continue
#read the pdb
#build proxy and mesh
ingr = MultiSphereIngr(name=wid,
pdb=pdbId,
nbMol=int(eval(count)),
positions=pos,
radii=rad,
encapsulatingRadius=R)
rMatrix.addIngredient(ingr)
print pdbId
o.setInnerRecipe(rMatrix)
#check lefty
env.boundingBox = [[0, 0, 0], [2000, 2000, 2000]]
env.name = "MycoplasmaGenitalium"
env.saveRecipe("C:\\Users\\ludov\\Downloads\\MG_1.0.json",
useXref=False,
format_output="json")
#save serialized
from autopack.IOutils import serializedRecipe, saveResultBinary
djson = serializedRecipe(env)
f = open("C:\\Users\\ludov\\Downloads\\MG_1.0_serialized.json", "w")
f.write(djson)
f.close()
saveResultBinary(env, "C:\\Users\\ludov\\Downloads\\MG_1.0_serialized.bin",
False, True)
#MG4 - nascent 753
#MG4 - processed I 753
# 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)
# 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 ,
# 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_C1"
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(5,
h.boundingBox,
wrkDir,
output,
rdf=True,
render=False,
twod=TWOD,
use_file=True) #,fbox_bb=fbox_bb)
# if not NOGUI :
# afviewer.displayFill()
else:
global fluo_pos
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 #============================================================================== #all option can be access through a Dictionary that hold : #options name #options default value #options value range #options type e.g. Vector,Float, Int,String #to get the value for the current value we can use the python function getattr #to change the value of the option we can use the python function setattr #all the packing options (General Parameters) are found in h.OPTIONS #for k in h.OPTIONS.keys(): # print h.OPTIONS[k]
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):
# print 'Collecting %d ...' % i
# n = gc.collect()
# print 'Unreachable objects:', n
# print 'Remaining Garbage:',
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):
# print 'Collecting %d ...' % i