BloodHIV1.0.json

{
 "recipe":{
  "paths":[
   [
    "autoPACKserver",
    "https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0"
   ]
  ],
  "version":"1.0",
  "name":"BloodHIV"
 },
 "options":{
  "cancelDialog":false,
  "_hackFreepts":false,
  "windowsSize":50,
  "use_gradient":true,
  "placeMethod":"pandaBullet",
  "saveResult":false,
  "runTimeDisplay":false,
  "overwritePlaceMethod":true,
  "innerGridMethod":"jordan3",
  "boundingBox":[
   [
    -800,
    -1272,
    -1734
   ],
   [
    881.659,
    1272,
    1734
   ]
  ],
  "gradients":[
   "gradRadSPIKE",
   "gradRadMA"
  ],
  "smallestProteinSize":50,
  "computeGridParams":true,
  "freePtsUpdateThrehod":0.15,
  "pickWeightedIngr":true,
  "_timer":false,
  "ingrLookForNeighbours":false,
  "pickRandPt":true,
  "largestProteinSize":47.92,
  "resultfile":"/opt/data/dev/cellPACK/cellPACK_data/cellPACK_database_1.1.0/results/HIV-1_0.1.6_3.apr.json",
  "use_periodicity":false,
  "EnviroOnly":false
 },
 "gradients":{
  "gradRadSPIKE":{
   "direction":[
    -480,
    -480,
    0
   ],
   "radius":1380,
   "description":"",
   "weight_mode":"linear",
   "pick_mode":"rnd",
   "gblob":4,
   "mode":"radial"
  },
  "gradRadMA":{
   "direction":[
    480,
    480,
    0
   ],
   "radius":1380,
   "description":"",
   "weight_mode":"linear",
   "pick_mode":"rnd",
   "gblob":4,
   "mode":"radial"
  }
 },
"cytoplasme":{
  "ingredients":{
   "Heparin":{
    "include":"Heparin.json",
    "name":"Heparin"
   },
   "Fibrinogen":{
    "include":"Fibrinogen.json",
    "name":"Fibrinogen"
   },
   "dLDL":{
    "include":"dLDL.json",
    "name":"dLDL"
   },
   "AntiTrypsin":{
    "include":"AntiTrypsin.json",
    "name":"AntiTrypsin"
   },
   "plv_Polio":{
    "include":"plv_Polio.json",
    "name":"plv_Polio"
   },
   "Hemoglobin":{
    "include":"Hemoglobin.json",
    "name":"Hemoglobin"
   },
   "i2tsc_63kD":{
    "include":"i2tsc_63kD.json",
    "name":"i2tsc_63kD"
   },
   "IgG_Antibody_1mer":{
    "include":"IgG_Antibody_1mer.json",
    "name":"IgG_Antibody_1mer"
   },
   "snake":{
    "include":"snake.json",
    "name":"snake"
   },
   "i1ysx_23kD":{
    "include":"i1ysx_23kD.json",
    "name":"i1ysx_23kD"
   },
   "SerumAlbumin":{
    "include":"SerumAlbumin.json",
    "name":"SerumAlbumin"
   },
   "Ceruloplasmin":{
    "include":"Ceruloplasmin.json",
    "name":"Ceruloplasmin"
   },
   "iLDL":{
    "include":"iLDL.json",
    "name":"iLDL"
   },
   "iIgA_Antibody_2mer":{
    "include":"iIgA_Antibody_2mer.json",
    "name":"iIgA_Antibody_2mer"
   },
   "Insulin":{
    "include":"Insulin.json",
    "name":"Insulin"
   },

   "FactorH1":{
    "include":"FactorH1.json",
    "name":"FactorH1"
   },
   "Transferrin":{
    "include":"Transferrin.json",
    "name":"Transferrin"
   },
   "i1smd_56kD":{
    "include":"i1smd_56kD.json",
    "name":"i1smd_56kD"
   },
   "i7aat_91kD":{
    "include":"i7aat_91kD.json",
    "name":"i7aat_91kD"
   },
   "iIgM_Antibody_5mer":{
    "include":"iIgM_Antibody_5mer.json",
    "name":"iIgM_Antibody_5mer"
   }
  }
}, 
 "compartments":{
  "HIV1_envelope_Pack_145_0_2_0":{
   "geom":"autoPACKserver/geometries/HIV1_envelope_Pack_145_0_2_0.dae",
   "name":"HIV1_envelope_Pack_145_0_2_0",
   "rep":"HIV1_envelope_Rep_145_0_2_0",
   "rep_file":"autoPACKserver/geometries/HIV1_envelope_Rep_145_0_2_0",
   "surface":{
    "ingredients":{
     "HIV1_MA_Hyb_0_1_0":{
      "include":"HIV1_MA_Hyb_0_1_1.json",
