def add(self, rights):
if rights:
try:
rights = rights.split(',')
except AttributeError:
pass
for right in rights:
set.add(self, right)
def add(self, set, item, i=None, predecessor=None, causal=None):
if predecessor is None:
if item not in set:
set.append(item)
else:
key = (item, i)
if item not in set:
self.links[key] = []
set.append(item)
self.links[key].append((predecessor, causal))
def reloadMirrors(self):
mirrors = sysconf.get("mirrors", {})
for channel in self._channels.values():
if isinstance(channel, MirrorsChannel):
cmirrors = channel.getMirrors()
if cmirrors:
for origin in cmirrors:
set = dict.fromkeys(cmirrors[origin])
set.update(dict.fromkeys(mirrors.get(origin, [])))
mirrors[origin] = set.keys()
msys = self._fetcher.getMirrorSystem()
msys.setMirrors(mirrors)
if not msys.getHistory():
msys.setHistory(sysconf.get("mirrors-history", []))
def __init__(self, reference_system, receptor_atoms=[], ligand_atoms=[]):
"""
Initialize absolute alchemical intermediate factory with reference system.
ARGUMENTS
reference_system (System) - reference system containing receptor and ligand
ligand_atoms (list) - list of atoms to be designated 'ligand' -- everything else in system is considered the 'environment'
receptor_atoms (list) - list of atoms to be considered in softening specific 'receptor' degrees of freedom -- shouldn't be the whole receptor, but a subset of atoms in binding site
"""
# Create pyopenmm System object.
self.reference_system = pyopenmm.System(reference_system)
# Store copy of atom sets.
self.receptor_atoms = copy.deepcopy(receptor_atoms)
self.ligand_atoms = copy.deepcopy(ligand_atoms)
# Store atom sets
self.ligand_atomset = Set(self.ligand_atoms)
self.receptor_atomset = Set(self.receptor_atoms)
# Make sure intersection of ligand and receptor atomsets is null.
intersection = Set.intersection(self.ligand_atomset, self.receptor_atomset)
if (len(intersection) > 0):
raise ParameterException("receptor and ligand atomsets must not overlap.")
return
def __new__(cls, *args, **kwargs):
if args:
new_args = (args[0], )
else:
new_args = ()
obj = set.__new__(cls, *new_args)
obj.__init__(*args, **kwargs)
return obj
def __init__(self, *args) : # Handle special case when this __init__ is used as a copy constructor, # i.e. with Set or ifilter instance as a sole argument # This is needed to overcome flawed standard sets implementation in Python 2.3+ if len(args) == 1 : x = args[0] if isinstance(x, (Set, itertools.ifilter)) : _Set.__init__(self, x) return # ALARM : dependence on the sets.Set implementation !!! xargs = [] for x in args : if isinstance(x, Keyword) : xargs.append(x) else : xargs.append(Keyword(x)) _Set.__init__(self, xargs)
def update_set (self, set):
if set == self.content_set:
return
model, iter = self.treeview.get_selection ().get_selected ()
if iter:
# save the selected content so that it will be selected again
# later
self.selected_content = model[iter][self.COLUMN_EDITABLE]
self.content_set = set.copy ()
self.__update_model ()
def findNeighbors(self) :
neighbors = []
nEdges = 0
for i in range(self.numElems()) :
allNeighbors = Set()
for v in self.elemVerts_[i] :
allNeighbors = Set.union(allNeighbors, self.vertToElemMap_[v])
# get rid of self-references
allNeighbors.discard(i)
