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"],