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,