graph-tool - AttributeError: 'PropertyDict' object has no attribute 'species'

Question

I have the following code to annotate a graph using property maps:

from graph_tool.all import *

# define graph
g = Graph()
g.set_directed(True)
species = g.new_vertex_property("string")
species_dict = {}
reaction_dict = {}

#add species and reactions
s1 = g.add_vertex()
species[s1] = 'limonene'
species_dict[g.vertex_index[s1]] = 'limonene'

g.vertex_properties["species"] = species
g.vp.species[s1]

When I run this I obtain the following error message:

File "/home/pmj27/projects/NOC/exergy/make_graph.py", line 45, in <module>
g.vp.species[s1]

AttributeError: 'PropertyDict' object has no attribute 'species'

Why is this? If I type g.vp into my IPython console I get {'species': <PropertyMap object with key type 'Vertex' and value type 'string', for Graph 0x7f285d90ea10, at 0x7f285d90ef90>} as answer, so there clearly is a property map.

graph-tool defines its own classes, presumably they have a different syntax? — P-M, Nov 03 '15 at 14:13
They are free to implement their own methods (e.g. `__getitem__` and `__getattr__` for `thing[item]` and `thing.attr`, respectively), but it would be unusual to throw a `SyntaxError` in those cases. — jonrsharpe, Nov 03 '15 at 14:18
This version is too old to support the attribute syntax. I have added an answer pointing this out below. BTW: The name of the library is graph-tool, not "graph tools". — Tiago Peixoto, Nov 06 '15 at 14:26
Thanks. I haven't gotten around to testing it yet due to some IT issues yet. — P-M, Nov 09 '15 at 13:41

Tiago Peixoto · Accepted Answer · 2015-11-05T18:16:01.603

1

The access to property maps via attributes (as g.vp.species[s1] in your example) is only available in more recent versions of graph-tool (currently 2.11, as of Nov 2015). In the version you are using (2.2.42), you must use the dictionary interface: g.vp["species"][s1].

edited Nov 05 '15 at 18:16

answered Nov 04 '15 at 18:04

Tiago Peixoto

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graph-tool - AttributeError: 'PropertyDict' object has no attribute 'species'

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