├── LICENSE ├── README.md ├── pypolybuilder ├── .gitignore ├── Angle.py ├── AngleParams.py ├── Atom.py ├── Bond.py ├── BondParams.py ├── Branch.py ├── BuildingBlock.py ├── BuildingBlockFactory.py ├── Connection.py ├── Dendrimer.py ├── Dihedral.py ├── DihedralParams.py ├── Exclusions.py ├── FFParams.py ├── GenerateGeometry.py ├── Itp.py ├── OptimizeGeometry.py ├── PSO.py ├── Polymer.py ├── Printer.py ├── TorsionOpt.py ├── Utils.py ├── __init__.py ├── __main__.py ├── __pycache__ │ ├── Angle.cpython-38.pyc │ ├── AngleParams.cpython-38.pyc │ ├── Atom.cpython-38.pyc │ ├── Bond.cpython-38.pyc │ ├── BondParams.cpython-38.pyc │ ├── Branch.cpython-38.pyc │ ├── BuildingBlock.cpython-38.pyc │ ├── BuildingBlockFactory.cpython-38.pyc │ ├── Connection.cpython-38.pyc │ ├── Dendrimer.cpython-38.pyc │ ├── Dihedral.cpython-38.pyc │ ├── DihedralParams.cpython-38.pyc │ ├── Exclusions.cpython-38.pyc │ ├── FFParams.cpython-38.pyc │ ├── Itp.cpython-38.pyc │ ├── OptimizeGeometry.cpython-38.pyc │ ├── Polymer.cpython-38.pyc │ ├── Printer.cpython-38.pyc │ ├── TorsionOpt.cpython-38.pyc │ ├── Utils.cpython-38.pyc │ ├── constants.cpython-38.pyc │ ├── pypoly_io.cpython-38.pyc │ ├── pypolybuilder.cpython-38.pyc │ └── vbga.cpython-38.pyc ├── asciilogo.txt ├── connect.in ├── constants.py ├── contributors.txt ├── demo │ ├── .gitignore │ └── gromacs_format │ │ ├── dendrimer │ │ ├── PAMAM │ │ │ ├── core_PAMAM.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_PAMAM-protonated.itp │ │ │ ├── inter_PAMAM.itp │ │ │ ├── list_param.itp │ │ │ ├── new-core_PAMAM-protonated.itp │ │ │ ├── old-core_PAMAM-protonated.itp │ │ │ ├── run │ │ │ │ ├── PAMAM.sh │ │ │ │ ├── PAMAM.top │ │ │ │ └── mdp │ │ │ │ │ ├── em.mdp │ │ │ │ │ ├── ion.mdp │ │ │ │ │ ├── md.mdp │ │ │ │ │ ├── minim.mdp │ │ │ │ │ ├── npt.mdp │ │ │ │ │ └── nvt.mdp │ │ │ ├── ter_PAMAM-protonated.itp │ │ │ └── ter_PAMAM.itp │ │ ├── PAMAMPPI_Janus_like │ │ │ ├── core_PAMAM.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_PAMAM.itp │ │ │ ├── inter_PPI.itp │ │ │ ├── list_param.itp │ │ │ ├── run │ │ │ │ ├── PAMAM_PPI.sh │ │ │ │ ├── PAMAM_PPI.top │ │ │ │ └── mdp │ │ │ │ │ ├── bck.em1.mdp │ │ │ │ │ ├── bck.em2.mdp │ │ │ │ │ ├── bck.md.mdp │ │ │ │ │ ├── bck.npt300.mdp │ │ │ │ │ ├── bck.nvt100.mdp │ │ │ │ │ ├── bck.nvt200.mdp │ │ │ │ │ ├── bck.nvt300.mdp │ │ │ │ │ ├── em.mdp │ │ │ │ │ ├── em1.mdp │ │ │ │ │ ├── em2.mdp │ │ │ │ │ ├── ion.mdp │ │ │ │ │ ├── md.mdp │ │ │ │ │ ├── minim.mdp │ │ │ │ │ ├── npt.mdp │ │ │ │ │ ├── npt300.mdp │ │ │ │ │ ├── nvt.mdp │ │ │ │ │ ├── nvt100.mdp │ │ │ │ │ ├── nvt200.mdp │ │ │ │ │ └── nvt300.mdp │ │ │ ├── ter_PAMAM.itp │ │ │ └── ter_PPI.itp │ │ ├── PAMAM_fix_connectors │ │ │ ├── default.gro │ │ │ ├── default.