def subtree_of(subtree, tree, exact=False, tolerance=0):
'''
Test to see if `subtree` is included in `tree` anywhere. Returns the
node id number of the first occurence of `subtree` included in `tree` or |None|
if it is not found.
Parameters
----------
subtree: Glycan
The structure to search for. The search attempts to match the complete structure of subtree.
tree: Glycan
The sturcture to search in. The search iterates over each residue in `tree` and calls a comparator
function, comparing the `subtree` to the substructure rooted at that residue.
exact: bool
If |True|, use :func:`exact_ordering_inclusion` to compare nodes. Otherwise use :func:`topological_inclusion`.
Defaults to |False|.
Returns
-------
|int| or |None| if no match
'''
if exact:
comparator = exact_ordering_inclusion
else:
comparator = topological_inclusion
tree_root = root(subtree)
for node in tree:
if comparator(tree_root, node):
return node.id
return None
def __init__(self, structure, figure=None, ax=None, layout=buchheim, symbol_nomenclature=cfg_symbols, **kwargs):
self.structure = structure
self.root = DrawTreeNode(root(structure))
self.figure = figure
self.ax = ax
self.layout_scheme = layout
self.symbol_nomenclature = symbol_nomenclature
def plot(tree, at=(1, 1), ax=None, orientation='h', center=False, label=False,
symbol_nomenclature='cfg', layout='balanced', **kwargs):
'''
Draw the parent outlink position and the child anomer symbol
Parameters
----------
tree: Glycan or Monosaccharide
The saccharide structure to draw.
orientation: str
A string corresponding to `h` or `horizontal` will draw the glycan horizontally
from right to left. `v` or `vertical` will draw the glycan from bottom to top.
Defaults to `h`
at: tuple
The x, y coordinates at which to draw the glycan's reducing_end. Defaults to `(0, 0)`
ax: :class:`matplotlib.axes.Axis`
A matplotlib axis on which to draw. Useful for adding glycans to existing figures. If
an axis is not provided, a new figure will be created and used.
center: bool
Should the plot limits be centered around this glycan? Defaults to |False| but will be
be set to |True| if `ax` is |None|
label: bool
Should the bond annotations for `tree` be drawn? Defaults to |False|
scale: (float, float) or float
Node scale coefficients. Pass a pair to scale x and y dimensions respectively.
stretch: (float, float) or float
Edge length coefficients. Pass a pair to scale x and y dimensions respectively. Order is
affected by `orientation`
'''
scale = kwargs.get("scale", DEFAULT_SYMBOL_SCALE_FACTOR)
if isinstance(symbol_nomenclature, basestring):
symbol_nomenclature = nomenclature_map.get(symbol_nomenclature)
if isinstance(layout, basestring):
layout = layout_map.get(layout)
tree_root = root(tree)
dtree = DrawTreeNode(tree_root)
if layout == topological:
for node in breadth_first_traversal(dtree):
node.mask_special_cases = False
layout(dtree)
if layout != topological:
dtree.fix_special_cases()
fig = None
# Create a figure if no axes are provided
if ax is None:
fig, ax = plt.subplots()
at = (0, 0)
center = True
ax.axis('off')
dtree.draw(at=at, ax=ax, scale=scale, label=False,
symbol_nomenclature=symbol_nomenclature, **kwargs)
dtree.axes = ax
dtree.data['orientation'] = orientation
if label:
dtree.draw_linkage_annotations(
at=at, ax=ax, scale=scale,
symbol_nomenclature=symbol_nomenclature, **kwargs)
if orientation in {"h", "horizontal"}:
dtree.transform(mtransforms.Affine2D().rotate_deg(90))
dtree._rotate_text(-90)
# If the figure is stand-alone, center it
if fig is not None or center:
xmin, xmax, ymin, ymax = dtree.extrema(at=at)
ax.set_xlim(xmin - 2, xmax + 2)
ax.set_ylim(ymin - 2, ymax + 2)
ax.autoscale_view()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
return (dtree, ax)
def pack(self):
d = self.processor(''.join(self.sequence_chunks))
name = self.defline
root_node = root(d)
return NamedGlycan(name=name, root=root_node, index_method=None)