Define relevant groups and rules.ipynb

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    "# Categories:\n",
    "Task 2: perform clash checks\n",
    "\n",
    "  * steric clash := all vs. all closer than 1.0A\n",
    "  * apolar clash := apolar vs. all closer than 2.9A\n",
    "  * polar clash := polor donor vs polor donor closer than 3.1A or polor acceptor vs. polar acceptor closer than 3.1A\n",
    "  * ionic clash := ionic pos vs. ionic pos closer than 3.5 or ionic neg vs. ionic neg closer than 3.5\n",
    "```\n",
    "# 1 = Apolar\n",
    "# 2 = Polar Donnor\n",
    "# 3 = Polar Donnor, Ionic Positive\n",
    "# 4 = Polar Acceptor\n",
    "# 5 = Polar Acceptor, Ionic Negative\n",
    "# 6 = Polar Mixt\n",
    "#\n",
    "#\n",
    "ALA-1HB: 1\n",
    "ALA-2HB: 1\n",
    "ALA-3HB: 1\n",
    "ALA-C: 4\n",
    "ALA-CA: 1\n",
    "ALA-CB: 1\n",
    "ALA-H: 2\n",
    "ALA-HA: 1\n",
    "ALA-HB1: 1\n",
    "ALA-HB2: 1\n",
    "ALA-HB3: 1\n",
    "ALA-N: 2\n",
    "ALA-O: 4\n",
    "ARG-1HH1: 3\n",
    "ARG-1HH2: 3\n",
    "ARG-2HB: 1\n",
    "ARG-2HD: 1\n",
    "ARG-2HG: 1\n",
    "ARG-2HH1: 3\n",
    "ARG-2HH2: 3\n",
    "ARG-3HB: 1\n",
    "ARG-3HD: 1\n",
    "ARG-3HG: 1\n",
    "ARG-C: 4\n",
    "ARG-CA: 1\n",
    "ARG-CB: 1\n",
    "ARG-CD: 1\n",
    "ARG-CG: 1\n",
    "ARG-CZ: 3\n",
    "ARG-H: 2\n",
    "ARG-HA: 1\n",
    "ARG-HB2: 1\n",
    "ARG-HB3: 1\n",
    "ARG-HD2: 1\n",
    "ARG-HD3: 1\n",
    "ARG-HE: 3\n",
    "ARG-HG2: 1\n",
    "ARG-HG3: 1\n",
    "ARG-N: 2\n",
    "ARG-NE: 3\n",
    "ARG-NH1: 3\n",
    "ARG-NH2: 3\n",
    "ARG-O: 4\n",
    "ASN-1HD2: 2\n",
    "ASN-2HB: 1\n",
    "ASN-2HD2: 2\n",
    "ASN-3HB: 1\n",
    "ASN-C: 4\n",
    "ASN-CA: 1\n",
    "ASN-CB: 1\n",
    "ASN-CG: 4\n",
    "ASN-H: 2\n",
    "ASN-HA: 1\n",
    "ASN-HB2: 1\n",
    "ASN-HB3: 1\n",
    "ASN-N: 2\n",
    "ASN-ND2: 2\n",
    "ASN-O: 4\n",
    "ASN-OD1: 4\n",
    "ASP-2HB: 1\n",
    "ASP-3HB: 1\n",
    "ASP-C: 4\n",
    "ASP-CA: 1\n",
    "ASP-CB: 1\n",
    "ASP-CG: 5\n",
    "ASP-H: 2\n",
    "ASP-HA: 1\n",
    "ASP-HB2: 1\n",
    "ASP-HB3: 1\n",
    "ASP-N: 2\n",
    "ASP-O: 4\n",
    "ASP-OD1: 5\n",
    "ASP-OD2: 5\n",
    "CYS-2HB: 1\n",
    "CYS-3HB: 1\n",
    "CYS-C: 4\n",
    "CYS-CA: 1\n",
    "CYS-CB: 1\n",
    "CYS-H: 2\n",
    "CYS-HA: 1\n",
    "CYS-HB2: 1\n",
    "CYS-HB3: 1\n",
    "CYS-HG: 6\n",
    "CYS-N: 2\n",
    "CYS-O: 4\n",
    "CYS-SG: 6\n",
    "CYX-2HB: 1\n",
    "CYX-3HB: 1\n",
    "CYX-C: 4\n",
    "CYX-CA: 1\n",
    "CYX-CB: 1\n",
    "CYX-H: 2\n",
    "CYX-HA: 1\n",
    "CYX-HB2: 1\n",
    "CYX-HB3: 1\n",
    "CYX-N: 2\n",
    "CYX-O: 4\n",
    "CYX-SG: 1\n",
    "TER-H1: 3\n",
    "TER-H2: 3\n",
    "TER-H3: 3\n",
    "TER-OXT: 5\n",
    "GLN-1HE2: 2\n",
    "GLN-2HB: 1\n",
    "GLN-2HE2: 2\n",
    "GLN-2HG: 1\n",
    "GLN-3HB: 1\n",
    "GLN-3HG: 1\n",
    "GLN-C: 4\n",
    "GLN-CA: 1\n",
    "GLN-CB: 1\n",
    "GLN-CD: 4\n",
    "GLN-CG: 1\n",
    "GLN-H: 2\n",
    "GLN-HA: 1\n",
    "GLN-HB2: 1\n",
    "GLN-HB3: 1\n",
    "GLN-N: 2\n",
    "GLN-NE2: 2\n",
    "GLN-O: 4\n",
    "GLN-OE1: 4\n",
    "GLU-2HB: 1\n",
    "GLU-2HG: 1\n",
    "GLU-3HB: 1\n",
    "GLU-3HG: 1\n",
    "GLU-C: 4\n",
    "GLU-CA: 1\n",
    "GLU-CB: 1\n",
    "GLU-CD: 5\n",
    "GLU-CG: 1\n",
    "GLU-H: 2\n",
    "GLU-HA: 1\n",
    "GLU-HB2: 1\n",
    "GLU-HB3: 1\n",
    "GLU-HG2: 1\n",
    "GLU-HG3: 1\n",
    "GLU-N: 2\n",
    "GLU-O: 4\n",
    "GLU-OE1: 5\n",
    "GLU-OE2: 5\n",
    "GLY-2HA: 1\n",
    "GLY-3HA: 1\n",
    "GLY-C: 4\n",
    "GLY-CA: 1\n",
    "GLY-H: 2\n",
    "GLY-HA2: 1\n",
    "GLY-HA3: 1\n",
    "GLY-N: 2\n",
    "GLY-O: 4\n",
    "HID-2HB: 1\n",
    "HID-3HB: 1\n",
    "HID-C: 4\n",
    "HID-CA: 1\n",
    "HID-CB: 1\n",
    "HID-CD2: 1\n",
    "HID-CE1: 1\n",
    "HID-CG: 1\n",
    "HID-H: 2\n",
    "HID-HA: 1\n",
    "HID-HB2: 1\n",
    "HID-HB3: 1\n",
    "HID-HD1: 1\n",
    "HID-HD2: 1\n",
    "HID-HE1: 1\n",
    "HID-N: 2\n",
    "HID-ND1: 6\n",
    "HID-NE2: 6\n",
    "HID-O: 4\n",
    "HIE-2HB: 1\n",
    "HIE-3HB: 1\n",
    "HIE-C: 4\n",
    "HIE-CA: 1\n",
    "HIE-CB: 1\n",
    "HIE-CD2: 1\n",
    "HIE-CE1: 1\n",
    "HIE-CG: 1\n",
    "HIE-H: 2\n",
    "HIE-HA: 1\n",
    "HIE-HB2: 1\n",
    "HIE-HB3: 1\n",
    "HIE-HD2: 1\n",
    "HIE-HE1: 1\n",
    "HIE-HE2: 1\n",
    "HIE-N: 2\n",
    "HIE-ND1: 6\n",
    "HIE-NE2: 6\n",
    "HIE-O: 4\n",
    "HIP-2HB: 1\n",
    "HIP-3HB: 1\n",
    "HIP-C: 4\n",
