filename = "/Users/ludo/DEV/autopack_git/autoPACK_database_1.0.0/recipes/NM_Analysis_FigureC1.3.xml"
fileName, fileExtension = os.path.splitext(filename)
n=os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe=n
h.load_XML(filename)
afviewer=None
if not NOGUI :
print h,helper
setattr(h,"helper",helper)
afviewer = AFViewer(ViewerType=h.helper.host,helper=h.helper)
afviewer.SetHistoVol(h,20.0,display=False)
h.host=h.helper.host
afviewer.displayPreFill()
h.saveResult = False
#resultfilename = h1.resultfile = wrkDir+os.sep+"autoFillRecipeScripts"+os.sep+"2DsphereFill"+os.sep+"results"+os.sep+"SpherefillResult.afr"
#resultfilename = h.resultfile = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/results/2DsphereFill_1.1.apr"
#resultfilename = h.resultfile = wrkDir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/MycoplasmaPackResult_3"
resultfilename = h.resultfile = "/Users/ludo/DEV/autoPACKresults/NM_Analysis_C2/NM_Analysis_C"
#h.smallestProteinSize=15
#h.exteriorRecipe.ingredients[0].uLength = 100.0
#overwrite the jiterMax usin jitterMax = [d[k]["rad"]/(15.*1.1547),d[k]["rad"]/(15.*1.1547),0.0]
#loopThroughIngr
def setJitter(ingr):
ingr.jitterMax =[ingr.encapsulatingRadius,ingr.encapsulatingRadius,0.0]
# if ingr.packingMode != "gradient":
# ingr.molarity = 0.0
# ingr.nbMol = 0
#filename = "/Users/ludo/Desktop/cell_hack.xml"
fileName, fileExtension = os.path.splitext(filename)
n=os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe=n
h.load_XML(filename)
afviewer=None
if not NOGUI :
print h,helper
setattr(h,"helper",helper)
afviewer = AFViewer(ViewerType=h.helper.host,helper=h.helper)
afviewer.SetHistoVol(h,20.0,display=False)
h.host=h.helper.host
afviewer.displayPreFill()
h.saveResult = False
#resultfilename = h1.resultfile = wrkDir+os.sep+"autoFillRecipeScripts"+os.sep+"2DsphereFill"+os.sep+"results"+os.sep+"SpherefillResult.afr"
#resultfilename = h.resultfile = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/results/2DsphereFill_1.1.apr"
resultfilename = h.resultfile = wrkDir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/MycoplasmaPackResult_3"
h.smallestProteinSize=25
#h.exteriorRecipe.ingredients[0].uLength = 100.0
#overwrite the jiterMax usin jitterMax = [d[k]["rad"]/(15.*1.1547),d[k]["rad"]/(15.*1.1547),0.0]
#loopThroughIngr
def setJitter(ingr):
# ingr.jitterMax =[ingr.encapsulatingRadius/(25.*1.1547),ingr.encapsulatingRadius/(25.*1.1547),0.0]
if ingr.packingMode != "gradient":
ingr.molarity = 0.0
ingr.nbMol = 0
print ingr.name
#h.loopThroughIngr(setJitter)
setupfile = autopack.retrieveFile(filename, cache="recipes")
else:
setupfile = filename
#overwrite result file
resultfile = "output_autopack_test"
print("ok use ", setupfile, filename)
fileName, fileExtension = os.path.splitext(setupfile)
print fileName
n = os.path.basename(fileName)
recipe = n
h = Environment(name=n)
h.loadRecipe(setupfile)
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
h.saveResult = False
# h.overwriteSurfacePts = False
# h.compartments[0].overwriteSurfacePts = False
#build the grid
#change the grid size ?
h.smallestProteinSize = 80.0
h.freePtsUpdateThrehod = 0.0
if doit:
#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)
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,
kwds=["compNum", "encapsulatingRadius"],
