# resultfile = "C:\Users\ludov\OneDrive\Documents\\backupC4DHiv\sphere139_random_127_tr.json"
n = "HIV_VLP"
h = Environment(name=n)
h.loadRecipe(setupfile)
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
fileName, fileExtension = os.path.splitext(setupfile)
rfile = h.resultfile
resultfilename = autopack.retrieveFile(rfile, cache="results")
if resultfilename is None:
print("no result for " + n + " " + h.version + " " + rfile)
sys.exit()
print("get the result file from ", resultfilename)
h.compartments[0].name = "HIVenvelop_140"
result, orgaresult, freePoint = h.loadResult(resultfilename=resultfilename)
# restore_grid=False,backward=True)#load text ?#this will restore the grid
ingredients = h.restore(result, orgaresult, freePoint)
#export the complete recipe as collada. each ingredient -> meshnode. Each instance->node instance
env = h
cxml = build_scene(
env,
"C:\Users\ludov\Google Drive\TSRI HIV Modeling\cellpack_models\HIV_VLP_140_214_random.dae"
)
#execfile("pathto/export_recipe_collada.py")
#I usually run this on with pmv,anaconda or mayapy
#execfile("/Users/ludo/DEV/git_upy/examples/export_collada.py")
#import upy
#helper = upy.getHelperClass()()
#helper.read("/Users/ludo/DEV/autopack_git/autoPACK_database_1.0.0/geometries/HIV1_capside_3j3q_Rep_Med_0_2_1.dae")
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
fileName, fileExtension = os.path.splitext(setupfile)
if export_json:
print("expot json recipe ", fileName)
h.saveRecipe(fileName + ".json", useXref=useXref, indent=True)
if check_result:
rfile = h.resultfile
resultfilename = autopack.retrieveFile(rfile, cache="results")
if resultfilename is None:
print("no result for " + n + " " + h.version + " " + rfile)
sys.exit()
print("get the result file from ", resultfilename)
result, orgaresult, freePoint = h.loadResult(
resultfilename=resultfilename, restore_grid=False,
backward=True) #load text ?#this will restore the grid
ingredients = h.restore(result, orgaresult, freePoint)
# print ("json ?",h.result_json)
# if export_json :
# fileName, fileExtension = os.path.splitext(resultfilename)
# h.store_asJson(n+"_result.json",indent=False)#fileName+"1.json",indent=False)
# print ("ok ",n+"_result.json",fileName+".json")
if mixedJson and export_json:
#special case for HIV
import json
import numpy
if HIV:
with open("/home/ludo/biomthiv.json",
'r') as fp: #doesnt work with symbol link ?
jsondic = json.load(fp) #,indent=4, separators=(',', ': ')
autopack.helper = helper from autopack.Environment import Environment filename = "/home/ludo/hivexp/BloodHIV1.0.json" #filename ="/home/ludo/hivexp/HIVimature1.0.json" fileName, fileExtension = os.path.splitext(filename) n = os.path.basename(fileName) h = Environment(name=n) #h.helper = helper recipe = n h.loadRecipe(filename) #previousresult = "/home/ludo/hivexp/BloodHIV1.0_mixed.json" #previousresult = "/home/ludo/hivexp/BloodHIV1.0_centered.json" previousresult = "/home/ludo/hivexp/BloodHIV1.0_mixed_tr.json" r = h.loadResult(previousresult, transpose=True) # ingredients = h.restore(*r) from autopack.lipids import lipidsCG #generate the membrane lcg = lipidsCG() comp = h.compartments[0] lcg.coverShape(comp.vertices, comp.vnormals) #remove lipids overlaping posrot = lcg.arrayOfBeads #save again with lipids ? #fix HIV1_CA_mono_0_1_0 #center is [405.609,1000.253,377.306] # if apply the center on all instance ? meanings rotate the center and apply it
# save a full recipe no Xref
#"nbMol": nbmol,
#"molarity" : ingr.molarity,
#"source": ingr.source,
#"positions":ingr.positions,
