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)
#raw_input()
if ANALYSIS:
# h.placeMethod="RAPID"
h.encapsulatingGrid=0
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
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)
# h.loopThroughIngr(excludeIngr)
# h.loopThroughIngr(excludeIngr)
# h.loopThroughIngr(setJitter)
# h.loopThroughIngr(setJitter)
# h.loopThroughIngr(setJitter)
helper = helperClass(vi="nogui")
autopack.helper = helper
from autopack.Environment import Environment
from autopack import transformation as tr
import numpy as np
filename = "/home/ludo/hivexp/HIVimature1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
h.smallestProteinSize = 40
resultfilename = h.resultfile = "/home/ludo/hivexp/hivfull"
previousresult = "/home/ludo/hivexp/HIVimature_results.json"
r = h.loadResult("/home/ludo/hivexp/HIVimature_results.json",
transpose=False) #
#ingredients = h.restore(*r)
#env is 0:6
#if need to offset ENV thats here.
#gag is 6:
#every 4th gag try to place gag_pol
#could try to rotate around a point
mrot = []
angle = 0
for i in range(6):