    "HIP-CA: 1\n",
    "HIP-CB: 1\n",
    "HIP-CD2: 6\n",
    "HIP-CE1: 6\n",
    "HIP-CG: 6\n",
    "HIP-H: 2\n",
    "HIP-HA: 1\n",
    "HIP-HB2: 1\n",
    "HIP-HB3: 1\n",
    "HIP-HD1: 6\n",
    "HIP-HD2: 6\n",
    "HIP-HE1: 6\n",
    "HIP-HE2: 6\n",
    "HIP-N: 2\n",
    "HIP-ND1: 6\n",
    "HIP-NE2: 6\n",
    "HIP-O: 4\n",
    "HIS-C: 4\n",
    "HIS-CA: 1\n",
    "HIS-CB: 1\n",
    "HIS-CD2: 1\n",
    "HIS-CE1: 1\n",
    "HIS-CG: 1\n",
    "HIS-N: 2\n",
    "HIS-ND1: 6\n",
    "HIS-NE2: 6\n",
    "HIS-O: 4\n",
    "HSC-C: 4\n",
    "HSC-CA: 1\n",
    "HSC-CB: 1\n",
    "HSC-CD2: 1\n",
    "HSC-CE1: 1\n",
    "HSC-CG: 1\n",
    "HSC-N: 2\n",
    "HSC-ND1: 6\n",
    "HSC-NE2: 6\n",
    "HSC-O: 4\n",
    "ILE-1HD1: 1\n",
    "ILE-1HG2: 1\n",
    "ILE-2HD1: 1\n",
    "ILE-2HG1: 1\n",
    "ILE-2HG2: 1\n",
    "ILE-3HD1: 1\n",
    "ILE-3HG1: 1\n",
    "ILE-3HG2: 1\n",
    "ILE-C: 4\n",
    "ILE-CA: 1\n",
    "ILE-CB: 1\n",
    "ILE-CD1: 1\n",
    "ILE-CG1: 1\n",
    "ILE-CG2: 1\n",
    "ILE-H: 2\n",
    "ILE-HA: 1\n",
    "ILE-HB: 1\n",
    "ILE-N: 2\n",
    "ILE-O: 4\n",
    "LEU-1HD1: 1\n",
    "LEU-1HD2: 1\n",
    "LEU-2HB: 1\n",
    "LEU-2HD1: 1\n",
    "LEU-2HD2: 1\n",
    "LEU-3HB: 1\n",
    "LEU-3HD1: 1\n",
    "LEU-3HD2: 1\n",
    "LEU-C: 4\n",
    "LEU-CA: 1\n",
    "LEU-CB: 1\n",
    "LEU-CD1: 1\n",
    "LEU-CD2: 1\n",
    "LEU-CG: 1\n",
    "LEU-H: 2\n",
    "LEU-HA: 1\n",
    "LEU-HB2: 1\n",
    "LEU-HB3: 1\n",
    "LEU-HG: 1\n",
    "LEU-N: 2\n",
    "LEU-O: 4\n",
    "LYS-1HZ: 3\n",
    "LYS-2HB: 1\n",
    "LYS-2HD: 1\n",
    "LYS-2HE: 1\n",
    "LYS-2HG: 1\n",
    "LYS-2HZ: 3\n",
    "LYS-3HB: 1\n",
    "LYS-3HD: 1\n",
    "LYS-3HE: 1\n",
    "LYS-3HG: 1\n",
    "LYS-3HZ: 3\n",
    "LYS-C: 4\n",
    "LYS-CA: 1\n",
    "LYS-CB: 1\n",
    "LYS-CD: 1\n",
    "LYS-CE: 1\n",
    "LYS-CG: 1\n",
    "LYS-H: 2\n",
    "LYS-HA: 1\n",
    "LYS-HB2: 1\n",
    "LYS-HB3: 1\n",
    "LYS-HD2: 1\n",
    "LYS-HD3: 1\n",
    "LYS-HE2: 1\n",
    "LYS-HE3: 1\n",
    "LYS-HG2: 1\n",
    "LYS-HG3: 1\n",
    "LYS-HZ1: 3\n",
    "LYS-HZ2: 3\n",
    "LYS-HZ3: 3\n",
    "LYS-N: 2\n",
    "LYS-NZ: 3\n",
    "LYS-O: 4\n",
    "MET-1HE: 1\n",
    "MET-2HB: 1\n",
    "MET-2HE: 1\n",
    "MET-2HG: 1\n",
    "MET-3HB: 1\n",
    "MET-3HE: 1\n",
    "MET-3HG: 1\n",
    "MET-C: 4\n",
    "MET-CA: 1\n",
    "MET-CB: 1\n",
    "MET-CE: 1\n",
    "MET-CG: 1\n",
    "MET-H: 2\n",
    "MET-HA: 1\n",
    "MET-HB2: 1\n",
    "MET-HB3: 1\n",
    "MET-HE1: 1\n",
    "MET-HE2: 1\n",
    "MET-HE3: 1\n",
    "MET-HG2: 1\n",
    "MET-HG3: 1\n",
    "MET-N: 2\n",
    "MET-O: 4\n",
    "MET-SD: 1\n",
    "PHE-2HB: 1\n",
    "PHE-3HB: 1\n",
    "PHE-C: 4\n",
    "PHE-CA: 1\n",
    "PHE-CB: 1\n",
    "PHE-CD1: 1\n",
    "PHE-CD2: 1\n",
    "PHE-CE1: 1\n",
    "PHE-CE2: 1\n",
    "PHE-CG: 1\n",
    "PHE-CZ: 1\n",
    "PHE-H: 2\n",
    "PHE-HA: 1\n",
    "PHE-HB2: 1\n",
    "PHE-HB3: 1\n",
    "PHE-HD1: 1\n",
    "PHE-HD2: 1\n",
    "PHE-HE1: 1\n",
    "PHE-HE2: 1\n",
    "PHE-HZ: 1\n",
    "PHE-N: 2\n",
    "PHE-O: 4\n",
    "PRO-2HB: 1\n",
    "PRO-2HD: 1\n",
    "PRO-2HG: 1\n",
    "PRO-3HB: 1\n",
    "PRO-3HD: 1\n",
    "PRO-3HG: 1\n",
    "PRO-C: 4\n",
    "PRO-CA: 1\n",
    "PRO-CB: 1\n",
    "PRO-CD: 1\n",
    "PRO-CG: 1\n",
    "PRO-HA: 1\n",
    "PRO-HB2: 1\n",
    "PRO-HB3: 1\n",
    "PRO-HD2: 1\n",
    "PRO-HD3: 1\n",
    "PRO-HG2: 1\n",
    "PRO-HG3: 1\n",
    "PRO-N: 2\n",
    "PRO-O: 4\n",
    "SER-2HB: 1\n",
    "SER-3HB: 1\n",
    "SER-C: 4\n",
    "SER-CA: 1\n",
    "SER-CB: 1\n",
    "SER-H: 2\n",
    "SER-HA: 1\n",
    "SER-HB2: 1\n",
    "SER-HB3: 1\n",
    "SER-HG: 6\n",
    "SER-N: 2\n",
    "SER-O: 4\n",
    "SER-OG: 6\n",
    "THR-1HG: 6\n",
    "THR-1HG2: 1\n",
    "THR-2HG2: 1\n",
    "THR-3HG2: 1\n",
    "THR-C: 4\n",
    "THR-CA: 1\n",
    "THR-CB: 1\n",
    "THR-CG2: 1\n",
    "THR-H: 2\n",
    "THR-HA: 1\n",
    "THR-HB: 1\n",
    "THR-HG1: 6\n",
    "THR-N: 2\n",
    "THR-O: 4\n",
    "THR-OG1: 6\n",
    "TRP-2HB: 1\n",
    "TRP-3HB: 1\n",
    "TRP-C: 4\n",
    "TRP-CA: 1\n",
    "TRP-CB: 1\n",
    "TRP-CD1: 1\n",
    "TRP-CD2: 1\n",
    "TRP-CE2: 1\n",
    "TRP-CE3: 1\n",
    "TRP-CG: 1\n",
    "TRP-CH2: 1\n",
    "TRP-CZ2: 1\n",
    "TRP-CZ3: 1\n",
    "TRP-H: 2\n",
    "TRP-HA: 1\n",
    "TRP-HB2: 1\n",
    "TRP-HB3: 1\n",
    "TRP-HD1: 1\n",
    "TRP-HE1: 1\n",
    "TRP-HE3: 1\n",
    "TRP-HH2: 1\n",
    "TRP-HZ2: 1\n",
    "TRP-HZ3: 1\n",