fullNeighbors = []
for j in allNeighbors :
numCommonNodes = Set.intersection(self.elemVerts_[i],
self.elemVerts_[j])
if len(numCommonNodes) == self.dim_ :
fullNeighbors.append(j)
nEdges = nEdges + len(fullNeighbors)
neighbors.append(fullNeighbors)
nEdges = nEdges/2
return (neighbors, nEdges)
def pattern_filter(pattern, xs, report_failed=None, check_errors=False,
range_match=False):
ps = pattern.split(",")
filtered_set = set([])
for p0 in ps:
p = p0.split("excluding")
if (len(p) == 1):
try:
pstr = p[0].strip()
p = re.compile(pstr + "$")
except:
sys.stderr.write("ERROR:`"+p[0].strip()+"' is not a valid regular expression ")
if (report_failed):
sys.stderr.write(report_failed)
sys.stderr.write("\n")
exit(1)
found = False
for item in xs:
if p.match(str(item)):
found = True
filtered_set.add((item,0))
elif range_match:
range_pattern = re.compile("(.*)__RANGE$")
m = range_pattern.match(str(item))
if m:
item_root = m.groups(0)[0]
item_pattern = re.compile(item_root + "_(.*)")
m = item_pattern.match(pstr)
if m:
n = int(m.groups(0)[0])
filtered_set.add((item, n))
if check_errors and report_failed and not found:
sys.stderr.write("Cannot match `" + p0 + "'" + report_failed +"\n")
if check_errors:
exit(1)
else:
in_pattern = re.compile(p[0].strip())
exc_pattern = re.compile(p[1].strip())
in_set = set([])
exc_set = set([])
for item in xs:
if in_pattern.match(str(item)):
in_set.add(item)
if exc_pattern.match(str(item)):
exc_set.add(item)
in_set = in_set - exc_set
filtered_set = set.union(filtered_set, in_set)
return list(filtered_set)
def _is_restraint(self, valence_atoms):
"""
Determine whether specified valence term connects the ligand with its environment.
Parameters
----------
valence_atoms : list of int
Atom indices involved in valence term (bond, angle or torsion).
Returns
-------
is_restraint : bool
True if the set of atoms includes at least one ligand atom and at least one non-ligand atom; False otherwise
Examples
--------
Various tests for a simple system.
>>> # Create a reference system.
>>> from repex import testsystems
>>> alanine_dipeptide = testsystems.AlanineDipeptideImplicit()
>>> [reference_system, positions] = [alanine_dipeptide.system, alanine_dipeptide.positions]
>>> # Create a factory.
>>> factory = AbsoluteAlchemicalFactory(reference_system, ligand_atoms=[0, 1, 2])
>>> factory._is_restraint([0,1,2])
False
>>> factory._is_restraint([1,2,3])
True
>>> factory._is_restraint([3,4])
False
>>> factory._is_restraint([2,3,4,5])
True
"""
valence_atomset = Set(valence_atoms)
intersection = Set.intersection(valence_atomset, self.ligand_atomset)
if (len(intersection) >= 1) and (len(intersection) < len(valence_atomset)):
return True
return False
def _is_restraint(self, valence_atoms):
"""
Determine whether specified valence term connects the ligand with its environment.
ARGUMENTS
valence_atoms (list of int) - atom indices involved in valence term (bond, angle or torsion)
RETURNS
True if the set of atoms includes at least one ligand atom and at least one non-ligand atom; False otherwise
EXAMPLES
Various tests.
>>> # Create a reference system.
>>> import testsystems
>>> [reference_system, coordinates] = testsystems.AlanineDipeptideImplicit()
>>> # Create a factory.
