Source code for

#!/usr/bin/env python
Usage: ``python -m >``

Renders the species from a model into the "dot" graph format which can be
visualized with Graphviz.

To create a PDF from the .dot file, use the Graphviz tools in the following
command pipeline::

    ccomps -x | dot | gvpack -m0 | neato -n2 -T pdf -o mymodel.pdf

You can also change the "dot" command to "circo" or "sfdp" for a different type
of layout. Note that you can pipe the output of render_species straight into a
Graphviz command pipeline without creating an intermediate .dot file, which is
especially helpful if you are making continuous changes to the model and need to
visualize your changes repeatedly::

    python -m | ccomps -x | dot |
      gvpack -m0 | neato -n2 -T pdf -o mymodel.pdf

Note that some PDF viewers will auto-reload a changed PDF, so you may not even
need to manually reopen it every time you rerun the tool.

import sys
import os
import re
    import pygraphviz
except ImportError:
    pygraphviz = None
import pysb.bng

[docs]def run(model): """ Render the species from a model into the "dot" graph format. Parameters ---------- model : pysb.core.Model The model to render. Returns ------- string The dot format output. """ pysb.bng.generate_equations(model) return render_species_as_dot(model.species,
def render_species_as_dot(species_list, graph_name=""): if pygraphviz is None: raise ImportError('pygraphviz library is required to run this ' 'function') graph = pygraphviz.AGraph(name="%s species" % graph_name, rankdir="LR", fontname='Arial') graph.edge_attr.update(fontname='Arial', fontsize=8) for si, cp in enumerate(species_list): sgraph_name = 'cluster_s%d' % si cp_label = re.sub(r'% ', '%<br align="left"/>', str(cp)) + '<br align="left"/>' sgraph_label = '<<font point-size="10" color="blue">s%d</font>' \ '<br align="left"/>' \ '<font face="Consolas" point-size="6">%s</font>>' % \ (si, cp_label) sgraph = graph.add_subgraph(name=sgraph_name, label=sgraph_label, color="gray75", sortv=sgraph_name) bonds = {} for mi, mp in enumerate(cp.monomer_patterns): monomer_node = '%s_%d' % (sgraph_name, mi) monomer_label = '<<table border="0" cellborder="1" cellspacing="0">' monomer_label += '<tr><td bgcolor="#a0ffa0"><b>%s</b></td></tr>' % \ for site in mp.monomer.sites: site_state = None cond = mp.site_conditions[site] if isinstance(cond, str): site_state = cond elif isinstance(cond, tuple): site_state = cond[0] site_label = site if site_state is not None: site_label += '=<font color="purple">%s</font>' % site_state monomer_label += '<tr><td port="%s">%s</td></tr>' % \ (site, site_label) for site, value in mp.site_conditions.items(): site_bonds = [] # list of bond numbers if isinstance(value, int): site_bonds.append(value) elif isinstance(value, tuple): site_bonds.append(value[1]) elif isinstance(value, list): site_bonds += value for b in site_bonds: bonds.setdefault(b, []).append((monomer_node, site)) monomer_label += '</table>>' sgraph.add_node(monomer_node, label=monomer_label, shape="none", fontname="Arial", fontsize=8) for bi, sites in bonds.items(): node_names, port_names = list(zip(*sites)) sgraph.add_edge(node_names, tailport=port_names[0], headport=port_names[1], label=str(bi)) return graph.string() usage = __doc__ usage = usage[1:] # strip leading newline if __name__ == '__main__': # sanity checks on filename if len(sys.argv) <= 1: print(usage, end=' ') exit() model_filename = sys.argv[1] if not os.path.exists(model_filename): raise Exception("File '%s' doesn't exist" % model_filename) if not'\.py$', model_filename): raise Exception("File '%s' is not a .py file" % model_filename) sys.path.insert(0, os.path.dirname(model_filename)) model_name = re.sub(r'\.py$', '', os.path.basename(model_filename)) # import it try: # FIXME if the model has the same name as some other "real" module # which we use, there will be trouble (use the imp package and import # as some safe name?) model_module = __import__(model_name) except Exception as e: print("Error in model script:\n") raise # grab the 'model' variable from the module try: model = model_module.__dict__['model'] except KeyError: raise Exception("File '%s' isn't a model file" % model_filename) print(run(model))