ingr = MultiSphereIngr(name=wid,
pdb=pdbId,
nbMol=int(eval(count)),
positions=pos,
radii=rad,
encapsulatingRadius=R)
rMatrix.addIngredient(ingr)
print pdbId
o.setInnerRecipe(rMatrix)
#check lefty
env.boundingBox = [[0, 0, 0], [2000, 2000, 2000]]
env.name = "MycoplasmaGenitalium"
env.saveRecipe("C:\\Users\\ludov\\Downloads\\MG_1.0.json",
useXref=False,
format_output="json")
#save serialized
from autopack.IOutils import serializedRecipe, saveResultBinary
djson = serializedRecipe(env)
f = open("C:\\Users\\ludov\\Downloads\\MG_1.0_serialized.json", "w")
f.write(djson)
f.close()
saveResultBinary(env, "C:\\Users\\ludov\\Downloads\\MG_1.0_serialized.bin",
False, True)
#MG4 - nascent 753
#MG4 - processed I 753
#MG4 - processed II 753
#MG4 - signal sequence 753
#MG4 - folded 776
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")
# h.loopThroughIngr(excludeIngr)
# h.loopThroughIngr(excludeIngr)
# h.loopThroughIngr(setJitter)
# h.loopThroughIngr(setJitter)
# h.loopThroughIngr(setJitter)
# h.loopThroughIngr(setJitter)
h.fill5(verbose=0, usePP=False)
h.collectResultPerIngredient()
rname = fileName + "_" + i.isoformat() + ".json"
rname = "C:\Users\ludovic\Documents\CellPackViewer_Cluster\Data\HIV\cellPACK\mycoDNA1.json"
h.saveRecipe(rname,
useXref=True,
mixed=True,
kwds=["source", "name"],
result=True,
grid=False,
packing_options=False,
indent=False,
quaternion=True)
#h.saveRecipe(fileName+"_"+i.isoformat()+".json",useXref=True,mixed=True,
# kwds=["source","name","positions","radii"],result=True,
# grid=False,packing_options=False,indent=False,quaternion=True)
else:
h.saveRecipe(fileName + "_" + i.isoformat() + ".json",
useXref=True,
mixed=True,
result=False,
grid=True,
packing_options=True,
indent=True,
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(
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)
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)
h.saveRecipe("/home/ludo/hivexp/BloodHIV1.0_mixed_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="/opt/data/dev/hivbdbox/test_ntr",bd_type="rigid")
#then run ~/Tools/bd_box-2.2/bin/bd_rigid test.prm --out_filename=err.log
from autopack.bd_box import rigid_box as bd_box
res_filename = "/opt/data/dev/hivbdbox/test_full_hack_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()
#"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"],
result=True,
transpose=False,
grid=False,
packing_options=False,
indent=False,
quaternion=True)
break
envdata = r[1][0][:6]
alldata = []
alldata.extend(envdata)
alldata.extend(data)
alldata.extend(respol)
r[1][0] = alldata
for d in r[1][0]:
d[1] = d[1].transpose()
ingredients = h.restore(*r)
h.saveRecipe("hivimmature_start_pol.json",
useXref=True,
mixed=True,
kwds=["source", "name"],
result=True,
grid=False,
packing_options=False,
indent=False,
quaternion=True)
#transpose
#
#h.buildGrid(boundingBox=h.boundingBox,gridFileIn=None,rebuild=True ,
# gridFileOut="/home/ludo/hivexp/gridOut",previousFill=True)
#
#gag.completion = 1.0
#env.completion = 1.0
##rest should pack around
#gag.nbMol = 0
#env.nbMol = 0
#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
#bd.addAutoPackIngredient(r.ingredients[1])
#bd.addAutoPackIngredient(r.ingredients[2])
#bd.addAutoPackIngredient(r.ingredients[3])
if r :
for ingr in r.ingredients:
h.saveResult = True
h.resultfile = "/home/ludo/Dev/bdbox/" + n + v
h.innerGridMethod = "bhtree" #jordan pure python ? sdf ?
# h.boundingBox = [[-250.0, -6500.0/2.0, -250.0], [250.0, 6500.0/2.0, 250.0]]
# h.boundingBox =[[-2482, -2389.0, 100.0], [2495, 2466, 2181.0]]
h.buildGrid(boundingBox=h.boundingBox,
gridFileIn=gridfile,
rebuild=True,
gridFileOut=None,
previousFill=False)
h.fill5(verbose=0, usePP=True)
h.collectResultPerIngredient()
h.saveRecipe(h.resultfile + "_mixed.json",
useXref=True,
mixed=True,
kwds=["compNum", "encapsulatingRadius"],
result=True,
grid=False,
packing_options=False,
indent=False)
#display ?
#export the complete recipe as collada. each ingredient -> meshnode. Each instance->node instance
env = h
from autopack import bd_box
#bd_box.executable_dmatrix="dmatrix"
#env.exportToBD_BOX(res_filename="/home/ludo/Dev/bdbox/"+n+v,bd_type="rigid")
#require no overlapp at all...
#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")
