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")