#"radii":ingr.radii}
rname = workingdir + "recipes\\BloodHIVMycoRB_full.1.0.json"
rname = workingdir + "recipes\\Mycoplasma1.7.json"
rname = workingdir + recipefile
#h.saveRecipe(rname,useXref=False,mixed=True,
# kwds=["source","name","nbMol","molarity","positions","radii"],result=True,
# grid=False,packing_options=False,indent=False,quaternion=True)
if resultfile != "":
r = h.loadResult(resultfile, transpose=transpose) #for c4d transpose
ingredients = h.restore(*r)
h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_1.json",
useXref=False,
mixed=True,
kwds=["source", "name"],
result=True,
transpose=True,
grid=False,
packing_options=False,
indent=False,
quaternion=True)
h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_2.json",
useXref=False,
mixed=True,
kwds=["source", "name"],
from autopack import transformation as tr
import numpy as np
filename = "/home/ludo/hivexp/HIVimature1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
h.smallestProteinSize = 40
resultfilename = h.resultfile = "/home/ludo/hivexp/hivfull"
previousresult = "/home/ludo/hivexp/HIVimature_results.json"
r = h.loadResult("/home/ludo/hivexp/HIVimature_results.json",
transpose=False) #
#ingredients = h.restore(*r)
#env is 0:6
#if need to offset ENV thats here.
#gag is 6:
#every 4th gag try to place gag_pol
#could try to rotate around a point
mrot = []
angle = 0
for i in range(6):
m = tr.rotation_matrix(math.radians(angle), [0, 0, 1],
point=[5.841, -1.458, 133.803])
mrot.append(m)
angle += 60
#tr.rotation_matrix(math.radians(60), [0,0,1], point=[5.841,-1.458,-133.803])
#h.loopThroughIngr(setNB) #h.loopThroughIngr(setNB) #h.loopThroughIngr(setNB) # #h.exteriorRecipe.ingredients[0].nbMol=2 #h.exteriorRecipe.ingredients[0].overwrite_nbMol_value=1 # #h.exteriorRecipe.ingredients[1].nbMol=2 #h.exteriorRecipe.ingredients[1].overwrite_nbMol_value=1 # #h.exteriorRecipe.ingredients[2].nbMol=2 #h.exteriorRecipe.ingredients[2].overwrite_nbMol_value=1 #h.fill5(verbose = 0,usePP=False) r=h.loadResult(rname,transpose=True)#)# or not ? ingredients = h.restore(*r) # h.collectResultPerIngredient() h.saveRecipe(path+"smallblood_results_tr.json",useXref=True,mixed=True,kwds=["source","name"],result=True,grid=False,packing_options=False,indent=False,quaternion=True) #h.exportToBD_BOX(res_filename=path+"test_tr",bd_type="rigid")#transpose ? from autopack.bd_box import rigid_box as bd_box res_filename = path+"test_tr" bd=bd_box(res_filename,bounding_box=h.boundingBox) bd.offset = [0,0,0] #bd.params["xbox"]["value"]=4000.0 #bd.params["ybox"]["value"]=4000.0 #bd.params["zbox"]["value"]=4000.0 bd.makePrmFile() r = h.exteriorRecipe
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
from autopack.Environment import Environment
filename = "/home/ludo/hivexp/BloodHIV1.0.json"
#filename ="/home/ludo/hivexp/HIVimature1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
#previousresult = "/home/ludo/hivexp/BloodHIV1.0_mixed.json"
previousresult = "/home/ludo/hivexp/BloodHIV1.0_centered.json"
r = h.loadResult(previousresult, transpose=False) #
ingredients = h.restore(*r)
#fix HIV1_CA_mono_0_1_0
#center is [405.609,1000.253,377.306]
# if apply the center on all instance ? meanings rotate the center and apply it
#h.saveRecipe("/home/ludo/hivexp/BloodHIV1.0_noref.json",useXref=False,mixed=True,result=False,grid=False,packing_options=True,indent=True,quaternion=True)
h.saveRecipe("/home/ludo/hivexp/BloodHIV1.0_mixed_tr.json",
useXref=True,
mixed=True,
kwds=["source", "name"],
result=True,
grid=False,
packing_options=False,