def __init__(self,target,usegrp=None,nstruct=10000,pid=10,**kwargs):
if os.path.isdir(target):
#the target is a valid population structure directory
if usegrp==None:
raise RuntimeError, "group key is not specified!"
firststr = files.modelstructures(os.path.join(target,"copy0.hms"),[usegrp])
self.idx = firststr.idx
self.genome = firststr.genome
self.usegrp = usegrp
self.nbead = len(self.idx)
self.nstruct = nstruct
self.radius = firststr[-1].r
print("reading %d structures info in %s,%s"%(nstruct,target,usegrp))
self._readStructures(target,pid,**kwargs)
elif os.path.isfile(target) and os.path.splitext(target)[1] == '.hss':
h5f = h5py.File(target,'r')
self.idx = h5f['idx'][:]
self.genome = pickle.loads(h5f['genome'].value)
self.usegrp = pickle.loads(h5f['usegrp'].value)
self.nbead = pickle.loads(h5f['nbead'].value)
self.nstruct = pickle.loads(h5f['nstruct'].value)
self.radius = h5f['radius'][:]
self.coordinates = h5f['coordinates'][:]
self.score = h5f['score'][:]
self.consecutiveViolations = h5f['consecutiveViolations'][:]
self.contactViolations = h5f['contactViolations'][:]
self.intraRestraints = h5f['intraRestraints'][:]
self.interRestraints = h5f['interRestraints'][:]
else:
raise RuntimeError, "Invalid filename or file directory!"
#-
return None
def __init__(self,target,usegrp=None,nstruct=10000,pid=10,**kwargs):
if os.path.isdir(target):
#the target is a valid population structure directory
if usegrp==None:
raise RuntimeError, "group key is not specified!"
firststr = files.modelstructures(os.path.join(target,"copy0.hms"),[usegrp])
self.idx = firststr.idx
self.genome = firststr.genome
self.usegrp = usegrp
self.nbead = len(self.idx)
self.nstruct = nstruct
self.radius = firststr[-1].r
print("reading %d structures info in %s,%s"%(nstruct,target,usegrp))
while nstruct%pid != 0:
pid = int(pid/2)
self._readStructures(target,pid,**kwargs)
elif os.path.isfile(target) and os.path.splitext(target)[1] == '.hss':
h5f = h5py.File(target,'r')
self.idx = h5f['idx'][:]
self.genome = pickle.loads(h5f['genome'].value)
self.usegrp = pickle.loads(h5f['usegrp'].value)
self.nbead = pickle.loads(h5f['nbead'].value)
self.nstruct = pickle.loads(h5f['nstruct'].value)
self.radius = h5f['radius'][:]
self.coordinates = h5f['coordinates'][:]
self.score = h5f['score'][:]
self.consecutiveViolations = h5f['consecutiveViolations'][:]
self.contactViolations = h5f['contactViolations'][:]
self.intraRestraints = h5f['intraRestraints'][:]
self.interRestraints = h5f['interRestraints'][:]
else:
raise RuntimeError, "Invalid filename or file directory!"
#-
return None
def _readInfo(self,target,start,end,usegrp,
coor_shared,
consecVio_shared,contactVio_shared,
score_shared,
intrares_shared,interres_shared,silence=True):
"""
Read in all information
"""
arr = np.frombuffer(coor_shared.get_obj())
modelcoor = arr.reshape((self.nstruct,self.nbead*2,3)) #10000 * 4640 * 3
for i in range(start,end):
try:
if not silence:
print(i)
sts = files.modelstructures(os.path.join(target,'copy'+str(i)+'.hms'),[usegrp])
modelcoor[i][:] = sts[0].xyz
score_shared[i] = sts[0].score
try:
consecVio_shared[i] = sts[0].consecutiveViolations
contactVio_shared[i] = sts[0].contactViolations
except:
consecVio_shared[i] = np.nan
contactVio_shared[i] = np.nan
try:
intrares_shared[i] = sts[0].intraRestraints
interres_shared[i] = sts[0].interRestraints
except:
intrares_shared[i] = np.nan
interres_shared[i] = np.nan
except RuntimeError:
print("Can't find result for copy %s , %s at %s" %(str(i),usegrp,os.path.join(target,'copy'+str(i)+'.hms')))
return 0
def _readInfo(self,target,start,end,usegrp,
coor_shared,
consecVio_shared,contactVio_shared,
score_shared,
intrares_shared,interres_shared,silence=True):
"""
Read in all information
"""
arr = np.frombuffer(coor_shared.get_obj())
modelcoor = arr.reshape((self.nstruct,self.nbead*2,3)) #10000 * 4640 * 3
for i in range(start,end):
try:
if not silence:
print(i)
sts = files.modelstructures(os.path.join(target,'copy'+str(i)+'.hms'),[usegrp])
modelcoor[i][:] = sts[0].xyz
score_shared[i] = sts[0].score
try:
consecVio_shared[i] = sts[0].consecutiveViolations
contactVio_shared[i] = sts[0].contactViolations
except:
consecVio_shared[i] = np.nan
contactVio_shared[i] = np.nan
try:
intrares_shared[i] = sts[0].intraRestraints
interres_shared[i] = sts[0].interRestraints
except:
intrares_shared[i] = np.nan
interres_shared[i] = np.nan
except RuntimeError:
print("Can't find result for copy %s , %s at %s" %(str(i),usegrp,os.path.join(target,'copy'+str(i)+'.hms')))
return 0