    "TRP-N: 2\n",
    "#TRP-NE1: 1\n",
    "TRP-NE1: 2\n",
    "TRP-O: 4\n",
    "TYR-2HB: 1\n",
    "TYR-3HB: 1\n",
    "TYR-C: 4\n",
    "TYR-CA: 1\n",
    "TYR-CB: 1\n",
    "TYR-CD1: 1\n",
    "TYR-CD2: 1\n",
    "TYR-CE1: 1\n",
    "TYR-CE2: 1\n",
    "TYR-CG: 1\n",
    "TYR-CZ: 1\n",
    "TYR-H: 2\n",
    "TYR-HA: 1\n",
    "TYR-HB2: 1\n",
    "TYR-HB3: 1\n",
    "TYR-HD1: 1\n",
    "TYR-HD2: 1\n",
    "TYR-HE1: 1\n",
    "TYR-HE2: 1\n",
    "TYR-HH: 6\n",
    "TYR-N: 2\n",
    "TYR-O: 4\n",
    "TYR-OH: 6\n",
    "VAL-1HG1: 1\n",
    "VAL-1HG2: 1\n",
    "VAL-2HG1: 1\n",
    "VAL-2HG2: 1\n",
    "VAL-3HG1: 1\n",
    "VAL-3HG2: 1\n",
    "VAL-C: 4\n",
    "VAL-CA: 1\n",
    "VAL-CB: 1\n",
    "VAL-CG1: 1\n",
    "VAL-CG2: 1\n",
    "VAL-H: 2\n",
    "VAL-HA: 1\n",
    "VAL-HB: 1\n",
    "VAL-N: 2\n",
    "VAL-O: 4\n",
    "WAT-O: 6\n",
    "WAT-H1: 6\n",
    "WAT-H2: 6\n",
    "```"
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   "outputs": [],
   "source": [
    "assignments = \"\"\"ALA-1HB: 1\n",
    "ALA-2HB: 1\n",
    "ALA-3HB: 1\n",
    "ALA-C: 4\n",
    "ALA-CA: 1\n",
    "ALA-CB: 1\n",
    "ALA-H: 2\n",
    "ALA-HA: 1\n",
    "ALA-HB1: 1\n",
    "ALA-HB2: 1\n",
    "ALA-HB3: 1\n",
    "ALA-N: 2\n",
    "ALA-O: 4\n",
    "ARG-1HH1: 3\n",
    "ARG-1HH2: 3\n",
    "ARG-2HB: 1\n",
    "ARG-2HD: 1\n",
    "ARG-2HG: 1\n",
    "ARG-2HH1: 3\n",
    "ARG-2HH2: 3\n",
    "ARG-3HB: 1\n",
    "ARG-3HD: 1\n",
    "ARG-3HG: 1\n",
    "ARG-C: 4\n",
    "ARG-CA: 1\n",
    "ARG-CB: 1\n",
    "ARG-CD: 1\n",
    "ARG-CG: 1\n",
    "ARG-CZ: 3\n",
    "ARG-H: 2\n",
    "ARG-HA: 1\n",
    "ARG-HB2: 1\n",
    "ARG-HB3: 1\n",
    "ARG-HD2: 1\n",
    "ARG-HD3: 1\n",
    "ARG-HE: 3\n",
    "ARG-HG2: 1\n",
    "ARG-HG3: 1\n",
    "ARG-N: 2\n",
    "ARG-NE: 3\n",
    "ARG-NH1: 3\n",
    "ARG-NH2: 3\n",
    "ARG-O: 4\n",
    "ASN-1HD2: 2\n",
    "ASN-2HB: 1\n",
    "ASN-2HD2: 2\n",
    "ASN-3HB: 1\n",
    "ASN-C: 4\n",
    "ASN-CA: 1\n",
    "ASN-CB: 1\n",
    "ASN-CG: 4\n",
    "ASN-H: 2\n",
    "ASN-HA: 1\n",
    "ASN-HB2: 1\n",
    "ASN-HB3: 1\n",
    "ASN-N: 2\n",
    "ASN-ND2: 2\n",
    "ASN-O: 4\n",
    "ASN-OD1: 4\n",
    "ASP-2HB: 1\n",
    "ASP-3HB: 1\n",
    "ASP-C: 4\n",
    "ASP-CA: 1\n",
    "ASP-CB: 1\n",
    "ASP-CG: 5\n",
    "ASP-H: 2\n",
    "ASP-HA: 1\n",
    "ASP-HB2: 1\n",
    "ASP-HB3: 1\n",
    "ASP-N: 2\n",
    "ASP-O: 4\n",
    "ASP-OD1: 5\n",
    "ASP-OD2: 5\n",
    "CYS-2HB: 1\n",
    "CYS-3HB: 1\n",
    "CYS-C: 4\n",
    "CYS-CA: 1\n",
    "CYS-CB: 1\n",
    "CYS-H: 2\n",
    "CYS-HA: 1\n",
    "CYS-HB2: 1\n",
    "CYS-HB3: 1\n",
    "CYS-HG: 6\n",
    "CYS-N: 2\n",
    "CYS-O: 4\n",
    "CYS-SG: 6\n",
    "CYX-2HB: 1\n",
    "CYX-3HB: 1\n",
    "CYX-C: 4\n",
    "CYX-CA: 1\n",
    "CYX-CB: 1\n",
    "CYX-H: 2\n",
    "CYX-HA: 1\n",
    "CYX-HB2: 1\n",
    "CYX-HB3: 1\n",
    "CYX-N: 2\n",
    "CYX-O: 4\n",
    "CYX-SG: 1\n",
    "TER-H1: 3\n",
    "TER-H2: 3\n",
    "TER-H3: 3\n",
    "TER-OXT: 5\n",
    "GLN-1HE2: 2\n",
    "GLN-2HB: 1\n",
    "GLN-2HE2: 2\n",
    "GLN-2HG: 1\n",
    "GLN-3HB: 1\n",
    "GLN-3HG: 1\n",
    "GLN-C: 4\n",
    "GLN-CA: 1\n",
    "GLN-CB: 1\n",
    "GLN-CD: 4\n",
    "GLN-CG: 1\n",
    "GLN-H: 2\n",
    "GLN-HA: 1\n",
    "GLN-HB2: 1\n",
    "GLN-HB3: 1\n",
    "GLN-N: 2\n",
    "GLN-NE2: 2\n",
    "GLN-O: 4\n",
    "GLN-OE1: 4\n",
    "GLU-2HB: 1\n",
    "GLU-2HG: 1\n",
    "GLU-3HB: 1\n",
    "GLU-3HG: 1\n",
    "GLU-C: 4\n",
    "GLU-CA: 1\n",
    "GLU-CB: 1\n",
    "GLU-CD: 5\n",
    "GLU-CG: 1\n",
    "GLU-H: 2\n",
    "GLU-HA: 1\n",
    "GLU-HB2: 1\n",
    "GLU-HB3: 1\n",
    "GLU-HG2: 1\n",
    "GLU-HG3: 1\n",
    "GLU-N: 2\n",
    "GLU-O: 4\n",
    "GLU-OE1: 5\n",
    "GLU-OE2: 5\n",
    "GLY-2HA: 1\n",
    "GLY-3HA: 1\n",
    "GLY-C: 4\n",
    "GLY-CA: 1\n",
    "GLY-H: 2\n",
    "GLY-HA2: 1\n",
    "GLY-HA3: 1\n",
    "GLY-N: 2\n",
    "GLY-O: 4\n",
    "HID-2HB: 1\n",
    "HID-3HB: 1\n",
    "HID-C: 4\n",
    "HID-CA: 1\n",
    "HID-CB: 1\n",
    "HID-CD2: 1\n",
    "HID-CE1: 1\n",
    "HID-CG: 1\n",
    "HID-H: 2\n",
    "HID-HA: 1\n",
    "HID-HB2: 1\n",
    "HID-HB3: 1\n",
    "HID-HD1: 1\n",
    "HID-HD2: 1\n",
    "HID-HE1: 1\n",
    "HID-N: 2\n",
    "HID-ND1: 6\n",
    "HID-NE2: 6\n",
    "HID-O: 4\n",
    "HIE-2HB: 1\n",
    "HIE-3HB: 1\n",
    "HIE-C: 4\n",
    "HIE-CA: 1\n",
    "HIE-CB: 1\n",
    "HIE-CD2: 1\n",
    "HIE-CE1: 1\n",
    "HIE-CG: 1\n",
    "HIE-H: 2\n",