>>> factory = AbsoluteAlchemicalFactory(reference_system, alchemical_atoms=[0, 1, 2])
>>> factory._is_restraint([0,1,2])
False
>>> factory._is_restraint([1,2,3])
True
>>> factory._is_restraint([3,4])
False
>>> factory._is_restraint([2,3,4,5])
True
"""
valence_atomset = Set(valence_atoms)
intersection = Set.intersection(valence_atomset, self.alchemical_atomset)
if (len(intersection) >= 1) and (len(intersection) < len(valence_atomset)):
return True
return False
def remove(self, *args):
print "removing %s" % args
return Set.remove(self, *args)
def __init__(self, *args):
print "starting with %s" % (args,)
Set.__init__(self, *args)
def test_difference_superset(self):
self.set -= Set((2, 4, 6, 8))
self.assertEqual(self.set, Set([]))
def test_difference_method_call(self):
self.set.difference_update(Set([3, 4, 5]))
self.assertEqual(self.set, Set([2, 6]))
def __init__(self, *args):
set.__init__(self, args)
def test_add_present(self):
self.set.add("c")
self.assertEqual(self.set, Set("abc"))
def test_sym_difference_method_call(self):
self.set.symmetric_difference_update(Set([3, 4, 5]))
self.assertEqual(self.set, Set([2, 3, 5, 6]))
def test_update_unit_tuple_non_overlap(self):
self.set.union_update(("a", "z"))
self.assertEqual(self.set, Set(self.values + ["z"]))
def test_update_unit_tuple_overlap(self):
self.set.union_update(("a", ))
self.assertEqual(self.set, Set(self.values))
def test_update_empty_tuple(self):
self.set.union_update(())
self.assertEqual(self.set, Set(self.values))
def test_discard_absent(self):
self.set.discard("d")
self.assertEqual(self.set, Set("abc"))
def test_discard_present(self):
self.set.discard("c")
self.assertEqual(self.set, Set("ab"))
def test_remove_present(self):
self.set.remove("b")
self.assertEqual(self.set, Set("ac"))
def test_add_absent(self):
self.set.add("d")
self.assertEqual(self.set, Set("abcd"))
class TestSubsetEqualEmpty(TestSubsets):
left = Set()
right = Set()
name = "both empty"
cases = "==", "<=", ">="
def db_update(self):
self._check_new_set()
for set in self.sets.values():
set.db_update()
class TestSubsetEqualNonEmpty(TestSubsets):
left = Set([1, 2])
right = Set([1, 2])
name = "equal pair"
cases = "==", "<=", ">="
def __init__(self, privacy=()):
if privacy is None or privacy == '!':
privacy = ()
if isinstance(privacy, basestring):
privacy = privacy.split(',')
set.__init__(self, privacy)
class TestSubsetEmptyNonEmpty(TestSubsets):
left = Set()
right = Set([1, 2])
name = "one empty, one non-empty"
cases = "!=", "<", "<="
def findspikes(xin, vin, thresh, t0=None, t1= None, dt=1.0, mode=None, interpolate=False, debug=False):
""" findspikes identifies the times of action potential in the trace v, with the
times in t. An action potential is simply timed at the first point that exceeds
the threshold... or is the peak.
4/1/11 - added peak mode
if mode is none or schmitt, we work as in the past.
if mode is peak, we return the time of the peak of the AP instead
7/15/11 - added interpolation flag
if True, the returned time is interpolated, based on a spline fit
if False, the returned time is just taken as the data time.
2012/10/9: Removed masked arrays and forced into ndarray from start
(metaarrays were really slow...)
"""
# if debug:
# # this does not work with pyside...
# import matplotlib
# matplotlib.use('Qt4Agg')
# import pylab
# from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
# from matplotlib.figure import Figure
#
# #MP.rcParams['interactive'] = False
st=numpy.array([])
spk = []
if xin is None:
return(st, spk)
xt = xin.view(numpy.ndarray)
v = vin.view(numpy.ndarray)
if t1 is not None and t0 is not None:
it0 = int(t0/dt)
it1 = int(t1/dt)
if not isinstance(xin, numpy.ndarray):
xt = xt[it0:it1]
v = v[it0:it1]
else:
xt = xt[it0:it1]
v = v[it0:it1]
# if debug:
# f = pylab.figure(1)
# print "xt: ", xt
# print "v: ", v
# pylab.plot(numpy.array(xt), v, 'k-')
# pylab.draw()
# pylab.show()
dv = numpy.diff(v, axis=0) # compute slope
dv /= dt
st=numpy.array([])
spk = []
spv = numpy.where(v > thresh)[0].tolist() # find points above threshold
sps = numpy.where(dv > 0.0)[0].tolist() # find points where slope is positive
sp = list(Set.intersection(Set(spv),Set(sps))) # intersection defines putative spikes
sp.sort() # make sure all detected events are in order (sets is unordered)
sp = tuple(sp) # convert to tuple
if sp is ():
return(st, spk) # nothing detected
dx = 1
mingap = int(0.0005/dt) # 0.5 msec between spikes (a little unphysiological...)
