if len(sys.argv) > 1:
filename = sys.argv[1]
resultfile = None
if filename in autopack.RECIPES:
n = filename
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
else:
resultfile = sys.argv[2]
setupfile = autopack.retrieveFile(filename, cache="recipes")
print("ok use ", setupfile, filename, resultfile)
fileName, fileExtension = os.path.splitext(setupfile)
n = os.path.basename(fileName)
h = Environment(name=n)
h.loadRecipe(setupfile)
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(
helper = autopack.helper
if helper is None and not NOGUI:
import upy
helperClass = upy.getHelperClass()
helper = helperClass()
else:
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
recipe = "D:\\Data\\cellPACK_data\\cellPACK_database_1.1.0\\recipes\\HIV_VLP.1.1.json" #127
filename = recipe #"/Users/ludo/DEV/autopack_git/autoPACK_database_1.0.0/recipes/NM_Analysis_FigureA1.0.xml"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
#recenter ingredient position according center.
#should manually do the mesh ?
for c in h.compartments:
for ingr in c.surfaceRecipe.ingredients:
ingr.positions = np.array(ingr.positions) - np.array(ingr.offset)
ingr.sphereFile = None
#save the recipe
h.version = "1.2"
h.saveRecipe(
"D:\\Data\\cellPACK_data\\cellPACK_database_1.1.0\\recipes\\HIV_VLP.1.2.json",
useXref=False,
format_output="json")
resultfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H" + tr + ".json" # or Tr workingdir = "D:\\Data\\cellPACK_data\\Mycoplasma\\" workingdir = "D:\\Data\\cellPACK_data_git\\influenza\Influenza\\" recipefile = "Influenza_3.json" resultfile = "" #workingdir ="C:\Users\ludov\OneDrive\Documents\cellVIEW-i\Data\\" #recipefile="christmas.json" fileName, fileExtension = os.path.splitext(recipefile) n = os.path.basename(fileName) h = Environment(name=n) #h.helper = helper recipe = n h.loadRecipe(workingdir + recipefile) # 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 != "":