    "HIE-HA: 1\n",
    "HIE-HB2: 1\n",
    "HIE-HB3: 1\n",
    "HIE-HD2: 1\n",
    "HIE-HE1: 1\n",
    "HIE-HE2: 1\n",
    "HIE-N: 2\n",
    "HIE-ND1: 6\n",
    "HIE-NE2: 6\n",
    "HIE-O: 4\n",
    "HIP-2HB: 1\n",
    "HIP-3HB: 1\n",
    "HIP-C: 4\n",
    "HIP-CA: 1\n",
    "HIP-CB: 1\n",
    "HIP-CD2: 6\n",
    "HIP-CE1: 6\n",
    "HIP-CG: 6\n",
    "HIP-H: 2\n",
    "HIP-HA: 1\n",
    "HIP-HB2: 1\n",
    "HIP-HB3: 1\n",
    "HIP-HD1: 6\n",
    "HIP-HD2: 6\n",
    "HIP-HE1: 6\n",
    "HIP-HE2: 6\n",
    "HIP-N: 2\n",
    "HIP-ND1: 6\n",
    "HIP-NE2: 6\n",
    "HIP-O: 4\n",
    "HIS-C: 4\n",
    "HIS-CA: 1\n",
    "HIS-CB: 1\n",
    "HIS-CD2: 1\n",
    "HIS-CE1: 1\n",
    "HIS-CG: 1\n",
    "HIS-N: 2\n",
    "HIS-ND1: 6\n",
    "HIS-NE2: 6\n",
    "HIS-O: 4\n",
    "HSC-C: 4\n",
    "HSC-CA: 1\n",
    "HSC-CB: 1\n",
    "HSC-CD2: 1\n",
    "HSC-CE1: 1\n",
    "HSC-CG: 1\n",
    "HSC-N: 2\n",
    "HSC-ND1: 6\n",
    "HSC-NE2: 6\n",
    "HSC-O: 4\n",
    "ILE-1HD1: 1\n",
    "ILE-1HG2: 1\n",
    "ILE-2HD1: 1\n",
    "ILE-2HG1: 1\n",
    "ILE-2HG2: 1\n",
    "ILE-3HD1: 1\n",
    "ILE-3HG1: 1\n",
    "ILE-3HG2: 1\n",
    "ILE-C: 4\n",
    "ILE-CA: 1\n",
    "ILE-CB: 1\n",
    "ILE-CD1: 1\n",
    "ILE-CG1: 1\n",
    "ILE-CG2: 1\n",
    "ILE-H: 2\n",
    "ILE-HA: 1\n",
    "ILE-HB: 1\n",
    "ILE-N: 2\n",
    "ILE-O: 4\n",
    "LEU-1HD1: 1\n",
    "LEU-1HD2: 1\n",
    "LEU-2HB: 1\n",
    "LEU-2HD1: 1\n",
    "LEU-2HD2: 1\n",
    "LEU-3HB: 1\n",
    "LEU-3HD1: 1\n",
    "LEU-3HD2: 1\n",
    "LEU-C: 4\n",
    "LEU-CA: 1\n",
    "LEU-CB: 1\n",
    "LEU-CD1: 1\n",
    "LEU-CD2: 1\n",
    "LEU-CG: 1\n",
    "LEU-H: 2\n",
    "LEU-HA: 1\n",
    "LEU-HB2: 1\n",
    "LEU-HB3: 1\n",
    "LEU-HG: 1\n",
    "LEU-N: 2\n",
    "LEU-O: 4\n",
    "LYS-1HZ: 3\n",
    "LYS-2HB: 1\n",
    "LYS-2HD: 1\n",
    "LYS-2HE: 1\n",
    "LYS-2HG: 1\n",
    "LYS-2HZ: 3\n",
    "LYS-3HB: 1\n",
    "LYS-3HD: 1\n",
    "LYS-3HE: 1\n",
    "LYS-3HG: 1\n",
    "LYS-3HZ: 3\n",
    "LYS-C: 4\n",
    "LYS-CA: 1\n",
    "LYS-CB: 1\n",
    "LYS-CD: 1\n",
    "LYS-CE: 1\n",
    "LYS-CG: 1\n",
    "LYS-H: 2\n",
    "LYS-HA: 1\n",
    "LYS-HB2: 1\n",
    "LYS-HB3: 1\n",
    "LYS-HD2: 1\n",
    "LYS-HD3: 1\n",
    "LYS-HE2: 1\n",
    "LYS-HE3: 1\n",
    "LYS-HG2: 1\n",
    "LYS-HG3: 1\n",
    "LYS-HZ1: 3\n",
    "LYS-HZ2: 3\n",
    "LYS-HZ3: 3\n",
    "LYS-N: 2\n",
    "LYS-NZ: 3\n",
    "LYS-O: 4\n",
    "MET-1HE: 1\n",
    "MET-2HB: 1\n",
    "MET-2HE: 1\n",
    "MET-2HG: 1\n",
    "MET-3HB: 1\n",
    "MET-3HE: 1\n",
    "MET-3HG: 1\n",
    "MET-C: 4\n",
    "MET-CA: 1\n",
    "MET-CB: 1\n",
    "MET-CE: 1\n",
    "MET-CG: 1\n",
    "MET-H: 2\n",
    "MET-HA: 1\n",
    "MET-HB2: 1\n",
    "MET-HB3: 1\n",
    "MET-HE1: 1\n",
    "MET-HE2: 1\n",
    "MET-HE3: 1\n",
    "MET-HG2: 1\n",
    "MET-HG3: 1\n",
    "MET-N: 2\n",
    "MET-O: 4\n",
    "MET-SD: 1\n",
    "PHE-2HB: 1\n",
    "PHE-3HB: 1\n",
    "PHE-C: 4\n",
    "PHE-CA: 1\n",
    "PHE-CB: 1\n",
    "PHE-CD1: 1\n",
    "PHE-CD2: 1\n",
    "PHE-CE1: 1\n",
    "PHE-CE2: 1\n",
    "PHE-CG: 1\n",
    "PHE-CZ: 1\n",
    "PHE-H: 2\n",
    "PHE-HA: 1\n",
    "PHE-HB2: 1\n",
    "PHE-HB3: 1\n",
    "PHE-HD1: 1\n",
    "PHE-HD2: 1\n",
    "PHE-HE1: 1\n",
    "PHE-HE2: 1\n",
    "PHE-HZ: 1\n",
    "PHE-N: 2\n",
    "PHE-O: 4\n",
    "PRO-2HB: 1\n",
    "PRO-2HD: 1\n",
    "PRO-2HG: 1\n",
    "PRO-3HB: 1\n",
    "PRO-3HD: 1\n",
    "PRO-3HG: 1\n",
    "PRO-C: 4\n",
    "PRO-CA: 1\n",
    "PRO-CB: 1\n",
    "PRO-CD: 1\n",
    "PRO-CG: 1\n",
    "PRO-HA: 1\n",
    "PRO-HB2: 1\n",
    "PRO-HB3: 1\n",
    "PRO-HD2: 1\n",
    "PRO-HD3: 1\n",
    "PRO-HG2: 1\n",
    "PRO-HG3: 1\n",
    "PRO-N: 2\n",
    "PRO-O: 4\n",
    "SER-2HB: 1\n",
    "SER-3HB: 1\n",
    "SER-C: 4\n",
    "SER-CA: 1\n",
    "SER-CB: 1\n",
    "SER-H: 2\n",
    "SER-HA: 1\n",
    "SER-HB2: 1\n",
    "SER-HB3: 1\n",
    "SER-HG: 6\n",
    "SER-N: 2\n",
    "SER-O: 4\n",
    "SER-OG: 6\n",
    "THR-1HG: 6\n",
    "THR-1HG2: 1\n",
    "THR-2HG2: 1\n",
    "THR-3HG2: 1\n",
    "THR-C: 4\n",
    "THR-CA: 1\n",
    "THR-CB: 1\n",
    "THR-CG2: 1\n",
    "THR-H: 2\n",
    "THR-HA: 1\n",
    "THR-HB: 1\n",
    "THR-HG1: 6\n",
    "THR-N: 2\n",
    "THR-O: 4\n",
    "THR-OG1: 6\n",
    "TRP-2HB: 1\n",
    "TRP-3HB: 1\n",
    "TRP-C: 4\n",
    "TRP-CA: 1\n",
    "TRP-CB: 1\n",
    "TRP-CD1: 1\n",
    "TRP-CD2: 1\n",
    "TRP-CE2: 1\n",
    "TRP-CE3: 1\n",
    "TRP-CG: 1\n",
    "TRP-CH2: 1\n",