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ └── list_param.itp │ │ ├── PPI │ │ │ ├── core_PPI-protonated.itp │ │ │ ├── core_PPI.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_PPI-protonated.itp │ │ │ ├── inter_PPI.itp │ │ │ ├── list_param.itp │ │ │ ├── run │ │ │ │ ├── PPI.sh │ │ │ │ ├── PPI.top │ │ │ │ └── mdp │ │ │ │ │ ├── em.mdp │ │ │ │ │ ├── ion.mdp │ │ │ │ │ ├── md.mdp │ │ │ │ │ ├── minim.mdp │ │ │ │ │ ├── npt.mdp │ │ │ │ │ └── nvt.mdp │ │ │ ├── ter_PPI-protonated.itp │ │ │ └── ter_PPI.itp │ │ └── SPL7013 │ │ │ ├── core_BDA.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_LYS.itp │ │ │ ├── list_param.itp │ │ │ ├── run │ │ │ ├── SPL.sh │ │ │ ├── SPL.top │ │ │ └── mdp │ │ │ │ ├── bck.em1.mdp │ │ │ │ ├── bck.em2.mdp │ │ │ │ ├── bck.md.mdp │ │ │ │ ├── bck.npt300.mdp │ │ │ │ ├── bck.nvt100.mdp │ │ │ │ ├── bck.nvt200.mdp │ │ │ │ ├── bck.nvt300.mdp │ │ │ │ ├── em.mdp │ │ │ │ ├── em1.mdp │ │ │ │ ├── em2.mdp │ │ │ │ ├── ion.mdp │ │ │ │ ├── md.mdp │ │ │ │ ├── minim.mdp │ │ │ │ ├── npt.mdp │ │ │ │ ├── npt300.mdp │ │ │ │ ├── nvt.mdp │ │ │ │ ├── nvt100.mdp │ │ │ │ ├── nvt200.mdp │ │ │ │ └── nvt300.mdp │ │ │ └── ter_NDSA.itp │ │ ├── polymer │ │ ├── Octane │ │ │ ├── C2.itp │ │ │ ├── C3.itp │ │ │ ├── connect.in │ │ │ ├── how_to_run_this_example.txt │ │ │ └── list_param.itp │ │ ├── PAMAM_PPI_Half │ │ │ ├── connect.in │ │ │ ├── coreHalf_PAMAM.itp │ │ │ ├── coreHalf_PPI.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_PAMAM.itp │ │ │ ├── inter_PPI.itp │ │ │ ├── list_param.itp │ │ │ ├── run │ │ │ │ ├── PAMAMPPI.top │ │ │ │ ├── PAMAM_PPI_half.sh │ │ │ │ └── mdp │ │ │ │ │ ├── em.mdp │ │ │ │ │ ├── ion.mdp │ │ │ │ │ ├── md.mdp │ │ │ │ │ ├── minim.mdp │ │ │ │ │ ├── npt.mdp │ │ │ │ │ └── nvt.mdp │ │ │ ├── ter_PAMAM.itp │ │ │ └── ter_PPI.itp │ │ ├── PAMAM_PolyEtyleneglycol │ │ │ ├── connect.in │ │ │ ├── coreHalf_PAMAM.itp │ │ │ ├── etyleneglycol.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── inter_PAMAM.itp │ │ │ ├── list_param.itp │ │ │ ├── run │ │ │ │ ├── PAMAM_PEG.sh │ │ │ │ ├── PAMAM_PEG.top │ │ │ │ └── mdp │ │ │ │ │ ├── em.mdp │ │ │ │ │ ├── ion.mdp │ │ │ │ │ ├── md.mdp │ │ │ │ │ ├── minim.mdp │ │ │ │ │ ├── npt.mdp │ │ │ │ │ └── nvt.mdp │ │ │ └── ter_PAMAM.itp │ │ ├── PNIPAM │ │ │ ├── bb_PNIP-end.itp │ │ │ ├── bb_PNIP-start.itp │ │ │ ├── bb_PNIP.itp │ │ │ ├── connect-5.in │ │ │ ├── connect.in │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── list_param.itp │ │ │ └── run │ │ │ │ ├── PNIPAM.sh │ │ │ │ ├── PNIPAM.top │ │ │ │ └── mdp │ │ │ │ ├── em.mdp │ │ │ │ ├── ion.mdp │ │ │ │ ├── md.mdp │ │ │ │ ├── minim.mdp │ │ │ │ ├── npt.mdp │ │ │ │ └── nvt.mdp │ │ ├── PNIPAM_fix_connection │ │ │ ├── connect-4.in │ │ │ ├── default.gro │ │ │ ├── default.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ └── list_param.itp │ │ ├── PolyEtyleneglycol │ │ │ ├── connect.in │ │ │ ├── etyleneglycol-end.itp │ │ │ ├── etyleneglycol-start.itp │ │ │ ├── etyleneglycol.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── list_param.itp │ │ │ └── run │ │ │ │ ├── .PAMAM.sh.swp │ │ │ │ ├── PEG.sh │ │ │ │ ├── PEG5x.top │ │ │ │ └── mdp │ │ │ │ ├── em.mdp │ │ │ │ ├── ion.mdp │ │ │ │ ├── md.mdp │ │ │ │ ├── minim.mdp │ │ │ │ ├── npt.mdp │ │ │ │ └── nvt.mdp │ │ ├── PolyUrethane │ │ │ ├── bb_PU_B.itp │ │ │ ├── bb_PU_E.itp │ │ │ ├── bb_PU_I.itp │ │ │ ├── connect-3.in │ │ │ ├── connect1.in │ │ │ ├── connect2.in │ │ │ ├── connect3.in │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── list_param.itp │ │ │ └── run │ │ │ │ ├── PU.sh │ │ │ │ ├── PU3x.top │ │ │ │ └── mdp │ │ │ │ ├── em.mdp │ │ │ │ ├── em1.mdp │ │ │ │ ├── em2.mdp │ │ │ │ ├── ion.mdp │ │ │ │ ├── md.mdp │ │ │ │ ├── minim.mdp │ │ │ │ ├── npt.mdp │ │ │ │ ├── npt300.mdp │ │ │ │ ├── nvt.mdp │ │ │ │ ├── nvt100.mdp │ │ │ │ ├── nvt200.mdp │ │ │ │ └── nvt300.mdp │ │ ├── Poly_p-benzamide │ │ │ ├── bb_PPD_B.itp │ │ │ ├── bb_PPD_I.itp │ │ │ ├── bb_TCO_E.itp │ │ │ ├── bb_TCO_I.itp │ │ │ ├── connect-4.in │ │ │ ├── connect.in │ │ │ ├── how_to_run_this_example.txt │ │ │ └── list_param.itp │ │ └── Toy_Ciclic_Polymer │ │ │ ├── connect.in │ │ │ ├── connect_BBs.in │ │ │ ├── connect_arm.in │ │ │ ├── connect_ring.in │ │ │ ├── default.gro │ │ │ ├── default.itp │ │ │ ├── etyleneglycol.itp │ │ │ ├── how_to_run_this_example.txt │ │ │ ├── list_param.itp │ │ │ ├── nc3.itp │ │ │ ├── ring.itp │ │ │ ├── run │ │ │ ├── mdp │ │ │ │ ├── em.mdp │ │ │ │ ├── ion.mdp │ │ │ │ ├── md.mdp │ │ │ │ ├── minim.mdp │ │ │ │ ├── npt.mdp │ │ │ │ └── nvt.mdp │ │ │ ├── toy.sh │ │ │ └── toy.top │ │ │ └── ter_etyleneglycol.itp │ │ └── test_tutorials.py ├── gromos2016h66.ff │ ├── 2016h66_orga.rtp │ ├── aminoacids.c.tdb │ ├── aminoacids.n.tdb │ ├── aminoacids.rtp │ ├── atomtypes.atp │ ├── elements.dat │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.itp │ ├── ions.itp │ ├── residuetypes.dat │ ├── spc.itp │ ├── specbond.dat │ └── xlateat.dat ├── init.py ├── pypoly_io.py ├── pypolybuilder.py ├── vbga.py └── vbga_u.py ├── setup.cfg ├── setup.py ├── tests ├── .coverage ├── angleTests.py ├── bb_cco.itp ├── bb_h.itp ├── bb_oh.itp ├── bondTests.py ├── buildingBlockFactoryTests.py ├── buildingBlockTests.py ├── connect.in ├── coords.gro ├── default.itp ├── dendritest.py ├── htmlcov │ ├── _home_vitor_dendribuilder_BuildingBlock.html │ ├── _home_vitor_dendribuilder_BuildingBlockFactory.html │ ├── _home_vitor_dendribuilder_angle.html │ ├── _home_vitor_dendribuilder_angle_params.html │ ├── _home_vitor_dendribuilder_atom.html │ ├── _home_vitor_dendribuilder_bond.html │ ├── _home_vitor_dendribuilder_bond_params.html │ ├── _home_vitor_dendribuilder_branch.html │ ├── _home_vitor_dendribuilder_connection.html │ ├── _home_vitor_dendribuilder_dendrimer.html │ ├── _home_vitor_dendribuilder_dihe_params.html │ ├── _home_vitor_dendribuilder_dihedral.html │ ├── _home_vitor_dendribuilder_exclusions.html │ ├── _home_vitor_dendribuilder_ff_params.html │ ├── _home_vitor_dendribuilder_itp.html │ ├── _home_vitor_dendribuilder_polymer.html │ ├── _home_vitor_dendribuilder_utils.html │ ├── angleTests.html │ ├── bondTests.html │ ├── buildingBlockFactoryTests.html │ ├── buildingBlockTests.html │ ├── coverage_html.js │ ├── dendritest.html │ ├── index.html │ ├── jquery.hotkeys.js │ ├── jquery.isonscreen.js │ ├── jquery.min.js │ ├── jquery.tablesorter.min.js │ ├── keybd_closed.png │ ├── keybd_open.png │ ├── polymerTests.html │ ├── status.dat │ ├── style.css │ └── testEnv.html ├── list_param.itp ├── polymerTests.py └── testEnv.py └── userGuide ├── Cyclic_Pol └── Cyclic_Pol.tex ├── Octane └── Octane.tex ├── PAMAM ├── PAMAM.pdf ├── PAMAM.tex ├── PAMAMBBs.png ├── PAMAMG2.png ├── PAMAMGs.pdf └── PAMAMSOL.pdf ├── PAMAM_PEG ├── PAMAMPEG.png ├── PAMAMPEG2.png ├── PAMAMPEGBBs.png ├── PAMAMPEGHalf.png ├── PAMAM_PEG.tex ├── PAMAM_PEG_PPB.pdf └── PAMAM_PEG_SOL.pdf ├── PAMAM_PPI-Janus ├── JANUSBBs.png ├── JANUSG1.png ├── JANUSPAMAMhalf.png ├── PAMAM_PPI-Janus.tex ├── PAMAM_PPI.pdf └── PAMAM_PPISOL.pdf ├── PAMAM_PPI-half ├── PAMAMPPIBBs.png ├── PAMAMPPIHalfs.png ├── PAMAMPPIPOL.png ├── PAMAMPPIPPB.pdf ├── PAMAMPPISOL.pdf └── PAMAM_PPI-half.tex ├── PEG ├── PEG.png ├── PEG.tex ├── PEGBBs.png ├── PEGPPB.png └── PEGSOL.png ├── PNIPAM ├── PNIPAM.tex ├── PNIPAMBBs.png ├── PNIPAMPOL.png ├── PNIPAMPPB.pdf ├── PNIPAMSIZE.pdf └── PNIPAMSOL.pdf ├── PPI ├── PPI.pdf ├── PPI.tex ├── PPIBBs.png ├── PPIG1.png └── 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