflets_side.png │ │ │ ├── 05_Leaflets_top.png │ │ │ ├── 05_Vesicle_leaflets_side.png │ │ │ ├── 05_Vesicle_leaflets_top.png │ │ │ ├── 06_Thickness_NS_same_neighbors_only_side.png │ │ │ ├── 06_Thickness_NS_same_neighbors_only_top.png │ │ │ ├── 06_Thickness_NS_same_side.png │ │ │ ├── 06_Thickness_NS_same_top.png │ │ │ ├── 06_Thickness_NS_same_used_side.png │ │ │ ├── 06_Thickness_NS_same_used_top.png │ │ │ ├── 06_Thickness_NS_same_xcm_only_side.png │ │ │ ├── 06_Thickness_NS_same_xcm_only_top.png │ │ │ ├── 06_Thickness_NS_same_xcm_side.png │ │ │ ├── 06_Thickness_NS_same_xcm_top.png │ │ │ ├── 06_Thickness_other_cutoff_side.png │ │ │ ├── 06_Thickness_other_neighbors_side.png │ │ │ ├── 06_Thickness_other_used_side.png │ │ │ ├── 06_Thickness_other_xcm_only_side.png │ │ │ ├── 06_Thickness_other_xcm_side.png │ │ │ ├── 06_Vesicle_NS_same_neighbors_only_side.png │ │ │ ├── 06_Vesicle_NS_same_neighbors_only_top.png │ │ │ ├── 06_Vesicle_NS_same_side.png │ │ │ ├── 06_Vesicle_NS_same_top.png │ │ │ ├── 06_Vesicle_NS_same_used_side.png │ │ │ ├── 06_Vesicle_NS_same_used_top.png │ │ │ ├── 06_Vesicle_NS_same_xcm_only_side.png │ │ │ ├── 06_Vesicle_NS_same_xcm_side.png │ │ │ ├── 06_Vesicle_NS_same_xcm_top.png │ │ │ ├── 06_Vesicle_other_cutoff_side.png │ │ │ ├── 06_Vesicle_other_neighbors_side.png │ │ │ ├── 06_Vesicle_other_used_side.png │ │ │ ├── 06_Vesicle_other_xcm_only_side.png │ │ │ ├── 06_Vesicle_other_xcm_side.png │ │ │ ├── 07_APLProt_01-system_start_NS_top.png │ │ │ ├── 07_APLProt_01-system_start_top.png │ │ │ ├── 07_APLProt_02-zoi_lipid_top.png │ │ │ ├── 07_APLProt_03-2D_interacting_neighbors_top.png │ │ │ ├── 07_APLProt_04-interacting_used_top.png │ │ │ ├── 07_APLProt_05-interacting_xcm_top.png │ │ │ ├── 07_APLProt_06-clipped_zoi_top.png │ │ │ ├── 07_APL_01-leaflets_lower_top.png │ │ │ ├── 07_APL_01-leaflets_upper_top.png │ │ │ ├── 07_APL_02-leaflets_both_side.png │ │ │ ├── 07_APL_02-leaflets_both_top.png │ │ │ ├── 07_APL_03-ref_side.png │ │ │ ├── 07_APL_03-ref_top.png │ │ │ ├── 07_APL_04-NS_side.png │ │ │ ├── 07_APL_04-NS_top.png │ │ │ ├── 07_APL_05-NS_nocutoff_side.png │ │ │ ├── 07_APL_05-NS_nocutoff_top.png │ │ │ ├── 07_APL_06-NS_projection_leaflets_side.png │ │ │ ├── 07_APL_06-NS_projection_leaflets_top.png │ │ │ ├── 07_APL_06-NS_projection_neighbors_side.png │ │ │ ├── 07_APL_06-NS_projection_neighbors_top.png │ │ │ ├── 07_APL_06-NS_projection_side.png │ │ │ ├── 07_APL_06-NS_projection_top.png │ │ │ ├── 07_APL_07-2D_neighbors_top.png │ │ │ ├── 07_APL_08-voro_complete_top.png │ │ │ ├── 07_APL_09-zoi_top.png │ │ │ ├── apl_lipids.svg │ │ │ ├── apl_protein.svg │ │ │ ├── arrow.svg │ │ │ ├── bilayer.gro │ │ │ ├── bilayer.ndx │ │ │ ├── bilayer.pdb │ │ │ ├── bilayer_prot.gro │ │ │ ├── bilayer_prot.ndx │ │ │ ├── bilayer_prot.pdb │ │ │ ├── fatslim_pymol.py │ │ │ ├── lipid-simplification.svg │ │ │ ├── normal-calculation.svg │ │ │ ├── run_me_NS.pml │ │ │ ├── run_me_apl.pml │ │ │ ├── run_me_apl_prot.pml │ │ │ ├── run_me_leaflets.pml │ │ │ ├── run_me_leaflets_vesicle.pml │ │ │ ├── run_me_simplification.pml │ │ │ ├── run_me_thickness.pml │ │ │ ├── run_me_thickness_vesicle.pml │ │ │ ├── system-simplification.svg │ │ │ ├── thickness_other.svg │ │ │ ├── thickness_results.svg │ │ │ ├── thickness_same.svg │ │ │ ├── vesicle.gro │ │ │ ├── vesicle.ndx │ │ │ └── vesicle.pdb │ │ ├── system_simplification.png │ │ ├── thickness_other.png │ │ ├── thickness_results.png │ │ └── thickness_same.png │ ├── installation.rst │ ├── leaflets.rst │ ├── overview.rst │ ├── thickness.rst │ ├── tutorials.rst │ └── tutorials │ │ ├── bilayer_chol.gro │ │ ├── bilayer_chol.ndx │ │ ├── bilayer_chol_leaflet_0000.ndx │ │ ├── bilayer_peptide.gro │ │ ├── bilayer_peptide.ndx │ │ ├── bilayer_peptide.xtc │ │ ├── bilayer_peptide_thickness.xvg │ │ ├── bilayer_prot.gro │ │ ├── bilayer_prot.ndx │ │ ├── bilayer_prot_apl_frame_00000.csv │ │ ├── dppc_vesicle.gro │ │ ├── dppc_vesicle.ndx │ │ ├── dppc_vesicle.xtc │ │ ├── dppc_vesicle_apl.xvg │ │ ├── dppc_vesicle_area.xvg │ │ ├── model_vesicle.gro │ │ ├── model_vesicle.ndx │ │ └── show_apl_map.py │ └── index.rst ├── extra └── fatslim-completion.bash ├── fatslim ├── fatslimlib ├── __init__.py ├── builtins.py ├── command.py ├── core_analysis.c ├── core_analysis.pxd ├── core_analysis.pyx ├── core_base.c ├── core_base.pxd ├── core_base.pyx ├── core_datareading.c ├── core_datareading.pyx ├── core_geometry.c ├── core_geometry.pxd ├── core_geometry.pyx ├── core_ns.c ├── core_ns.pxd ├── core_ns.pyx ├── datareading.py ├── test │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── bilayer.gro │ │ ├── bilayer.ndx │ │ ├── bilayer_allatom.gro │ │ ├── bilayer_allatom.ndx │ │ ├── bilayer_chol.gro │ │ ├── bilayer_chol.ndx │ │ ├── bilayer_chol_apl_group.xvg │ │ ├── bilayer_chol_apl_nogroup.xvg │ │ ├── bilayer_ganglio.gro │ │ ├── bilayer_ganglio.ndx │ │ ├── bilayer_multi.gro │ │ ├── bilayer_multi.ndx │ │ ├── bilayer_peptide.gro │ │ ├── bilayer_peptide.ndx │ │ ├── bilayer_peptide_hydrogen.ndx │ │ ├── bilayer_prot.gro │ │ ├── bilayer_prot.ndx │ │ ├── bilayer_prot_area.xvg │ │ ├── deformed.gro │ │ ├── deformed.ndx │ │ ├── dppc_vesicle.gro │ │ ├── dppc_vesicle.ndx │ │ ├── dppc_vesicle.trr │ │ ├── dppc_vesicle.xtc │ │ ├── dppc_vesicle_apl.xvg │ │ ├── dppc_vesicle_area.xvg │ │ ├── dppc_vesicle_thickness.xvg │ │ ├── model_big.gro │ │ ├── model_big.ndx │ │ ├── model_bilayer.gro │ │ ├── model_bilayer.ndx │ │ ├── model_bilayer_apl_raw.csv │ │ ├── model_bilayer_prot.gro │ │ ├── model_bilayer_prot.ndx │ │ ├── model_bilayer_thickness.xvg │ │ ├── model_bilayer_thickness_raw.csv │ │ ├── model_bilayer_vesicle.gro │ │ ├── model_bilayer_vesicle.ndx │ │ ├── model_multibilayer.gro │ │ ├── model_multibilayer.ndx │ │ ├── model_vesicle.gro │ │ └── model_vesicle.ndx │ ├── test_00_cosmogony.py │ ├── test_01_datareading.py │ ├── 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