├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── VERSION.txt ├── insane ├── __init__.py ├── _data.py ├── _lipid_data.py ├── cli.py ├── constants.py ├── converters.py ├── core.py ├── data │ └── diacylester.dat ├── lipids.dat ├── lipids.py ├── options.py ├── pbc.py ├── structure.py └── utils.py ├── maintainers ├── travis_zip.sh └── zippackage.sh ├── setup.py └── tests ├── data ├── inputs │ └── 1a0s │ │ ├── 1a0s.pdb │ │ ├── CG1a0s-box.pdb │ │ ├── CG1a0s.pdb │ │ ├── CG1a0s.top │ │ └── Protein_A.itp └── simple_case │ ├── -o bilayer.pdb -x 15 -y 15 -z 10 -l DOPC:0.5 -l DOPS:0.5 -sol W │ ├── bilayer.pdb │ ├── stderr │ └── stdout │ ├── -o test.gro -box 10,15,20 -l LOLO -alname LOLO -alhead C.P -allink G.G -altail CC.CDC │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 10,15,20 -l POPC │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 10,15,20 -sol W -l POPC │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 10,15,20 -sol W │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 10,15,20 -sol WF │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 10,15,20 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 25,15,10,0,0,5,0,5,5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 25,15,10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 25,20,15,90,60,60 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -box 25 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc cubic -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc cubic -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc hexagonal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc hexagonal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc optimal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc optimal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc rectangular -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc rectangular -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc square -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -hole 4 -pbc square -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc cubic -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc cubic -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc hexagonal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc hexagonal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc optimal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc optimal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc rectangular -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc rectangular -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc square -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -disc 8 -pbc square -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -box 2,3,4 -d 10 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -box 20,30,40 -d 3 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -box 20,30,40 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -center │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -dm 3 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -orient -od 0.2 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -orient │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -ring │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -rotate 30 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -rotate 40 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb -p CG1a0s.top -l POPC -rotate princ │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -f CG1a0s.pdb │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc cubic -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc cubic -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc hexagonal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc hexagonal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc optimal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc optimal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc rectangular -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc rectangular -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc square -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -hole 4 -pbc square -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -l POPC -l DPPC -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -l POPC:2 -l DPPC:1 -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc cubic -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc cubic -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc cubic -f CG1a0s.pdb -p CG1a0s.top │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc hexagonal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc hexagonal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc hexagonal -f CG1a0s.pdb -p CG1a0s.top │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc keep -f CG1a0s-box.pdb │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc optimal -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc optimal -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc optimal -f CG1a0s.pdb -p CG1a0s.top │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc rectangular -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc rectangular -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc rectangular -f CG1a0s.pdb -p CG1a0s.top │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc square -d 10 -dz 5 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc square -d 10 │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro -pbc square -f CG1a0s.pdb -p CG1a0s.top │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.gro │ ├── stderr │ ├── stdout │ └── test.gro │ ├── -o test.pdb -box 10,15,20 │ ├── stderr │ ├── stdout │ └── test.pdb │ ├── -o test.pdb -f CG1a0s.pdb -p CG1a0s.top -l POPC -box 20,30,40 -d 3 │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.pdb │ ├── -o test.pdb -f CG1a0s.pdb -p CG1a0s.top -l POPC -ring │ ├── 1a0s.pdb │ ├── CG1a0s-box.pdb │ ├── CG1a0s.pdb │ ├── CG1a0s.top │ ├── Protein_A.itp │ ├── stderr │ ├── stdout │ └── test.pdb │ ├── here.pdb │ └── multi-custom-lipids │ ├── stderr │ ├── stdout │ └── test.gro ├── easy_copy.py ├── run_tests.py ├── test_absolute.py ├── test_pbc.py ├── test_regression.py ├── test_utils.py └── utils.py /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Tsjerk/Insane/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Tsjerk/Insane/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: 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