    "TRP-CZ2: 1\n",
    "TRP-CZ3: 1\n",
    "TRP-H: 2\n",
    "TRP-HA: 1\n",
    "TRP-HB2: 1\n",
    "TRP-HB3: 1\n",
    "TRP-HD1: 1\n",
    "TRP-HE1: 1\n",
    "TRP-HE3: 1\n",
    "TRP-HH2: 1\n",
    "TRP-HZ2: 1\n",
    "TRP-HZ3: 1\n",
    "TRP-N: 2\n",
    "#TRP-NE1: 1\n",
    "TRP-NE1: 2\n",
    "TRP-O: 4\n",
    "TYR-2HB: 1\n",
    "TYR-3HB: 1\n",
    "TYR-C: 4\n",
    "TYR-CA: 1\n",
    "TYR-CB: 1\n",
    "TYR-CD1: 1\n",
    "TYR-CD2: 1\n",
    "TYR-CE1: 1\n",
    "TYR-CE2: 1\n",
    "TYR-CG: 1\n",
    "TYR-CZ: 1\n",
    "TYR-H: 2\n",
    "TYR-HA: 1\n",
    "TYR-HB2: 1\n",
    "TYR-HB3: 1\n",
    "TYR-HD1: 1\n",
    "TYR-HD2: 1\n",
    "TYR-HE1: 1\n",
    "TYR-HE2: 1\n",
    "TYR-HH: 6\n",
    "TYR-N: 2\n",
    "TYR-O: 4\n",
    "TYR-OH: 6\n",
    "VAL-1HG1: 1\n",
    "VAL-1HG2: 1\n",
    "VAL-2HG1: 1\n",
    "VAL-2HG2: 1\n",
    "VAL-3HG1: 1\n",
    "VAL-3HG2: 1\n",
    "VAL-C: 4\n",
    "VAL-CA: 1\n",
    "VAL-CB: 1\n",
    "VAL-CG1: 1\n",
    "VAL-CG2: 1\n",
    "VAL-H: 2\n",
    "VAL-HA: 1\n",
    "VAL-HB: 1\n",
    "VAL-N: 2\n",
    "VAL-O: 4\n",
    "WAT-O: 6\n",
    "WAT-H1: 6\n",
    "WAT-H2: 6\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "num2type = { '1': 'Apolar',\n",
    "             '2': 'Polar Donor',\n",
    "             '3': 'Polar Donnor, Ionic Positive',\n",
    "             '4': 'Polar Acceptor',\n",
    "             '5': 'Polar Acceptor, Ionic Negative',\n",
    "             '6': 'Polar Mixt',\n",
    "            }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# want atom groups: apolar, polorDonor, etc.\n",
    "types = { num2type[n]: [] for n in num2type }\n",
    "\n",
    "for a in assignments.split('\\n'):\n",
    "    spec, n = a.split(': ')\n",
    "    res, at = spec.split('-')\n",
    "    types[num2type[n]].append((res, at))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Apolar': [('ALA', '1HB'),\n",
       "  ('ALA', '2HB'),\n",
       "  ('ALA', '3HB'),\n",
       "  ('ALA', 'CA'),\n",
       "  ('ALA', 'CB'),\n",
       "  ('ALA', 'HA'),\n",
       "  ('ALA', 'HB1'),\n",
       "  ('ALA', 'HB2'),\n",
       "  ('ALA', 'HB3'),\n",
       "  ('ARG', '2HB'),\n",
       "  ('ARG', '2HD'),\n",
       "  ('ARG', '2HG'),\n",
       "  ('ARG', '3HB'),\n",
       "  ('ARG', '3HD'),\n",
       "  ('ARG', '3HG'),\n",
       "  ('ARG', 'CA'),\n",
       "  ('ARG', 'CB'),\n",
       "  ('ARG', 'CD'),\n",
       "  ('ARG', 'CG'),\n",
       "  ('ARG', 'HA'),\n",
       "  ('ARG', 'HB2'),\n",
       "  ('ARG', 'HB3'),\n",
       "  ('ARG', 'HD2'),\n",
       "  ('ARG', 'HD3'),\n",
       "  ('ARG', 'HG2'),\n",
       "  ('ARG', 'HG3'),\n",
       "  ('ASN', '2HB'),\n",
       "  ('ASN', '3HB'),\n",
       "  ('ASN', 'CA'),\n",
       "  ('ASN', 'CB'),\n",
       "  ('ASN', 'HA'),\n",
       "  ('ASN', 'HB2'),\n",
       "  ('ASN', 'HB3'),\n",
       "  ('ASP', '2HB'),\n",
       "  ('ASP', '3HB'),\n",
       "  ('ASP', 'CA'),\n",
       "  ('ASP', 'CB'),\n",
       "  ('ASP', 'HA'),\n",
       "  ('ASP', 'HB2'),\n",
       "  ('ASP', 'HB3'),\n",
       "  ('CYS', '2HB'),\n",
       "  ('CYS', '3HB'),\n",
       "  ('CYS', 'CA'),\n",
       "  ('CYS', 'CB'),\n",
       "  ('CYS', 'HA'),\n",
       "  ('CYS', 'HB2'),\n",
       "  ('CYS', 'HB3'),\n",
       "  ('CYX', '2HB'),\n",
       "  ('CYX', '3HB'),\n",
       "  ('CYX', 'CA'),\n",
       "  ('CYX', 'CB'),\n",
       "  ('CYX', 'HA'),\n",
       "  ('CYX', 'HB2'),\n",
       "  ('CYX', 'HB3'),\n",
       "  ('CYX', 'SG'),\n",
       "  ('GLN', '2HB'),\n",
       "  ('GLN', '2HG'),\n",
       "  ('GLN', '3HB'),\n",
       "  ('GLN', '3HG'),\n",
       "  ('GLN', 'CA'),\n",
       "  ('GLN', 'CB'),\n",
       "  ('GLN', 'CG'),\n",
       "  ('GLN', 'HA'),\n",
       "  ('GLN', 'HB2'),\n",
       "  ('GLN', 'HB3'),\n",
       "  ('GLU', '2HB'),\n",
       "  ('GLU', '2HG'),\n",
       "  ('GLU', '3HB'),\n",
       "  ('GLU', '3HG'),\n",
       "  ('GLU', 'CA'),\n",
       "  ('GLU', 'CB'),\n",
       "  ('GLU', 'CG'),\n",
       "  ('GLU', 'HA'),\n",
       "  ('GLU', 'HB2'),\n",
       "  ('GLU', 'HB3'),\n",
       "  ('GLU', 'HG2'),\n",
       "  ('GLU', 'HG3'),\n",
       "  ('GLY', '2HA'),\n",
       "  ('GLY', '3HA'),\n",
       "  ('GLY', 'CA'),\n",
       "  ('GLY', 'HA2'),\n",
       "  ('GLY', 'HA3'),\n",
       "  ('HID', '2HB'),\n",
       "  ('HID', '3HB'),\n",
       "  ('HID', 'CA'),\n",
       "  ('HID', 'CB'),\n",
