if filename in autopack.RECIPES:
n = filename
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
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,
maskGrid.stepSize = [space, space, space]
maskGrid.origin = (boundingBox[1] - boundingBox[0]) / 2.0
#maskGrid.normalize()
h['amin'], h['amax'], h['amean'], h['arms'] = maskGrid.stats()
w.write(filename, maskGrid)
#filename = "/Users/ludo/Desktop/cell.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2D1.1.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2Dgradients1.0.xml"
#filename = "/Users/ludo/DEV/autopack_git/data/Mycoplasma/recipe/Mycoplasma1.3.xml"
#filename = "/Users/ludo/Desktop/cell_hack.xml"
filename = "/Users/ludo/Downloads/autopack_ouput/hiv_experiment/HIV1.6.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 = True
#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"
else :
setupfile =filename
else :
#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)
#
if len(sys.argv) > 1:
filename = sys.argv[1]
resultfile = None
if filename in autopack.RECIPES:
n = filename
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
setupfile = autopack.retrieveFile(filename, cache="recipes")
print("ok use ", setupfile, filename)
fileName, fileExtension = os.path.splitext(setupfile)
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
fileName, fileExtension = os.path.splitext(setupfile)
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
#h.loopThroughIngr(setCompartment)
load = False
pack = True
if len(sys.argv) > 1: #and doit :
filename = sys.argv[1]
resultfile = None
if filename in autopack.RECIPES:
n = filename
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
setupfile = autopack.retrieveFile(filename, cache="recipes")
print("ok use ", setupfile, filename)
fileName, fileExtension = os.path.splitext(setupfile)
n = os.path.basename(fileName)
h = Environment(name=n)
h.loadRecipe(setupfile)
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
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
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
setupfile = autopack.retrieveFile(filename, cache="recipes")
print("ok use ", setupfile, filename)
fileName, fileExtension = os.path.splitext(setupfile)
n = os.path.basename(fileName)
else:
setupfile = filename = "C:\Users\ludov\Google Drive\TSRI HIV Modeling\HIVsphere_simple_r140.json"
# resultfile = "C:\Users\ludov\Google Drive\TSRI HIV Modeling\cellpack_models\Sphere_140_m330_random_tr.json"
# resultfile = "C:\Users\ludov\Google Drive\TSRI HIV Modeling\cellpack_models\Sphere_140_10_random_tr.json"
resultfile = "C:\Users\ludov\Google Drive\TSRI HIV Modeling\cellpack_models\HIV_VLP_140_214_random_tr.json"
# resultfile = "C:\Users\ludov\OneDrive\Documents\\backupC4DHiv\sphere140_rand_49_tr.json"
# setupfile = filename = "C:\Users\ludov\Google Drive\TSRI HIV Modeling\HIVsphere_simple_r139.json"
# resultfile = "C:\Users\ludov\OneDrive\Documents\\backupC4DHiv\sphere139_random_127_tr.json"
n = "HIV_VLP"
h = Environment(name=n)
h.loadRecipe(setupfile)
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
fileName, fileExtension = os.path.splitext(setupfile)
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)
h.compartments[0].name = "HIVenvelop_140"
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)
localdir = wrkDir = autopack.__path__[0]
helper = autopack.helper
if helper is None:
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
from autopack.Environment import Environment
filename = "/home/ludo/hivexp/BloodHIV1.0.json"
#filename ="/home/ludo/hivexp/HIVimature1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
#previousresult = "/home/ludo/hivexp/BloodHIV1.0_mixed.json"
#previousresult = "/home/ludo/hivexp/BloodHIV1.0_centered.json"
previousresult = "/home/ludo/hivexp/BloodHIV1.0_mixed_tr.json"
r = h.loadResult(previousresult, transpose=True) #
ingredients = h.restore(*r)
from autopack.lipids import lipidsCG
#generate the membrane
lcg = lipidsCG()
comp = h.compartments[0]
lcg.coverShape(comp.vertices, comp.vnormals)
#remove lipids overlaping
centroids = np.loadtxt(data_folder + os.sep + fname + "_cl.txt")
nProxy = len(centroids)
R = np.linalg.norm(centroids, axis=1).max() + proxy_radius
return [
centroids.tolist(),
], [
(np.ones(nProxy) * proxy_radius).tolist(),
], R, mesh, fname, center
