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=(',', ': ')
matrices = jsondic.values() #3*4
newm = []
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
#h.saveRecipe("/home/ludo/hivexp/BloodHIV1.0_noref.json",useXref=False,mixed=True,result=False,grid=False,packing_options=True,indent=True,quaternion=True)