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graph.py
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graph.py
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from operator import itemgetter
from io import StringIO, BytesIO
from numpy import linspace, random
from colorsys import hsv_to_rgb
from math import sqrt, ceil
from typing import Optional, Any, Union, Tuple, Dict
USE_NEIGHBOUR_VALENCES = True
USE_DIFFERENT_ELEMENT_SHAPES = False
OPAQUE = 1.0
RAISE_IF_MISSING_GRAPH_TOOL = False
def graph(data, vertex_text=None, decorate_graph=True, use_random_colors: bool = True, shuffle_equivalence_classes: bool = True):
try:
from graph_tool.all import Graph
except ImportError as e:
if RAISE_IF_MISSING_GRAPH_TOOL:
raise
else:
from sys import stderr
stderr.write('Package graph_tool could not be imported. Error was: {0}'.format(e))
return None
g = Graph(directed=False)
vertex_types = g.new_vertex_property("string")
g.vertex_properties['type'] = vertex_types
if decorate_graph:
vertex_equivalence_classes = g.new_vertex_property("vector<double>")
g.vertex_properties['equivalence_class'] = vertex_equivalence_classes
if USE_DIFFERENT_ELEMENT_SHAPES:
vertex_shapes = g.new_vertex_property("int")
g.vertex_properties['shape'] = vertex_shapes
equivalence_classes = [
atom['equivalenceGroup']
for atom in list(data.atoms.values())
]
unique_equivalence_classes = {}
assigned_equivalence_classes = {}
next_equivalence_class = 0
for (atom_index, atom) in sorted(list(data.atoms.items()), key=itemgetter(0)):
if atom['equivalenceGroup'] == -1:
unique_equivalence_classes[atom_index] = next_equivalence_class
next_equivalence_class += 1
else:
if atom['equivalenceGroup'] not in assigned_equivalence_classes:
assigned_equivalence_classes[atom['equivalenceGroup']] = next_equivalence_class
next_equivalence_class += 1
unique_equivalence_classes[atom_index] = assigned_equivalence_classes[atom['equivalenceGroup']]
range_unique_equivalence_classes = list(range(len(set(unique_equivalence_classes.values()))))
equivalence_class_permutation = dict(
list(zip(
range_unique_equivalence_classes,
(random.permutation(range_unique_equivalence_classes) if shuffle_equivalence_classes else range_unique_equivalence_classes), # pylint: disable=no-member
)),
)
unique_elements = set([atom['type'] for atom in list(data.atoms.values())])
symbol_index_for_element = dict(
list(map(
lambda n_element: (n_element[1], n_element[0] % 15), # There are only 15 different symbols
enumerate(unique_elements),
)),
)
hues = linspace( # pylint: disable=no-member
0.0,
1.0,
len(
set(
list(unique_equivalence_classes.values()),
),
) // 2 + 1,
).tolist()
colours = list(map(
lambda c: hsv_to_rgb(*c),
[(H, S, 0.5) for H in hues for S in (0.3, 0.9)],
))
# Shuffle the colours around the graph
colours = (
[
# Numpy cast all tuples to lists; needs to be reverted
tuple(colour)
for colour in random.permutation(colours).tolist()
]
if use_random_colors
else colours
)
if vertex_text == 'element_valence':
vertex_text_fct = lambda atom_index, atom: '{element}{valence}'.format(
element=atom['type'],
valence=len(atom['conn']) if USE_NEIGHBOUR_VALENCES else '',
)
elif vertex_text == 'element_equivalence':
vertex_text_fct = lambda atom_index, atom: '{element}{equivalence}'.format(
element=atom['type'],
equivalence=unique_equivalence_classes[atom_index],
)
elif vertex_text == 'name_equivalence':
vertex_format_str = '{symbol} ({equivalence})'
vertex_text_fct = lambda atom_index, atom: vertex_format_str.format(
symbol=atom['symbol'],
equivalence=unique_equivalence_classes[atom_index],
)
else:
raise Exception('Unvalid vertex_text')
vertices = {}
for (atom_index, atom) in sorted(list(data.atoms.items()), key=itemgetter(0)):
v = g.add_vertex()
vertex_types[v] = vertex_text_fct(atom_index, atom)
vertices[atom_index] = v
if decorate_graph:
vertex_equivalence_classes[v] = colours[unique_equivalence_classes[atom_index]] + (OPAQUE,)
if USE_DIFFERENT_ELEMENT_SHAPES:
#vertex_shapes[v] = symbol_index_for_element[atom['type']]
pass
for (i, j) in [bond['atoms'] for bond in data.bonds]:
g.add_edge(vertices[i], vertices[j])
return g
def graph_img(data, molecule_graph: Optional[Any] = None, return_pos: bool = False, pos: Optional[Any] = None, **kwargs: Dict[str, Any]) -> Union[None, str, Tuple[str, Any, Any]]:
try:
from graph_tool.draw import graph_draw
except ImportError as e:
if RAISE_IF_MISSING_GRAPH_TOOL:
raise
else:
from sys import stderr
stderr.write('Package graph_tool could not be imported. Error was: {0}'.format(e))
return None
if molecule_graph is None:
molecule_graph = graph(data, **kwargs)
if molecule_graph is not None:
io = StringIO()
output_pos = graph_draw(
molecule_graph,
pos=pos,
vertex_text=molecule_graph.vertex_properties['type'],
vertex_font_size=10.0,
vertex_size=50.0,
output=io,
fmt='svg',
output_size=tuple([150 * ceil(sqrt(len(data.atoms)))]*2),
vertex_fill_color=molecule_graph.vertex_properties['equivalence_class'],
**(
dict(vertex_shape=molecule_graph.vertex_properties['shape'])
if USE_DIFFERENT_ELEMENT_SHAPES
else {}
)
)
if not return_pos:
return io.getvalue()
else:
return (io.getvalue(), molecule_graph, output_pos)
else:
return None
def graph_gt(data, **kwargs):
molecule_graph = graph(data, vertex_text='element_valence', decorate_graph=False)
if molecule_graph is not None:
io = BytesIO()
molecule_graph.save(io)
return io.getvalue()
else:
return None