       "  ('HID', 'CD2'),\n",
       "  ('HID', 'CE1'),\n",
       "  ('HID', 'CG'),\n",
       "  ('HID', 'HA'),\n",
       "  ('HID', 'HB2'),\n",
       "  ('HID', 'HB3'),\n",
       "  ('HID', 'HD1'),\n",
       "  ('HID', 'HD2'),\n",
       "  ('HID', 'HE1'),\n",
       "  ('HIE', '2HB'),\n",
       "  ('HIE', '3HB'),\n",
       "  ('HIE', 'CA'),\n",
       "  ('HIE', 'CB'),\n",
       "  ('HIE', 'CD2'),\n",
       "  ('HIE', 'CE1'),\n",
       "  ('HIE', 'CG'),\n",
       "  ('HIE', 'HA'),\n",
       "  ('HIE', 'HB2'),\n",
       "  ('HIE', 'HB3'),\n",
       "  ('HIE', 'HD2'),\n",
       "  ('HIE', 'HE1'),\n",
       "  ('HIE', 'HE2'),\n",
       "  ('HIP', '2HB'),\n",
       "  ('HIP', '3HB'),\n",
       "  ('HIP', 'CA'),\n",
       "  ('HIP', 'CB'),\n",
       "  ('HIP', 'HA'),\n",
       "  ('HIP', 'HB2'),\n",
       "  ('HIP', 'HB3'),\n",
       "  ('HIS', 'CA'),\n",
       "  ('HIS', 'CB'),\n",
       "  ('HIS', 'CD2'),\n",
       "  ('HIS', 'CE1'),\n",
       "  ('HIS', 'CG'),\n",
       "  ('HSC', 'CA'),\n",
       "  ('HSC', 'CB'),\n",
       "  ('HSC', 'CD2'),\n",
       "  ('HSC', 'CE1'),\n",
       "  ('HSC', 'CG'),\n",
       "  ('ILE', '1HD1'),\n",
       "  ('ILE', '1HG2'),\n",
       "  ('ILE', '2HD1'),\n",
       "  ('ILE', '2HG1'),\n",
       "  ('ILE', '2HG2'),\n",
       "  ('ILE', '3HD1'),\n",
       "  ('ILE', '3HG1'),\n",
       "  ('ILE', '3HG2'),\n",
       "  ('ILE', 'CA'),\n",
       "  ('ILE', 'CB'),\n",
       "  ('ILE', 'CD1'),\n",
       "  ('ILE', 'CG1'),\n",
       "  ('ILE', 'CG2'),\n",
       "  ('ILE', 'HA'),\n",
       "  ('ILE', 'HB'),\n",
       "  ('LEU', '1HD1'),\n",
       "  ('LEU', '1HD2'),\n",
       "  ('LEU', '2HB'),\n",
       "  ('LEU', '2HD1'),\n",
       "  ('LEU', '2HD2'),\n",
       "  ('LEU', '3HB'),\n",
       "  ('LEU', '3HD1'),\n",
       "  ('LEU', '3HD2'),\n",
       "  ('LEU', 'CA'),\n",
       "  ('LEU', 'CB'),\n",
       "  ('LEU', 'CD1'),\n",
       "  ('LEU', 'CD2'),\n",
       "  ('LEU', 'CG'),\n",
       "  ('LEU', 'HA'),\n",
       "  ('LEU', 'HB2'),\n",
       "  ('LEU', 'HB3'),\n",
       "  ('LEU', 'HG'),\n",
       "  ('LYS', '2HB'),\n",
       "  ('LYS', '2HD'),\n",
       "  ('LYS', '2HE'),\n",
       "  ('LYS', '2HG'),\n",
       "  ('LYS', '3HB'),\n",
       "  ('LYS', '3HD'),\n",
       "  ('LYS', '3HE'),\n",
       "  ('LYS', '3HG'),\n",
       "  ('LYS', 'CA'),\n",
       "  ('LYS', 'CB'),\n",
       "  ('LYS', 'CD'),\n",
       "  ('LYS', 'CE'),\n",
       "  ('LYS', 'CG'),\n",
       "  ('LYS', 'HA'),\n",
       "  ('LYS', 'HB2'),\n",
       "  ('LYS', 'HB3'),\n",
       "  ('LYS', 'HD2'),\n",
       "  ('LYS', 'HD3'),\n",
       "  ('LYS', 'HE2'),\n",
       "  ('LYS', 'HE3'),\n",
       "  ('LYS', 'HG2'),\n",
       "  ('LYS', 'HG3'),\n",
       "  ('MET', '1HE'),\n",
       "  ('MET', '2HB'),\n",
       "  ('MET', '2HE'),\n",
       "  ('MET', '2HG'),\n",
       "  ('MET', '3HB'),\n",
       "  ('MET', '3HE'),\n",
       "  ('MET', '3HG'),\n",
       "  ('MET', 'CA'),\n",
       "  ('MET', 'CB'),\n",
       "  ('MET', 'CE'),\n",
       "  ('MET', 'CG'),\n",
       "  ('MET', 'HA'),\n",
       "  ('MET', 'HB2'),\n",
       "  ('MET', 'HB3'),\n",
       "  ('MET', 'HE1'),\n",
       "  ('MET', 'HE2'),\n",
       "  ('MET', 'HE3'),\n",
       "  ('MET', 'HG2'),\n",
       "  ('MET', 'HG3'),\n",
       "  ('MET', 'SD'),\n",
       "  ('PHE', '2HB'),\n",
       "  ('PHE', '3HB'),\n",
       "  ('PHE', 'CA'),\n",
       "  ('PHE', 'CB'),\n",
       "  ('PHE', 'CD1'),\n",
       "  ('PHE', 'CD2'),\n",
       "  ('PHE', 'CE1'),\n",
       "  ('PHE', 'CE2'),\n",
       "  ('PHE', 'CG'),\n",
       "  ('PHE', 'CZ'),\n",
       "  ('PHE', 'HA'),\n",
       "  ('PHE', 'HB2'),\n",
       "  ('PHE', 'HB3'),\n",
       "  ('PHE', 'HD1'),\n",
       "  ('PHE', 'HD2'),\n",
       "  ('PHE', 'HE1'),\n",
       "  ('PHE', 'HE2'),\n",
       "  ('PHE', 'HZ'),\n",
       "  ('PRO', '2HB'),\n",
       "  ('PRO', '2HD'),\n",
       "  ('PRO', '2HG'),\n",
       "  ('PRO', '3HB'),\n",
       "  ('PRO', '3HD'),\n",
       "  ('PRO', '3HG'),\n",
       "  ('PRO', 'CA'),\n",
       "  ('PRO', 'CB'),\n",
       "  ('PRO', 'CD'),\n",
       "  ('PRO', 'CG'),\n",
       "  ('PRO', 'HA'),\n",
       "  ('PRO', 'HB2'),\n",
       "  ('PRO', 'HB3'),\n",
       "  ('PRO', 'HD2'),\n",
       "  ('PRO', 'HD3'),\n",
       "  ('PRO', 'HG2'),\n",
       "  ('PRO', 'HG3'),\n",
       "  ('SER', '2HB'),\n",
