def model_contour(p,res=4.0,emmap=False,t=-1.):
blurrer = StructureBlurrer()
modelmap = blurrer.gaussian_blur_real_space(p, res,densMap=emmap,normalise=True)
c1 = None
if t != -1.0:
c1 = t*emmap.std()#0.0
return modelmap,c1
def blur_model(p,res=4.0,emmap=False):
pName = os.path.basename(p).split('.')[0]
print 'reading the model'
structure_instance=PDBParser.read_PDB_file(pName,p,hetatm=False,water=False)
print 'filtering the model'
blurrer = StructureBlurrer()
if res is None: sys.exit('Map resolution required..')
#emmap = blurrer.gaussian_blur(structure_instance, res,densMap=emmap_1,normalise=True)
modelmap = blurrer.gaussian_blur_real_space(structure_instance, res,sigma_coeff=0.187,densMap=emmap,normalise=True)
return pName,modelmap, structure_instance
def blur_model(p, res=4.0, emmap=False):
pName = os.path.basename(p).split('.')[0]
structure_instance = PDBParser.read_PDB_file(pName,
p,
hetatm=False,
water=False)
blurrer = StructureBlurrer()
if res is None:
sys.exit('Map resolution required..')
modelmap = blurrer.gaussian_blur_real_space(structure_instance,
res,
densMap=emmap,
normalise=True)
return pName, modelmap
def _ccc(self, mapname, modelname, res):
path_test = "./"
m = os.path.join(path_test, mapname)
emmap1 = MapParser.readMRC(m)
p = os.path.join(path_test, modelname)
structure_instance = PDBParser.read_PDB_file('pdbfile',
p,
hetatm=False,
water=False)
blurrer = StructureBlurrer()
t = 1.5
c1 = None
c2 = None
#calculate map contour
zeropeak, ave, sigma1 = emmap1._peak_density()
if not zeropeak is None: c1 = zeropeak + (t * sigma1)
mt = 0.1
if res > 20.0: mt = 2.0
elif res > 10.0: mt = 1.0
elif res > 6.0: mt = 0.5
#emmap2 = blurrer.gaussian_blur(structure_instance, res, densMap=emmap1)
emmap2 = blurrer.gaussian_blur_real_space(structure_instance,
res,
sigma_coeff=0.187,
densMap=emmap1,
normalise=True)
# calculate model contour - emmap1 apparently?
c2 = mt * emmap2.std()
sc = ScoringFunctions()
_, ovr = sc.CCC_map(emmap1, emmap2, c1, c2, 3, cmode=False)
ccc, _ = sc.CCC_map(emmap1, emmap2, c1, c2, cmode=False)
print("Printing CCC", ccc, ovr, c1, c2)
return (ccc, ovr)