# normal operating mode is fixed voltage threshold
# for this we need to just get the FIRST positive crossing,
if mode is 'schmitt':
sthra = list(numpy.where(numpy.diff(sp) > mingap))
sthr = [sp[x] for x in sthra[0]] # bump indices by 1
for k in sthr:
x = xt[k-1:k+1]
y = v[k-1:k+1]
if interpolate:
dx = 0
m = (y[1]-y[0])/dt # local slope
b = y[0]-(x[0]*m)
s0 = (thresh-b)/m
else:
s0 = x[1]
st = numpy.append(st, x[1])
elif mode is 'peak':
pkwidth = 1.0e-3 # in same units as dt - usually msec
kpkw = int(pkwidth/dt)
z = (numpy.array(numpy.where(numpy.diff(spv) > 1)[0])+1).tolist()
z.insert(0, 0) # first element in spv is needed to get starting AP
spk = []
for k in z:
zk = spv[k]
spkp = numpy.argmax(v[zk:zk+kpkw])+zk # find the peak position
x = xt[spkp-1:spkp+2]
y = v[spkp-1:spkp+2]
if interpolate:
try:
# mimic Igor FindPeak routine with B = 1
m1 = (y[1]-y[0])/dt # local slope to left of peak
b1 = y[0]-(x[0]*m1)
m2 = (y[2]-y[1])/dt # local slope to right of peak
b2 = y[1]-(x[1]*m2)
mprime = (m2-m1)/dt # find where slope goes to 0 by getting the line
bprime = m2-((dt/2.0)*mprime)
st = numpy.append(st, -bprime/mprime+x[1])
spk.append(spkp)
except:
continue
else:
st = numpy.append(st, x[1]) # always save the first one
spk.append(spkp)
return(st, spk)
class TestSubsetPartial(TestSubsets):
left = Set([1])
right = Set([1, 2])
name = "one a non-empty proper subset of other"
cases = "!=", "<", "<="
def __init__(self, sequence=tuple()):
DependencyCell.__init__(self)
set.__init__(self, sequence)
class TestSubsetNonOverlap(TestSubsets):
left = Set([1])
right = Set([2])
name = "neither empty, neither contains"
cases = "!="
def __init__(self, rights=None):
set.__init__(self)
self.add(rights)
def setUp(self):
self.set = Set((1, 2, 3))
self.other = 19
self.otherIsIterable = False
def __init__(self,iterable=None):
Set.__init__(self,iterable)
def setUp(self):
self.set = Set((1, 2, 3))
self.other = {1: 2, 3: 4}
self.otherIsIterable = True
def add(self, *args):
print "adding %s" % args
return Set.add(self, *args)
def setUp(self):
self.set = Set((1, 2, 3))
self.other = operator.add
self.otherIsIterable = False
def test_difference_subset(self):
self.set -= Set((2, 4))
self.assertEqual(self.set, Set([6]))
def setUp(self):
self.set = Set((1, 2, 3))
self.other = (2, 4, 6)
self.otherIsIterable = True
def db_has_changed(self):
self._check_new_set()
for set in self.sets.values():
if set.db_has_changed():
return True
return False
def setUp(self):
self.set = Set((1, 2, 3))
self.other = 'abc'
self.otherIsIterable = True
def db_revert(self):
self._new_set = None
for set in self.sets.values():
set.db_revert()
def add(self, thing):
print '%s ok' % thing
Set.add(self, thing)
def uniq(alist):
set = {}
return [set.setdefault(e,e) for e in alist if e not in set]
def __repr__(self):
return '%s(%s), %s' % (self.__class__.__name__, Set.__repr__(self))
def setUp(self):
self.set = Set((1, 2, 3))
self.other = [Set('ab'), ImmutableSet('cd')]
