tables.py

class _RxnTable(object):

    _rsys_meth = None

    def __init__(
        self,
        idx_rxn_pairs,
        substances,
        colors=None,
        missing=None,
        missing_color="eee8aa",
    ):
        self.idx_rxn_pairs = idx_rxn_pairs
        self.substances = substances
        self.colors = colors or {}
        self.missing = missing or []
        self.missing_color = missing_color

    @classmethod
    def from_ReactionSystem(cls, rsys, color_categories=True):
        idx_rxn_pairs, unconsidered_ri = getattr(rsys, cls._rsys_meth)()
        colors = rsys._category_colors() if color_categories else {}
        missing = [not rsys.substance_participation(sk) for sk in rsys.substances]
        return (
            cls(idx_rxn_pairs, rsys.substances, colors=colors, missing=missing),
            unconsidered_ri,
        )

    def _repr_html_(self):
        from .web import css

        return css(self, substances=self.substances, colors=self.colors)

    def _cell_label_html(self, printer, ori_idx, rxn):
        """Reaction formatting callback. (reaction index -> string)"""
        pretty = rxn.unicode(self.substances, with_param=True, with_name=False)
        return '<a title="%d: %s">%s</a>' % (
            ori_idx,
            pretty,
            printer._print(rxn.name or rxn.param),
        )

    def _cell_html(self, printer, A, ri, ci=None):
        args = []
        if ci is not None and ri > ci:
            r = "-"
        else:
            if ci is None:  # A is a vector
                c = A[ri]
                is_missing = self.missing[ri]
            else:  # A is a matrix
                c = A[ri][ci]
                is_missing = self.missing[ri] or self.missing[ci]

            if c is None:
                r = ""
            else:
                r = ", ".join(self._cell_label_html(printer, *r) for r in c)

            if is_missing:
                args.append('style="background-color: #%s;"' % self.missing_color)

        return "<td %s>%s</td>" % (" ".join(args), r)


class UnimolecularTable(_RxnTable):
    """Table of unimolecular reactions in a ReactionSystem

    Parameters
    ----------
    rsys : ReactionSystem
    sinks_sources_disjoint : tuple, None or True
        Colors sinks & sources. When ``True`` :meth:`sinks_sources_disjoint` is called.
    html_cell_label : Reaction formatting callback
        The function takes an integer, a Reaction instance and a dict of Substances as
        parameters and return a string.

    Returns
    -------
    string: html representation
    list: reactions not considered
    """

    _rsys_meth = "_unimolecular_reactions"

    def _html(self, printer, **kwargs):
        if "substances" not in kwargs:
            kwargs["substances"] = self.substances
        ss = printer._get("substances", **kwargs)
        rows = "\n".join(
            "<tr><td>%s</td>%s</tr>"
            % (printer._print(s), self._cell_html(printer, self.idx_rxn_pairs, rowi))
            for rowi, s in enumerate(ss.values())
        )
        return "<table>%s</table>" % rows


class BimolecularTable(_RxnTable):
    """Table of bimolecular reactions

    Parameters
    ----------
    idx_rxn_pairs : iterable of (int, Reaction) pairs
    substances : dict
        Mapping substance key to Substance instance.
    sinks_sources_disjoint : tuple, None or True
        Colors sinks & sources. When ``True`` :meth:`sinks_sources_disjoint` is called.

    Returns
    -------
    string: html representation
    list: reactions not considered
    """

    _rsys_meth = "_bimolecular_reactions"

    def _html(self, printer, **kwargs):
        if "substances" not in kwargs:
            kwargs["substances"] = self.substances
        ss = printer._get("substances", **kwargs)
        header = "<th></th>" + "".join(
            "<th>%s</th>" % printer._print(s) for s in ss.values()
        )
        rows = [
            "<tr><td>%s</td>%s</tr>"
            % (
                printer._print(s),
                "".join(
                    self._cell_html(printer, self.idx_rxn_pairs, rowi, ci)
                    for ci in range(len(ss))
                ),
            )
            for rowi, s in enumerate(ss.values())
        ]
        return "<table>%s</table>" % "\n".join([header, "\n".join(rows)])