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")
centroids = np.loadtxt(data_folder + os.sep + fname + "_cl.txt")
nProxy = len(centroids)
R = np.linalg.norm(centroids, axis=1).max() + proxy_radius
return [
centroids.tolist(),
], [
(np.ones(nProxy) * proxy_radius).tolist(),
], R, mesh, fname, center
#X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
#print(X.count_amino_acids())
#print(X.get_amino_acids_percent())
#print(X.molecular_weight())
left = []
env = Environment(name="MG")
#c Cytosol
#d DNA
#e Extracellular Space
#m Membrane
#tc Terminal Organelle Cytosol
#tm Terminal Organelle Membrane
#rCyto = Recipe()
## sorted(numbers, key=str.lower)
#for ing_name in sorted(ingrs_dic, key=unicode.lower): # ingrs_dic:
# # either xref or defined
# ing_dic = ingrs_dic[ing_name]
# ingr = io_ingr.makeIngredientFromJson(inode=ing_dic, recipe=env.name)
# rCyto.addIngredient(ingr)
# # setup recipe