Source code for chempy.util.graph

# -*- coding: utf-8 -*-
Convenince functions for representing reaction systems as graphs.
import os
import subprocess
import shutil
import tempfile

[docs]def rsys2dot(rsys, tex=False, rprefix='r', rref0=1, nodeparams='[label="{}",shape=diamond]', colors=('maroon', 'darkgreen'), penwidths=None, include_inactive=True): """ Returns list of lines of DOT (graph description language) formated graph. Parameters ========== rsys: ReactionSystem tex: bool (default False) If set True, output will be LaTeX formated (Substance need to have latex_name attribute set) rprefix: string Reaction enumeration prefix, default: r rref0: integer Reaction enumeration inital counter value, default: 1 nodeparams: string DOT formated param list, default: [label={} shape=diamond] Returns ======= list of lines of DOT representation of the graph representation. """ lines = ['digraph "' + str( + '" {\n'] ind = ' ' # indentation if penwidths is None: penwidths = [1.0]* categories = rsys.categorize_substances(checks=()) def add_substance(key): fc = 'black' if key in categories['depleted']: fc = colors[0] if key in categories['accumulated']: fc = colors[1] label = ('$%s$' if tex else '%s') % getattr(rsys.substances[key], 'latex_name' if tex else 'name') lines.append(ind + '"{key}" [fontcolor={fc} label="{lbl}"];\n'.format(key=key, fc=fc, lbl=label)) for sk in rsys.substances: add_substance(sk) def add_vertex(key, num, reac, penwidth): snum = str(num) if num > 1 else '' fmt = ','.join( ['label="{}"'.format(snum)] + (['penwidth={}'.format(penwidth)] if penwidth != 1 else []) ) lines.append(ind + '"{}" -> "{}" [color={},fontcolor={},{}];\n'.format( *((key, rid, colors[0], colors[0], fmt) if reac else (rid, key, colors[1], colors[1], fmt)) )) if include_inactive: reac_stoichs = rsys.all_reac_stoichs() prod_stoichs = rsys.all_prod_stoichs() else: reac_stoichs = rsys.active_reac_stoichs() prod_stoichs = rsys.active_prod_stoichs() for ri, rxn in enumerate(rsys.rxns): rid = rprefix + str(ri+rref0) lines.append(ind + '{') lines.append(ind*2 + 'node ' + nodeparams.format( or rid)) lines.append(ind*2 + rid) lines.append(ind + '}\n') for idx, key in enumerate(rsys.substances): num = reac_stoichs[ri, idx] if num == 0: continue add_vertex(key, num, True, penwidths[ri]) for idx, key in enumerate(rsys.substances): num = prod_stoichs[ri, idx] if num == 0: continue add_vertex(key, num, False, penwidths[ri]) lines.append('}\n') return lines
[docs]def rsys2graph(rsys, fname, output_dir=None, prog=None, save=False, **kwargs): """ Convenience function to call `rsys2dot` and write output to file and render the graph Parameters ---------- rsys : ReactionSystem fname : str filename output_dir : str (optional) path to directory (default: temporary directory) prog : str (optional) default: 'dot' save : bool removes temporary directory if False, default: False \\*\\*kwargs : Keyword arguments passed along to py:func:`rsys2dot`. Returns ------- str Outpath Examples -------- >>> rsys2graph(rsys, sbstncs, '/tmp/out.png') # doctest: +SKIP """ lines = rsys2dot(rsys, **kwargs) created_tempdir = False try: if output_dir is None: output_dir = tempfile.mkdtemp() created_tempdir = True basename, ext = os.path.splitext(os.path.basename(fname)) outpath = os.path.join(output_dir, fname) dotpath = os.path.join(output_dir, basename + '.dot') with open(dotpath, 'wt') as ofh: ofh.writelines(lines) if ext == '.tex': cmds = [prog or 'dot2tex'] else: cmds = [prog or 'dot', '-T'+outpath.split('.')[-1]] p = subprocess.Popen(cmds + [dotpath, '-o', outpath]) retcode = p.wait() if retcode: fmtstr = "{}\n returned with exit status {}" raise RuntimeError(fmtstr.format(' '.join(cmds), retcode)) return outpath finally: if save is True or save == 'True': pass else: if save is False or save == 'False': if created_tempdir: shutil.rmtree(output_dir) else: # interpret save as path to copy pdf to. shutil.copy(outpath, save)