       "  ('SER', '3HB'),\n",
       "  ('SER', 'CA'),\n",
       "  ('SER', 'CB'),\n",
       "  ('SER', 'HA'),\n",
       "  ('SER', 'HB2'),\n",
       "  ('SER', 'HB3'),\n",
       "  ('THR', '1HG2'),\n",
       "  ('THR', '2HG2'),\n",
       "  ('THR', '3HG2'),\n",
       "  ('THR', 'CA'),\n",
       "  ('THR', 'CB'),\n",
       "  ('THR', 'CG2'),\n",
       "  ('THR', 'HA'),\n",
       "  ('THR', 'HB'),\n",
       "  ('TRP', '2HB'),\n",
       "  ('TRP', '3HB'),\n",
       "  ('TRP', 'CA'),\n",
       "  ('TRP', 'CB'),\n",
       "  ('TRP', 'CD1'),\n",
       "  ('TRP', 'CD2'),\n",
       "  ('TRP', 'CE2'),\n",
       "  ('TRP', 'CE3'),\n",
       "  ('TRP', 'CG'),\n",
       "  ('TRP', 'CH2'),\n",
       "  ('TRP', 'CZ2'),\n",
       "  ('TRP', 'CZ3'),\n",
       "  ('TRP', 'HA'),\n",
       "  ('TRP', 'HB2'),\n",
       "  ('TRP', 'HB3'),\n",
       "  ('TRP', 'HD1'),\n",
       "  ('TRP', 'HE1'),\n",
       "  ('TRP', 'HE3'),\n",
       "  ('TRP', 'HH2'),\n",
       "  ('TRP', 'HZ2'),\n",
       "  ('TRP', 'HZ3'),\n",
       "  ('#TRP', 'NE1'),\n",
       "  ('TYR', '2HB'),\n",
       "  ('TYR', '3HB'),\n",
       "  ('TYR', 'CA'),\n",
       "  ('TYR', 'CB'),\n",
       "  ('TYR', 'CD1'),\n",
       "  ('TYR', 'CD2'),\n",
       "  ('TYR', 'CE1'),\n",
       "  ('TYR', 'CE2'),\n",
       "  ('TYR', 'CG'),\n",
       "  ('TYR', 'CZ'),\n",
       "  ('TYR', 'HA'),\n",
       "  ('TYR', 'HB2'),\n",
       "  ('TYR', 'HB3'),\n",
       "  ('TYR', 'HD1'),\n",
       "  ('TYR', 'HD2'),\n",
       "  ('TYR', 'HE1'),\n",
       "  ('TYR', 'HE2'),\n",
       "  ('VAL', '1HG1'),\n",
       "  ('VAL', '1HG2'),\n",
       "  ('VAL', '2HG1'),\n",
       "  ('VAL', '2HG2'),\n",
       "  ('VAL', '3HG1'),\n",
       "  ('VAL', '3HG2'),\n",
       "  ('VAL', 'CA'),\n",
       "  ('VAL', 'CB'),\n",
       "  ('VAL', 'CG1'),\n",
       "  ('VAL', 'CG2'),\n",
       "  ('VAL', 'HA'),\n",
       "  ('VAL', 'HB')],\n",
       " 'Polar Acceptor': [('ALA', 'C'),\n",
       "  ('ALA', 'O'),\n",
       "  ('ARG', 'C'),\n",
       "  ('ARG', 'O'),\n",
       "  ('ASN', 'C'),\n",
       "  ('ASN', 'CG'),\n",
       "  ('ASN', 'O'),\n",
       "  ('ASN', 'OD1'),\n",
       "  ('ASP', 'C'),\n",
       "  ('ASP', 'O'),\n",
       "  ('CYS', 'C'),\n",
       "  ('CYS', 'O'),\n",
       "  ('CYX', 'C'),\n",
       "  ('CYX', 'O'),\n",
       "  ('GLN', 'C'),\n",
       "  ('GLN', 'CD'),\n",
       "  ('GLN', 'O'),\n",
       "  ('GLN', 'OE1'),\n",
       "  ('GLU', 'C'),\n",
       "  ('GLU', 'O'),\n",
       "  ('GLY', 'C'),\n",
       "  ('GLY', 'O'),\n",
       "  ('HID', 'C'),\n",
       "  ('HID', 'O'),\n",
       "  ('HIE', 'C'),\n",
       "  ('HIE', 'O'),\n",
       "  ('HIP', 'C'),\n",
       "  ('HIP', 'O'),\n",
       "  ('HIS', 'C'),\n",
       "  ('HIS', 'O'),\n",
       "  ('HSC', 'C'),\n",
       "  ('HSC', 'O'),\n",
       "  ('ILE', 'C'),\n",
       "  ('ILE', 'O'),\n",
       "  ('LEU', 'C'),\n",
       "  ('LEU', 'O'),\n",
       "  ('LYS', 'C'),\n",
       "  ('LYS', 'O'),\n",
       "  ('MET', 'C'),\n",
       "  ('MET', 'O'),\n",
       "  ('PHE', 'C'),\n",
       "  ('PHE', 'O'),\n",
       "  ('PRO', 'C'),\n",
       "  ('PRO', 'O'),\n",
       "  ('SER', 'C'),\n",
       "  ('SER', 'O'),\n",
       "  ('THR', 'C'),\n",
       "  ('THR', 'O'),\n",
       "  ('TRP', 'C'),\n",
       "  ('TRP', 'O'),\n",
       "  ('TYR', 'C'),\n",
       "  ('TYR', 'O'),\n",
       "  ('VAL', 'C'),\n",
       "  ('VAL', 'O')],\n",
       " 'Polar Acceptor, Ionic Negative': [('ASP', 'CG'),\n",
       "  ('ASP', 'OD1'),\n",
       "  ('ASP', 'OD2'),\n",
       "  ('TER', 'OXT'),\n",
       "  ('GLU', 'CD'),\n",
       "  ('GLU', 'OE1'),\n",
       "  ('GLU', 'OE2')],\n",
       " 'Polar Donnor, Ionic Positive': [('ARG', '1HH1'),\n",
       "  ('ARG', '1HH2'),\n",
       "  ('ARG', '2HH1'),\n",
       "  ('ARG', '2HH2'),\n",
       "  ('ARG', 'CZ'),\n",
       "  ('ARG', 'HE'),\n",
       "  ('ARG', 'NE'),\n",
       "  ('ARG', 'NH1'),\n",
       "  ('ARG', 'NH2'),\n",
       "  ('TER', 'H1'),\n",
       "  ('TER', 'H2'),\n",
       "  ('TER', 'H3'),\n",
       "  ('LYS', '1HZ'),\n",
       "  ('LYS', '2HZ'),\n",
       "  ('LYS', '3HZ'),\n",
       "  ('LYS', 'HZ1'),\n",
       "  ('LYS', 'HZ2'),\n",
       "  ('LYS', 'HZ3'),\n",
       "  ('LYS', 'NZ')],\n",
       " 'Polar Donor': [('ALA', 'H'),\n",
       "  ('ALA', 'N'),\n",
       "  ('ARG', 'H'),\n",
