# h.boundingBox[1]+=numpy.array([500.0,500.0,0.0])
d=analyse.doloop(1000,h.boundingBox,wrkDir,output,rdf=True,
render=False,twod=TWOD,use_file=True)#,fbox_bb=fbox_bb)
# if not NOGUI :
# afviewer.displayFill()
else :
gridfile = localdir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/grid_store"
h.placeMethod="RAPID"
h.saveResult = True
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=None,rebuild=True ,
# gridFileOut=gridfile,previousFill=False)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,
gridFileOut=None,previousFill=False)
h.fill5(verbose = 0,usePP=True)
# if not NOGUI :
# afviewer.displayFill()
#analyse.grid_pack(h.boundingBox,wrkDir,seed=0, fill=1,vTestid = 0,vAnalysis = 1)#build grid and fill
#for i in range(2):
# print 'Collecting %d ...' % i
# n = gc.collect()
# print 'Unreachable objects:', n
# print 'Remaining Garbage:',
# pprint.pprint(gc.garbage)
# del gc.garbage[:]
# print
#execfile("/Users/ludo/DEV/autoPACK_github/autopack/scripts/testAF_xml.py")
# modeCloseMA_ENV(h,100,m,ma_results,eid=4)#50/50
# modeCloseENV(h,100,m,ma_results,eid=5)#50/50
# modeCloseMA_ENV(h,100,m,ma_results,eid=6,w1=0.3333,w2=0.33333,w3=0.44)
# modeCloseMA_ENV(h,100,m,ma_results,eid=7,w1=0.6,w2=0.2,w3=0.2)
# a) MA free 0%, MA-MA 100%, ENV free 0%, ENV-ENV 0%, ENV-MA 100%
# modeCloseMA_ENV(h,1,m,[],eid=7,w1=0.6,w2=0.2,w3=0.2)
# if not NOGUI :
# afviewer.displayPreFill()
# afviewer.displayFill()
# displayResult(h,0,2,0)
elif disp:
#execfile("/Users/ludo/DEV/testGaussCluster.py")
h.FillName = [
"test",
] * (h.cFill + 1)
n = 0
displayResult(h, n, n, 50)
#a,fluos,locis,npx,limits=displayOne(helper,n,n,50,20.0,None,space=100,redo=True)
# execfile("/Users/ludo/Downloads/autopack_ouput/hiv_experiment/hiv_exp.py")
else:
resultfilename = h.resultfile = "/Users/ludo/Downloads/autopack_ouput/hiv_experiment/hiv_exp"
h.buildGrid(boundingBox=h.boundingBox,
gridFileIn=None,
rebuild=False,
gridFileOut=None,
previousFill=True)
h.fill5(seedNum=10, verbose=0, usePP=False)
if not NOGUI:
afviewer.displayPreFill()
afviewer.displayFill()
output=localdir+os.sep+"autoFillRecipeScripts/2DsphereFill/results/paper/"
analyse.g.Resolution = 1.0
d=analyse.doloop(100,h.boundingBox,wrkDir,output,rdf=True,render=False,twod=TWOD)
if not NOGUI :
afviewer.displayFill()
else :
gridfile = localdir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/grid_store"
h.placeMethod="RAPID"
h.saveResult = True
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=None,rebuild=True ,
# gridFileOut=gridfile,previousFill=False)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,
gridFileOut=None,previousFill=False)
h.fill5(verbose = 0,usePP=True)
# if not NOGUI :
# afviewer.displayFill()
#analyse.grid_pack(h.boundingBox,wrkDir,seed=0, fill=1,vTestid = 0,vAnalysis = 1)#build grid and fill
#for i in range(2):
# print 'Collecting %d ...' % i
# n = gc.collect()
# print 'Unreachable objects:', n
# print 'Remaining Garbage:',
# pprint.pprint(gc.garbage)
# del gc.garbage[:]
# print
#execfile("/Users/ludo/DEV/autopack_git/autopack/scripts/testAF_xml.py")
#h.boundingBox=[[ -2482, -2389, -500.26],[ 2495, 2466, 500.02]]
h.buildGrid(boundingBox=h.boundingBox,
gridFileIn=None,
rebuild=True,
gridFileOut=None,
previousFill=False)
# h.loopThroughIngr(excludeIngr)
# h.loopThroughIngr(excludeIngr)
# 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)
# if not NOGUI :
# afviewer.displayFill()
else :
autopack.testPeriodicity = False
gridfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\grid_store"
h.placeMethod="RAPID"
h.saveResult = True
resultfilename = h.resultfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_july"
h.innerGridMethod = "trimesh"
h.smallestProteinSize = 80.0
h.freePtsUpdateThrehod=0.0
#remove HUE,RIBO,DNAPOLY,PEPTIDE,RNA,DNA,Lipo
filterOutFiber(h)
h.loopThroughIngr(setJitter)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,gridFileOut=gridfile,previousFill=False)
h.fill5(verbose = 0,usePP=usePP)
h.collectResultPerIngredient()
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)
from autopack.IOutils import serializedRecipe, saveResultBinary, toBinary
djson, all_pos, all_rot = serializedRecipe(h,False,True,True,True)#transpose, use_quaternion, result=False, lefthand=False
with open("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_serialized.json","w") as f:
f.write(djson)
from autopack.Serializable import sCompartment,sIngredientGroup,sIngredient,sIngredientFiber
sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos1, all_rot1 = serializedRecipe(h,True,True,True,True);toBinary(all_pos1, all_rot1,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serializedTR_L.bin")
sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos2, all_rot2 = serializedRecipe(h,False,True,True,True);toBinary(all_pos2, all_rot2,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serialized_L.bin")
sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos3, all_rot3 = serializedRecipe(h,False,True,True,False);toBinary(all_pos3, all_rot3,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serialized.bin")
sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos4, all_rot4 = serializedRecipe(h,True,True,True,False);toBinary(all_pos4, all_rot4,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serializedTR.bin")