#X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
#print(X.count_amino_acids())
#print(X.get_amino_acids_percent())
#print(X.molecular_weight())
left = []
env = Environment(name="MG")
#c Cytosol
#d DNA
#e Extracellular Space
#m Membrane
#tc Terminal Organelle Cytosol
#tm Terminal Organelle Membrane
#rCyto = Recipe()
## sorted(numbers, key=str.lower)
#for ing_name in sorted(ingrs_dic, key=unicode.lower): # ingrs_dic:
# # either xref or defined
# ing_dic = ingrs_dic[ing_name]
# ingr = io_ingr.makeIngredientFromJson(inode=ing_dic, recipe=env.name)
# rCyto.addIngredient(ingr)
# # setup recipe
else :
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
#filename = "/Users/ludo/Desktop/cell.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2D1.1.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2Dgradients1.0.xml"
filename = "/Users/ludo/DEV/autopack_git/data/Mycoplasma/recipe/Mycoplasma1.3.xml"
#filename = "/Users/ludo/Desktop/cell_hack.xml"
#filename = "/Users/ludo/DEV/autopack_git/autoPACK_database_1.0.0/recipes/NM_Analysis_FigureC1.3.xml"
filename = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n=os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe=n
h.loadRecipe(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"
recipefile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_1.0.json" tr = "" #"_tr" transpose = True resultfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H" + tr + ".json" # or Tr workingdir = "D:\\Data\\cellPACK_data\\Mycoplasma\\" workingdir = "D:\\Data\\cellPACK_data_git\\influenza\Influenza\\" recipefile = "Influenza_3.json" resultfile = "" #workingdir ="C:\Users\ludov\OneDrive\Documents\cellVIEW-i\Data\\" #recipefile="christmas.json" fileName, fileExtension = os.path.splitext(recipefile) n = os.path.basename(fileName) h = Environment(name=n) #h.helper = helper recipe = n h.loadRecipe(workingdir + recipefile) # save a full recipe no Xref #"nbMol": nbmol, #"molarity" : ingr.molarity, #"source": ingr.source, #"positions":ingr.positions, #"radii":ingr.radii} rname = workingdir + "recipes\\BloodHIVMycoRB_full.1.0.json" rname = workingdir + "recipes\\Mycoplasma1.7.json" rname = workingdir + recipefile #h.saveRecipe(rname,useXref=False,mixed=True,
helper = autopack.helper
if helper is None:
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
from autopack.Environment import Environment
from autopack import transformation as tr
import numpy as np
filename = "/home/ludo/hivexp/HIVimature1.0.json"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
h.smallestProteinSize = 40
resultfilename = h.resultfile = "/home/ludo/hivexp/hivfull"
previousresult = "/home/ludo/hivexp/HIVimature_results.json"
r = h.loadResult("/home/ludo/hivexp/HIVimature_results.json",
transpose=False) #
#ingredients = h.restore(*r)
#env is 0:6
#if need to offset ENV thats here.
#gag is 6:
#every 4th gag try to place gag_pol
#wrkDir = AutoFill.__path__[0]
localdir = wrkDir = autopack.__path__[0]
path="/opt/data/dev/BD_EXP/"
helper = autopack.helper
if helper is None :
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
from autopack.Environment import Environment
filename = path+"smallBlood.json"
fileName, fileExtension = os.path.splitext(filename)
n=os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe=n
h.loadRecipe(filename)
h.placeMethod="pandaBullet"
rname=path+"smallblood_results.json"
#h.buildGrid(boundingBox=h.boundingBox,gridFileIn=None,rebuild=True ,gridFileOut=path+"gridOut",previousFill=False,lookup=2)
#
#def setNB(ingr):
# ingr.nbMol = 0
# ingr.molarity = 0.0
# ingr.overwrite_nbMol_value = 0.0
recipe = parVals['running_settings']['recipePath']
if recipe != '':
#remove 1.1.json from recipe
setupfile = recipe
filename = setupfile
else: # don't do it as else
#Or we can also use the server for gathering the file
recipe = recipename # put recipe here
version = version # put version here
filename = autopack.RECIPES[recipe][version]["setupfile"]
setupfile = autopack.retrieveFile(filename, cache="recipes")
fileName, fileExtension = os.path.splitext(setupfile)
n = os.path.basename(fileName)
h = Environment(name=n)
h.loadRecipe(setupfile)
h.dump = False
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)
helperClass = upy.getHelperClass()
helper =helperClass()
else :
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