self.otherIsIterable = True
def setUp(self):
self.values = ["a", "b", "c"]
self.set = Set(self.values)
def test_sym_difference_overlap(self):
self.set ^= Set((3, 4, 5))
self.assertEqual(self.set, Set([2, 3, 5, 6]))
def __contains__(self, x) : if isinstance(x, Keyword) : return _Set.__contains__(self, x) else : return _Set.__contains__(self, Keyword(x))
def setUp(self):
self.set = Set(["hello"])
def setUp(self):
self.set = Set(["zero", 0, None])
def __init__(self, iterable=None):
Set.__init__(self)
self._data = WeakKeyDictionary()
if iterable is not None:
self._update(iterable)
def test_difference_overlap(self):
self.set -= Set((3, 4, 5))
self.assertEqual(self.set, Set([2, 6]))
def makeChacoGraphFile(filename) :
f = file(filename + '.ele')
nodeToEleMap = {}
elemVerts = []
# read header
while 1 :
line = f.readline()
if line[0]=='#': continue
header = line.split()
nElems = int(header[0])
d = int(header[1])-1
break
# read lines, building elements and the element-to-node map
while 1:
line = f.readline()
if not line : break
if line[0]=='#': continue
toks = line.split()
ele = int(toks[0])
verts = Set()
for i in range(d+1) :
node = int(toks[i+1])
verts.add(node)
if nodeToEleMap.has_key(node) :
nodeToEleMap[node].add(ele)
else :
nodeToEleMap[node] = Set()
nodeToEleMap[node].add(ele)
elemVerts.append(verts)
# For each node, assign one of the adjoining elements as its "owner."
# The node will later be assigned to the same processer as the owner.
# The choice of owner is arbitrary; here, we simply choose the
# adjoining element having the largest index.
#
# We write the ownership information to a file, with the format:
# line 1: <num nodes>
# line 2: <node 1 number> <node 1 owner>
# etc.
nodeOwnerFile = file(filename + '.owner', 'w')
nodeOwnerFile.write('%d\n' % len(nodeToEleMap.keys()))
for node in nodeToEleMap.keys() :
owner = max(nodeToEleMap[node])
nodeOwnerFile.write('%d %d\n' % (node, owner))
# determine lists of neighbors for each element
neighbors = []
nEdges = 0
for i in range(nElems) :
allNeighbors = Set()
for v in elemVerts[i] :
allNeighbors = Set.union(allNeighbors, nodeToEleMap[v])
# get rid of self-references
allNeighbors.discard(i)
fullNeighbors = []
for j in allNeighbors :
numCommonNodes = Set.intersection(elemVerts[i], elemVerts[j])
if len(numCommonNodes) == d :
fullNeighbors.append(j)
nEdges = nEdges + len(fullNeighbors)
neighbors.append(fullNeighbors)
nEdges = nEdges/2
graphFile = file(filename + '.graph', 'w')
graphFile.write('%d %d\n' % (nElems, nEdges))
for i in range(nElems) :
line = ''
for j in neighbors[i] :
line = line + '%d ' % (j+1)
graphFile.write(line + '\n');
graphFile.flush()
return (elemVerts, nodeToEleMap)
def __init__(self,iterable=None):
'''Construct a multiset from an optional iterable.'''
Set.__init__(self,iterable)
def setUp(self):
self.set = Set()
def test_difference_non_overlap(self):
self.set -= Set([8])
self.assertEqual(self.set, Set([2, 4, 6]))