      "name":"HIV1_MA_Hyb_0_1_0"
     },
     "HIV1_ENV_4nco_0_1_1":{
      "include":"HIV1_ENV_4nco_0_1_4.json",
      "name":"HIV1_ENV_4nco_0_1_1"
     },
     "HIV1_NEF_Hyb_0_2_0":{
      "include":"HIV1_NEF_Hyb_0_2_1.json",
      "name":"HIV1_NEF_Hyb_0_2_0"
     },
     "HIV1_HLA_1dlh_0_1_0":{
      "include":"HIV1_HLA_1dlh_0_1_1.json",
      "name":"HIV1_HLA_1dlh_0_1_0"
     },
     "HIV1_VPU_Hyb_0_1_0":{
      "include":"HIV1_VPU_Hyb_0_1_1.json",
      "name":"HIV1_VPU_Hyb_0_1_0"
     }
    }
   },
   "interior":{
    "ingredients":{
     "HIV1_PR_7hvp_0_1_0":{
      "include":"HIV1_PR_7hvp_0_1_1.json",
      "name":"HIV1_PR_7hvp_0_1_0"
     },
     "HIV1_SP1_hack_0_1_0":{
      "include":"HIV1_SP1_hack_0_1_1.json",
      "name":"HIV1_SP1_hack_0_1_0"
     },
     "HIV1_VIF_Modbase_0_1_0":{
      "include":"HIV1_VIF_Modbase_0_1_1.json",
      "name":"HIV1_VIF_Modbase_0_1_0"
     },
     "HIV1_VPR_1esx_0_1_0":{
      "include":"HIV1_VPR_1esx_0_1_1.json",
      "name":"HIV1_VPR_1esx_0_1_0"
     },
     "HIV1_P6_SwissMod_0_1_0":{
      "include":"HIV1_P6_SwissMod_0_1_1.json",
      "name":"HIV1_P6_SwissMod_0_1_0"
     },
     "HIV1_CAhexCyclophilA_0_1_0":{
      "include":"HIV1_CAhexCyclophilA_0_1_1.json",
      "name":"HIV1_CAhexCyclophilA_0_1_0"
     },
     "HIV1_NC_1f6u_0_1_0":{
      "include":"HIV1_NC_1f6u_0_1_1.json",
      "name":"HIV1_NC_1f6u_0_1_0"
     },
     "HIV1_CAhex_0_1_0":{
      "include":"HIV1_CAhex_0_1_1.json",
      "name":"HIV1_CAhex_0_1_0"
     },
     "HIV1_SP2_hack_0_1_0":{
      "include":"HIV1_SP2_hack_0_1_1.json",
      "name":"HIV1_SP2_hack_0_1_0"
     },
     "HIV1_RT_3hvt_0_1_0":{
      "include":"HIV1_RT_3hvt_0_1_1.json",
      "name":"HIV1_RT_3hvt_0_1_0"
     },
     "HIV1_NEFsol_Hyb_0_2_0":{
      "include":"HIV1_NEFsol_Hyb_0_2_1.json",
      "name":"HIV1_NEFsol_Hyb_0_2_0"
     },
     "HIV1_P6_VPR_0_1_0":{
      "include":"HIV1_P6_VPR_0_1_1.json",
      "name":"HIV1_P6_VPR_0_1_0"
     },
     "HIV1_NC_1a1t_0_1_0":{
      "include":"HIV1_NC_1a1t_0_1_1.json",
      "name":"HIV1_NC_1a1t_0_1_0"
     },
     "HIV1_CyclophilinA_1ak4_0_1_0":{
      "include":"HIV1_CyclophilinA_1ak4_0_1_1.json",
      "name":"HIV1_CyclophilinA_1ak4_0_1_0"
     },
     "HIV1_IN_1ex4_0_1_0":{
      "include":"HIV1_IN_1ex4_0_1_1.json",
      "name":"HIV1_IN_1ex4_0_1_0"
     }
    }
   }
  },
  "HIV1_capsid_3j3q_PackOuter_0_1_1":{
   "geom":"autoPACKserver/geometries/HIV1_capsid_3j3q_PackOuter_0_1_2.dae",
   "name":"HIV1_capsid_3j3q_PackOuter_0_1_1",
   "surface":{
    "ingredients":{
     "HIV1_CA_mono_0_1_0":{
      "include":"HIV1_CA_mono_0_1_0.json",
      "name":"HIV1_CA_mono_0_1_0"
     }
    }
   }
  },
  "HIV1_capsid_3j3q_PackInner_0_1_0":{
   "geom":"autoPACKserver/geometries/HIV1_capsid_3j3q_PackInner_0_1_1.dae",
   "name":"HIV1_capsid_3j3q_PackInner_0_1_0",
   "interior":{
    "ingredients":{
     "HIV1_RT_3hvt_0_1_0":{
      "include":"HIV1_RT_3hvt_0_1_1.json",
      "name":"HIV1_RT_3hvt_0_1_0"
     },
     "HIV1_NC_1a1t_0_1_0":{
      "include":"HIV1_NC_1a1t_0_1_1.json",
      "name":"HIV1_NC_1a1t_0_1_0"
     },
     "HIV1_NC_1f6u_0_1_0":{
      "include":"HIV1_NC_1f6u_0_1_1.json",
      "name":"HIV1_NC_1f6u_0_1_0"
     },
     "HIV1_TAT_1jfw_0_1_0":{
      "include":"HIV1_TAT_1jfw_0_1_1.json",
      "name":"HIV1_TAT_1jfw_0_1_0"
     },
     "HIV1_IN_1ex4_0_1_0":{
      "include":"HIV1_IN_1ex4_0_1_1.json",
      "name":"HIV1_IN_1ex4_0_1_0"
     }
    }
   }
  }
 }
}