#filename = "/Users/ludo/Desktop/cell.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2D1.1.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2Dgradients1.0.xml"
#filename = "/Users/ludo/DEV/autopack_git/data/Mycoplasma/recipe/Mycoplasma1.3.xml"
#filename = "/Users/ludo/Desktop/cell_hack.xml"
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"
import upy
helperClass = upy.getHelperClass()
helper =helperClass()
else :
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
#filename = "/Users/ludo/Desktop/cell.xml"
#filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2D1.1.xml"
filename = wrkDir+os.sep+"autoFillRecipeScripts/2DsphereFill/Test_Spheres2Dgradients1.0.xml"
#filename = "/Users/ludo/DEV/autopack_git/data/Mycoplasma/recipe/Mycoplasma1.3.xml"
#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"
if len(sys.argv) > 1:
filename = sys.argv[1]
resultfile = None
if filename in autopack.RECIPES:
n = filename
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
else:
resultfile = sys.argv[2]
setupfile = autopack.retrieveFile(filename, cache="recipes")
print("ok use ", setupfile, filename, resultfile)
fileName, fileExtension = os.path.splitext(setupfile)
n = os.path.basename(fileName)
h = Environment(name=n)
h.loadRecipe(setupfile)
h.setupfile = filename
if resultfile is not None:
h.resultfile = resultfile
fileName, fileExtension = os.path.splitext(setupfile)
if export_json:
print("expot json recipe ", fileName)
h.saveRecipe(fileName + ".json", useXref=useXref, indent=True)
if check_result:
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)
# pathToCP="/opt/data/dev/cellPACK/cellPACK_data_git/cellPACK_database_1.1.0/" pathToCP="D:\\DATA\\cellPACK_data\\cellPACK_database_1.1.0\\" #D:\Data\cellPACK_data\cellPACK_database_1.1.0\other # filename = "/home/ludo/hivexp/BloodHIV1.0.json" filename = "/opt/data/dev/cellPACK/cellPACK_data_git/cellPACK_database_1.1.0/recipes/Mycoplasma1.6.json" filename = "/opt/data/dev/cellPACK/cellPACK_data_git/cellPACK_database_1.1.0/recipes/DNAplectoneme.1.0.json" filename = pathToCP+os.sep+"recipes"+os.sep+"Mycoplasma1.6_full.json" filename = pathToCP+os.sep+"recipes"+os.sep+"Mycoplasma1.7.json" filename = "C:\\Dev\\flexpack_dev_1.1\\data\\cellpack\\recipes\\Mycoplasma1.7.json" #path = "/home/ludo/hivexp/" fileName, fileExtension = os.path.splitext(filename) n=os.path.basename(fileName) h = Environment(name=n) h.totalNBBeads = 0 ##h.helper = helper #recipe=n h.loadRecipe(filename) # ##for each ingredient, PDB, make a sphere Tree using SBL #sbl_binary_U="sbl-ballcovor-pdb-U.exe" #sbl_binary_A="sbl-ballcovor-pdb-A.exe" #sbl_binary_C="sbl-ballcovor-pdb-C.exe" #sbl_binary_T="sbl-ballcovor-txt.exe" # #sbl_arg_file=" -f " #sbl_arg_nballs=" --n-inner-balls " #sbl_arg_outer=" --outer " #sbl_arg_interpolated=" --interpolated "
helper = autopack.helper
if helper is None and not NOGUI:
import upy
helperClass = upy.getHelperClass()
helper = helperClass()
else:
import upy
helperClass = upy.getHelperClass()
helper = helperClass(vi="nogui")
autopack.helper = helper
recipe = "D:\\Data\\cellPACK_data\\cellPACK_database_1.1.0\\recipes\\HIV_VLP.1.1.json" #127
filename = recipe #"/Users/ludo/DEV/autopack_git/autoPACK_database_1.0.0/recipes/NM_Analysis_FigureA1.0.xml"
fileName, fileExtension = os.path.splitext(filename)
n = os.path.basename(fileName)
h = Environment(name=n)
#h.helper = helper
recipe = n
h.loadRecipe(filename)
#recenter ingredient position according center.
#should manually do the mesh ?
for c in h.compartments:
for ingr in c.surfaceRecipe.ingredients:
ingr.positions = np.array(ingr.positions) - np.array(ingr.offset)
ingr.sphereFile = None
#save the recipe
h.version = "1.2"
h.saveRecipe(
"D:\\Data\\cellPACK_data\\cellPACK_database_1.1.0\\recipes\\HIV_VLP.1.2.json",
useXref=False,
format_output="json")
v = sys.argv[2]
filename = autopack.RECIPES[n][v]["setupfile"]
resultfile = autopack.RECIPES[n][v]["resultfile"]
setupfile = autopack.retrieveFile(filename, cache="recipes")
# or the filename directly
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.freePtsUpdateThrehod = 0.0
afviewer = None
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
h.analyse = analyse
analyse.g.Resolution = 1.0
# firs time we build the grid
h.buildGrid(boundingBox=h.boundingBox,
gridFileIn=None,