h.encapsulatingGrid=0
autopack.testPeriodicity = False
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
output="/Users/ludo/DEV/autoPACKresults/NM_Analysis_C2"
analyse.g.Resolution = 1.0
h.boundingBox=numpy.array(h.boundingBox)
fbox_bb=numpy.array(h.boundingBox)
# h.boundingBox[0]-=numpy.array([500.0,500.0,0.0])
# 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):
ingr.nbMol = 0
print ingr.name
#h.loopThroughIngr(setJitter)
#raw_input()
if ANALYSIS:
# h.placeMethod="RAPID"
h.encapsulatingGrid=0
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
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):
#Or we can also use the server for gathering the file
recipe = "NM_Analysis_FigureB"
version = "1.1"
filename = autopack.RECIPES[recipe][version]["setupfile"]
resultfile= autopack.RECIPES[recipe][version]["resultfile"]
setupfile = autopack.retrieveFile(filename,cache="recipes")
#you could overwrite here the filename
#filename = "something.json"
fileName, fileExtension = os.path.splitext(setupfile)
n=os.path.basename(fileName)
h = Environment(name=n)
h.loadRecipe(setupfile)
afviewer=None
h.placeMethod="pandaBullet"
h.encapsulatingGrid=0
#default for periodicity
h.use_periodicity = False
autopack.testPeriodicity = True
autopack.biasedPeriodicity = [1,1,0]
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
h.analyse = analyse
analyse.g.Resolution = 1.0
#h.smallestProteinSize=30.0#get it faster? same result ?
h.boundingBox=np.array(h.boundingBox)
#==============================================================================
# the parameter for a run
#==============================================================================
fileName, fileExtension = os.path.splitext(setupfile)
if load:
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)
elif pack:
#pack
gridfile = "/home/ludo/Dev/bdbox/grid_store"
h.placeMethod = "RAPID" #does it use all vertices ?
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,
