def check_required_attributes(self, entity_set_index, attribute_list):
"""Check that all the elements of the given entity_set have all
the attributes in the attribute_list.
"""
# get_entities will validate entity_set_index
entities = self.get_entities(entity_set_index)
if type(entities) == types.GeneratorType:
# @@ figure out how to check generator attributes !!
return
# check each attribute
typeList = [types.ListType, types.DictType] #, types.InstanceType]
from mglutil.util.misc import isInstance
for attr in attribute_list:
# get returns the subset of entities
# for which the expression is true
ents = entities.get(lambda x: hasattr(x, attr))
if ents == None or len(ents) != len(entities):
raise AttributeError, \
"All Entities do not have required Entity attribute (%s) " % attr
ent0 = entities[0]
if type(getattr(ent0, attr)) in typeList \
or isInstance(getattr(ent0, attr)) is True:
if len(getattr(ent0, attr)) == 0:
raise ValueError, \
"Required Entity attribute (%s) has zero length" % attr
def check_required_attributes(self, entity_set_index, attribute_list):
"""Check that all the elements of the given entity_set have all
the attributes in the attribute_list.
"""
# get_entities will validate entity_set_index
entities = self.get_entities( entity_set_index)
if type(entities) == types.GeneratorType:
# @@ figure out how to check generator attributes !!
return
# check each attribute
typeList = [types.ListType, types.DictType]#, types.InstanceType]
from mglutil.util.misc import isInstance
for attr in attribute_list:
# get returns the subset of entities
# for which the expression is true
ents = entities.get( lambda x: hasattr(x, attr))
if ents==None or len(ents)!=len(entities):
raise AttributeError, \
"All Entities do not have required Entity attribute (%s) " % attr
ent0 = entities[0]
if type(getattr(ent0, attr)) in typeList \
or isInstance(getattr(ent0, attr)) is True:
if len(getattr(ent0, attr))==0:
raise ValueError, \
"Required Entity attribute (%s) has zero length" % attr
def process(self, nodes, criteria, sets=None):
# print "in process with len(nodes)=", len(nodes), ' and criteria=', criteria
# print "type(criteria)==", type(criteria)
msg_to_return = ""
if type(criteria) == str:
selected, msg = self.do_op(nodes, criteria, sets=sets)
# print " back in process with len(selected) = ", len(selected)
msg_to_return += msg
# elif type(criteria)==types.InstanceType:
elif isInstance(criteria) is True:
selected = criteria
return selected, msg_to_return
def process(self, nodes, criteria, sets=None):
#print "in process with len(nodes)=", len(nodes), ' and criteria=', criteria
#print "type(criteria)==", type(criteria)
msg_to_return = ""
if type(criteria)==types.StringType:
selected, msg = self.do_op(nodes, criteria, sets=sets)
#print " back in process with len(selected) = ", len(selected)
msg_to_return += msg
#elif type(criteria)==types.InstanceType:
elif isInstance(criteria) is True:
selected = criteria
return selected, msg_to_return
def _strArg(self, arg):
"""
Method to turn a command argument into a string for logging purposes
Add support for TreeNodes and TreeNodeSets
"""
#if type(arg)==types.InstanceType:
from mglutil.util.misc import isInstance
if isInstance(arg) is True:
if issubclass(arg.__class__, TreeNode):
return '"' + arg.full_name() + '", ', None
if issubclass(arg.__class__, TreeNodeSet):
stringRepr = arg.getStringRepr()
if stringRepr:
return '"' + stringRepr + '", ', None
else:
name = ""
mols, elems = self.vf.getNodesByMolecule(arg)
for elem in elems:
name = name + elem.full_name() +';'
return '"' + name + '", ', None
return Command._strArg(self, arg)
def _strArg(self, arg):
"""
Method to turn a command argument into a string for logging purposes
Add support for TreeNodes and TreeNodeSets
"""
#if type(arg)==types.InstanceType:
from mglutil.util.misc import isInstance
if isInstance(arg) is True:
if issubclass(arg.__class__, TreeNode):
return '"' + arg.full_name() + '", ', None
if issubclass(arg.__class__, TreeNodeSet):
stringRepr = arg.getStringRepr()
if stringRepr:
return '"' + stringRepr + '", ', None
else:
name = ""
mols, elems = self.vf.getNodesByMolecule(arg)
for elem in elems:
name = name + elem.full_name() + ';'
return '"' + name + '", ', None
return Command._strArg(self, arg)
def setroot(self, atom):
"""
setroot to 'C11' or 'hsg1:A:ILE2:CA'
"""
if type(atom)==types.StringType:
if find(atom, ':')>-1:
#have to use full_name list
#check that it is an atom
mols = ProteinSet([self])
nodes = mols.NodesFromName(atom)
if not nodes:
return 'invalid root name'
if nodes.__class__!=AtomSet:
return 'invalid root name: not atom level'
else:
nodes = self.allAtoms.get(lambda x, n = atom:x.name==n)
if not nodes:
return 'invalid root name'
if len(nodes)>1:
return 'root name must be unique'
atom = nodes[0]
#elif type(atom)!=types.InstanceType:
elif isInstance(atom) is False:
return atom, ' invalid root atom'
elif atom.__class__!=Atom:
return atom, ' can only select an Atom instance as root'
#fix this rnum0 stuff
#in case toggling back and forth
if hasattr(self, 'autoRoot') and hasattr(self.autoRoot, 'rnum0'):
delattr(self.autoRoot, 'rnum0')
#if there is an old root, remove rnum0
if hasattr(self, 'ROOT') and hasattr(self.ROOT, 'rnum0'):
delattr(self.ROOT, 'rnum0')
self.ROOT = atom
self.ROOT.rnum0 = 0
return self.ROOT
def setroot(self, atom):
"""
setroot to 'C11' or 'hsg1:A:ILE2:CA'
"""
if type(atom) == bytes:
if find(atom, ':') > -1:
#have to use full_name list
#check that it is an atom
mols = ProteinSet([self])
nodes = mols.NodesFromName(atom)
if not nodes:
return 'invalid root name'
if nodes.__class__ != AtomSet:
return 'invalid root name: not atom level'
else:
nodes = self.allAtoms.get(lambda x, n=atom: x.name == n)
if not nodes:
return 'invalid root name'
if len(nodes) > 1:
return 'root name must be unique'
atom = nodes[0]
#elif type(atom)!=types.InstanceType:
elif isInstance(atom) is False:
return atom, ' invalid root atom'
elif atom.__class__ != Atom:
return atom, ' can only select an Atom instance as root'
#fix this rnum0 stuff
#in case toggling back and forth
if hasattr(self, 'autoRoot') and hasattr(self.autoRoot, 'rnum0'):
delattr(self.autoRoot, 'rnum0')
#if there is an old root, remove rnum0
if hasattr(self, 'ROOT') and hasattr(self.ROOT, 'rnum0'):
delattr(self.ROOT, 'rnum0')
self.ROOT = atom
self.ROOT.rnum0 = 0
return self.ROOT