       "  ('ARG', 'N'),\n",
       "  ('ASN', '1HD2'),\n",
       "  ('ASN', '2HD2'),\n",
       "  ('ASN', 'H'),\n",
       "  ('ASN', 'N'),\n",
       "  ('ASN', 'ND2'),\n",
       "  ('ASP', 'H'),\n",
       "  ('ASP', 'N'),\n",
       "  ('CYS', 'H'),\n",
       "  ('CYS', 'N'),\n",
       "  ('CYX', 'H'),\n",
       "  ('CYX', 'N'),\n",
       "  ('GLN', '1HE2'),\n",
       "  ('GLN', '2HE2'),\n",
       "  ('GLN', 'H'),\n",
       "  ('GLN', 'N'),\n",
       "  ('GLN', 'NE2'),\n",
       "  ('GLU', 'H'),\n",
       "  ('GLU', 'N'),\n",
       "  ('GLY', 'H'),\n",
       "  ('GLY', 'N'),\n",
       "  ('HID', 'H'),\n",
       "  ('HID', 'N'),\n",
       "  ('HIE', 'H'),\n",
       "  ('HIE', 'N'),\n",
       "  ('HIP', 'H'),\n",
       "  ('HIP', 'N'),\n",
       "  ('HIS', 'N'),\n",
       "  ('HSC', 'N'),\n",
       "  ('ILE', 'H'),\n",
       "  ('ILE', 'N'),\n",
       "  ('LEU', 'H'),\n",
       "  ('LEU', 'N'),\n",
       "  ('LYS', 'H'),\n",
       "  ('LYS', 'N'),\n",
       "  ('MET', 'H'),\n",
       "  ('MET', 'N'),\n",
       "  ('PHE', 'H'),\n",
       "  ('PHE', 'N'),\n",
       "  ('PRO', 'N'),\n",
       "  ('SER', 'H'),\n",
       "  ('SER', 'N'),\n",
       "  ('THR', 'H'),\n",
       "  ('THR', 'N'),\n",
       "  ('TRP', 'H'),\n",
       "  ('TRP', 'N'),\n",
       "  ('TRP', 'NE1'),\n",
       "  ('TYR', 'H'),\n",
       "  ('TYR', 'N'),\n",
       "  ('VAL', 'H'),\n",
       "  ('VAL', 'N')],\n",
       " 'Polar Mixt': [('CYS', 'HG'),\n",
       "  ('CYS', 'SG'),\n",
       "  ('HID', 'ND1'),\n",
       "  ('HID', 'NE2'),\n",
       "  ('HIE', 'ND1'),\n",
       "  ('HIE', 'NE2'),\n",
       "  ('HIP', 'CD2'),\n",
       "  ('HIP', 'CE1'),\n",
       "  ('HIP', 'CG'),\n",
       "  ('HIP', 'HD1'),\n",
       "  ('HIP', 'HD2'),\n",
       "  ('HIP', 'HE1'),\n",
       "  ('HIP', 'HE2'),\n",
       "  ('HIP', 'ND1'),\n",
       "  ('HIP', 'NE2'),\n",
       "  ('HIS', 'ND1'),\n",
       "  ('HIS', 'NE2'),\n",
       "  ('HSC', 'ND1'),\n",
       "  ('HSC', 'NE2'),\n",
       "  ('SER', 'HG'),\n",
       "  ('SER', 'OG'),\n",
       "  ('THR', '1HG'),\n",
       "  ('THR', 'HG1'),\n",
       "  ('THR', 'OG1'),\n",
       "  ('TYR', 'HH'),\n",
       "  ('TYR', 'OH'),\n",
       "  ('WAT', 'O'),\n",
       "  ('WAT', 'H1'),\n",
       "  ('WAT', 'H2')]}"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "with open('types.json','w') as fh:\n",
    "    json.dump(types, fh)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pdbchecker, json"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Check it out!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "u = pdbchecker.get_PDB_universe('1aki')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AtomGroup with 449 atoms>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pdbchecker.get_apolar(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pdbchecker.get_polar_acceptor(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pdbchecker.get_polar_acceptor_ionic_negative(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pdbchecker.get_polar_donor(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pdbchecker.get_polar_donor_ionic_positive(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AtomGroup with 292 atoms>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pdbchecker.get_polar_mixt(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import subprocess\n",
    "import MDAnalysis as mda\n",
    "\n",
    "code = '1914'  # example with gaps\n",
    "\n",
    "# Get PDB file by code\n",
    "p = subprocess.Popen(('./getpdb.sh', code))\n",
    "p.communicate()\n",
    "p = subprocess.Popen(('gunzip',  'pdb'+code+'.ent.gz'))\n",
    "p.communicate()\n",
    "p = subprocess.Popen(('mv', 'pdb'+code+'.ent', 'pdb'+code+'.pdb'))\n",
    "p.communicate()\n",
    "u = mda.Universe('pdb'+code+'.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pdbchecker"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Residue Gap between residues: 2034 2047 19.1994\n",
      "Residue Gap between residues: 2097 3001 14.0736\n",
      "Residue Gap between residues: 3008 4004 13.8024\n"
     ]
    }
   ],
   "source": [
    "pdbchecker.get_gaps(u)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "language_info": {
   "codemirror_mode": {
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   "file_extension": ".py",
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