def add_sep_part(sep, pos, lst):
if sep is not None and not isNone(sep) and \
not (sep.type == token.STRING and sep.value in ("' '", '" "')):
temp = []
for arg in pos:
temp.append(_unicode(arg.clone()))
if sys.version_info >= (2, 6):
warnings.warn(
"Calling unicode() on what may be a bytes object")
temp.append(Comma())
del temp[-1]
sep = sep.clone()
sep.prefix = " "
args = Node(syms.listmaker, temp)
new_list = Node(syms.atom,
[Leaf(token.LSQB, "["), args,
Leaf(token.RSQB, "]")])
join_arg = Node(syms.trailer, [LParen(), new_list, RParen()])
sep_join = Node(syms.power,
[sep, Node(syms.trailer, [Dot(), Name("join")])])
lst.append(sep_join)
lst.append(join_arg)
else:
if pos:
pos[0].prefix = " "
for arg in pos:
lst.append(arg.clone())
lst.append(Comma())
del lst[-1]
def transform(self, node, results):
method = results['method']
method_name = method.value
if method_name == 'numframes':
method_name = 'n_frames'
syms = self.syms
args = [pytree.Node(syms.trailer, [Dot(), Name(method_name)])]
new = pytree.Node(syms.power, args)
return new
def add_end_part(end, file, parent, loc):
if isNone(end):
return
if end.type == token.STRING and end.value in ("' '", '" "', "u' '", 'u" "',
"b' '", 'b" "'):
return
if file is None:
touch_import(None, "sys", parent)
file = Node(syms.power,
[Name("sys"),
Node(syms.trailer, [Dot(), Name("stdout")])])
end_part = Node(syms.power, [
file,
Node(syms.trailer, [Dot(), Name("write")]),
Node(syms.trailer, [LParen(), end, RParen()])
])
end_part.prefix = " "
parent.insert_child(loc, Leaf(token.SEMI, ";"))
parent.insert_child(loc + 1, end_part)
def DottedName(full_name: str, prefix: Optional[str]) -> Node:
names = [name.strip() for name in full_name.split(".")]
dotted_name = []
for name in names:
dotted_name.append(Name(name))
dotted_name.append(Dot())
dotted_name.pop()
return Node(syms.dotted_name, dotted_name, prefix=prefix)
def transform(self, node, results):
head = results['head']
method = results['method']
tail = results['tail']
syms = self.syms
method_name = 'dihedrals'
head = [n.clone() for n in head]
tail = [n.clone() for n in tail]
args = head + [pytree.Node(syms.trailer, [Dot(), Name(method_name, prefix = method.prefix)])]
new = pytree.Node(syms.power, args)
return new
def transform(self, node, results):
method = results['method'][0]
method_name = method.value
#with the exception of applyPBC, all camelcase changes here involve replacing a capital letter with an underscore and the lower case version of that letter
if not method_name == 'applyPBC':
method_name = re.sub(r'([A-Z]{1})', r'_\1', method_name).lower()
else:
method_name = 'apply_PBC'
syms = self.syms
args = [pytree.Node(syms.trailer, [Dot(), Name(method_name)])]
new = pytree.Node(syms.power, args)
return new
def package_tree(self, package):
""" Return pytree tree for accessing the package
Example:
>>> package_tree("Orange.feature.scoring")
[Name('Orange'), trailer('.' 'feature'), trailer('.', 'scoring')]
"""
path = package.split('.')
nodes = [Name(path[0])]
for name in path[1:]:
new = pytree.Node(self.syms.trailer, [Dot(), Name(name)])
nodes.append(new)
return nodes
def transform(self, node, results):
head = results['head']
method = results['method'][0]
tail = results['tail']
syms = self.syms
method_name = method.value
if method_name == 'torsion':
method_name = 'dihedral'
head = [n.clone() for n in head]
tail = [n.clone() for n in tail]
args = head + [
pytree.Node(syms.trailer, [
Dot(),
Name(method_name, prefix=method.prefix),
Dot(),
Name('value'),
LParen(),
RParen()
])
]
new = pytree.Node(syms.power, args)
return new
def transform(self, node, results):
head = results['head']
method = results['method'][0]
tail = results['tail']
syms = self.syms
method_name = method.value
head = [n.clone() for n in head]
tail = [n.clone() for n in tail]
if method_name == 'set_radius': #different plural conversion
method_name = 'set_radii'
elif method_name == 'set_mass': #another different plural form
method_name = 'set_masses'
else:
method_name += 's' #standard plural conversion for all others
args = head + [pytree.Node(syms.trailer, [Dot(), Name(method_name, prefix = method.prefix)])] + tail
new = pytree.Node(syms.power, args)
return new
def transform(self, node, results):
if 'method' in results.keys():
method = results['method']
syms = self.syms
method_name = method.value
replacement_dict = {'calc_torsions': 'calc_dihedrals'}
method_name = replacement_dict[method_name]
args = [
pytree.Node(
syms.trailer,
[Dot(), Name(method_name, prefix=method.prefix)])
]
new = pytree.Node(syms.power, args)
return new
elif 'import_name' in results.keys():
import_name = results['import_name']
import_name.replace(Name(' calc_dihedrals'))
def transform(self, node, results):
head = results['head']
method = results['method'][0]
tail = results['tail']
syms = self.syms
method_name = method.value
head = [n.clone() for n in head]
tail = [n.clone() for n in tail]
replacement_dict = {
'numberOfAtoms': 'n_atoms',
'numberOfResidues': 'n_residues',
'numberOfSegments': 'n_segments'
}
method_name = replacement_dict[method_name]
args = head + [
pytree.Node(syms.trailer,
[Dot(), Name(method_name, prefix=method.prefix)])
]
new = pytree.Node(syms.power, args)
return new
def AttrChain(name: str) -> List[Node]:
first, *rest = name.split(".")
children = [Name(first)]
for attr in rest:
children.append(Node(syms.trailer, [Dot(), Name(attr)]))
return children
