def __init__(self, criteria_sets=None, vertex_tags=None):
"""
Arguments: see :class:`molmod.graphs.CustomPattern`
"""
if vertex_tags is None:
vertex_tags = {}
pattern_graph = Graph([(0, 1), (0, 2), (0, 3), (0, 4)])
CustomPattern.__init__(self, pattern_graph, criteria_sets, vertex_tags)
def __init__(self, size, criteria_sets=None, vertex_tags=None, strong=False):
"""
Argument:
| ``size`` -- the size of the ring
"""
if vertex_tags is None:
vertex_tags = {}
self.size = size
self.strong = strong
pattern_graph = Graph([(i, (i+1)%size) for i in range(size)])
CustomPattern.__init__(self, pattern_graph, criteria_sets, vertex_tags)
def make_graph_distance_matrix(system):
"""Return a bond graph distance matrix.
Parameters
----------
system : System
Molecule (with bonds) for which the graph distances must be computed.
The graph distance is used for comparison because it allows the pattern
matching to make optimal choices of which pairs of atoms to compare next, i.e.
both bonded or nearby the last matched pair.
"""
from molmod.graphs import Graph
return Graph(system.bonds, system.natom).distances
def get_graph(self):
"""Return the bond graph represented by the data structure"""
return Graph(self.bonds)
def __init__(self, size, criteria_sets=None, node_tags={}, strong=False):
self.size = size
self.strong = strong
subgraph = Graph([(i,(i+1)%size) for i in xrange(size)])
SubgraphPattern.__init__(self, subgraph, criteria_sets, node_tags)
def __init__(self, criteria_sets=None, node_tags={}):
subgraph = Graph([(0, 1), (0, 2), (0, 3), (0, 4)])
SubgraphPattern.__init__(self, subgraph, criteria_sets, node_tags)
def get_graph(self):
return Graph(self.bonds)
