Example #1
0
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")
Example #2
0
        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