center_c = np.array(data) - np.average(data,axis=0) np.savetxt(data_folder+os.sep+pdbname+"_cl.txt",data) else : data=np.loadtxt(pdb_directory+os.sep+pdbname+"_cl.txt") center_c = data - np.average(data,0) pointscloud, mesh_pts = helper.PointCloudObject("atoms_"+name, vertices=center_c,parent=parent) if os.path.isfile(pdb_directory+os.sep+pdbname+"_kmeans15.txt") : cluster = np.loadtxt(pdb_directory+os.sep+pdbname+"_kmeans15.txt") if (cluster.shape==(3,)) : cluster = [cluster,] pointscloud, mesh_pts = helper.PointCloudObject("cluster_"+name, vertices=cluster,parent=parent) #h.loopThroughIngr(doIngredientVOX) print h.totalNBBeads/22.0#avg nbbeads*total ninstance ~ 40000 h.loopThroughIngr(dsClusterAtoms) #execfile("C:\\Users\\ludov\\OneDrive\\Documents\\autoPACK\\autopack\\scripts\\sblSphereTree.py") #DEBUG VISUAL #BUILD ATOMcLOUD FOR SPHERETREE AND ATOMCOORDAINTES FOR EVERY INGREDIENTS #from autopack.IOutils import serializedRecipe, saveResultBinary #djson = serializedRecipe(h, False, True, lefthand = True) #f=open("/opt/data/dev/cellPACK/cellPACK_data_git/cellPACK_database_1.1.0/recipes/Mycoplasma1.6_serialized.json", "w") #f.write(djson[0]) #f.close() #h.saveRecipe("/home/ludo/hivexp/BloodHIV1.0.full.json", useXref=False, mixed=True, kwds=["source","name"], result=False, grid=True, packing_options=True, indent=False, quaternion=True) #h.saveRecipe("/opt/data/dev/cellPACK/cellPACK_data_git/cellPACK_database_1.1.0/recipes/Mycoplasma1.6_full.json", useXref=False, mixed=True, result=False, grid=True, packing_options=True, indent=False, quaternion=True)
ingr.jitterMax =[ingr.encapsulatingRadius,ingr.encapsulatingRadius,0.0] # if ingr.packingMode != "gradient": # ingr.molarity = 0.0 # ingr.nbMol = 0 # print ingr.name def setCompartment(ingr): # ingr.checkCompartment=True # ingr.compareCompartment=True#slow down a little. # ingr.nbMol*=2 ingr.rejectionThreshold=100#[1,1,0]# # ingr.jitterMax =[ingr.encapsulatingRadius/(25.*1.1547),ingr.encapsulatingRadius/(25.*1.1547),0.0] # ingr.cutoff_boundary=ingr.encapsulatingRadius # ingr.cutoff_boundary=500+ingr.encapsulatingRadius ingr.nbJitter = 6 # h.loopThroughIngr(setCompartment) #setJitter #raw_input() if ANALYSIS: # h.placeMethod="RAPID" 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)
d=analyse.doloop(5,h.boundingBox,wrkDir,output,rdf=True, render=False,twod=TWOD,use_file=True)#,fbox_bb=fbox_bb) # if not NOGUI : # afviewer.displayFill() else : autopack.testPeriodicity = False gridfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\grid_store" h.placeMethod="RAPID" h.saveResult = True resultfilename = h.resultfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_july" h.innerGridMethod = "trimesh" h.smallestProteinSize = 80.0 h.freePtsUpdateThrehod=0.0 #remove HUE,RIBO,DNAPOLY,PEPTIDE,RNA,DNA,Lipo filterOutFiber(h) h.loopThroughIngr(setJitter) h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,gridFileOut=gridfile,previousFill=False) h.fill5(verbose = 0,usePP=usePP) h.collectResultPerIngredient() h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_1.json",useXref=False,mixed=True, kwds=["source","name"],result=True, transpose = True, grid=False,packing_options=False,indent=False,quaternion=True) h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_2.json",useXref=False,mixed=True, kwds=["source","name"],result=True, transpose = False, grid=False,packing_options=False,indent=False,quaternion=True) from autopack.IOutils import serializedRecipe, saveResultBinary, toBinary djson, all_pos, all_rot = serializedRecipe(h,False,True,True,True)#transpose, use_quaternion, result=False, lefthand=False with open("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_serialized.json","w") as f: f.write(djson) from autopack.Serializable import sCompartment,sIngredientGroup,sIngredient,sIngredientFiber sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos1, all_rot1 = serializedRecipe(h,True,True,True,True);toBinary(all_pos1, all_rot1,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serializedTR_L.bin") sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos2, all_rot2 = serializedRecipe(h,False,True,True,True);toBinary(all_pos2, all_rot2,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serialized_L.bin") sCompartment.static_id = 0;sIngredientFiber.static_id = 0;sIngredient.static_id = [0, 0, 0];sIngredientGroup.static_id= 0;djson, all_pos3, all_rot3 = serializedRecipe(h,False,True,True,False);toBinary(all_pos3, all_rot3,"C:\\Users\\ludov\\OneDrive\\Documents\\OnlinePacking_Tobias\\cellVIEW-OP\\Data\\Mpn_2.0_serialized.bin")