utils

Utility module for plotting reactions/compounds/networks dotfiles.

rnets.plotter.utils.C_WHITE

Default white color.

Type:

Color

rnets.plotter.utils.C_BLACK

Default black color.

Type:

Color

rnets.plotter.utils.COLORSCH

Default colorscheme.

Type:

sequence of Color

rnets.plotter.utils.GRAPH_ATTR_DEF

Default graph global attributes.

Type:

Opts

rnets.plotter.utils.NODE_ATTR_DEF

Default node global attributes.

Type:

Opts

rnets.plotter.utils.EDCE_ATTR_DEF

Default edge global attributes.

Type:

Opts

rnets.plotter.utils.BOX_TMP

HTML box template.

Type:

str

rnets.plotter.utils.LABEL_TMP

HTML label template.

Type:

str

class rnets.plotter.utils.EdgeArgs(react: Reaction, width: float | None, color: Color | None, reversed: bool = False)

Situational tuple to store the filter arguments for the filter function.

Notes

Internal use to avoid type checker complaints.

class rnets.plotter.utils.EdgeCfg(opts: Opts | None = {'weight': '2.'}, solid_color: Color | None = None, width: float = 1.0, max_width: float | None = 5.0)

Dot edge general configuration.

opts

Dot additional global edge options. Defauts to None.

Type:

dict of str as keys and str as values or None, optional

solid_color

If set, all lines will be draw with that color, else, the color will be decided based on the reaction energy. Defaults to None.

Type:

Color or None, optional

width

Minimum width of the edges. Defaults to 1..

Type:

float, optional

max_width

If set, the width or the arrows will be decided based on their kinetic constant (k, see calc_pseudo_k_constant), using width as the minimum width and this max_width as the maximum width, if None, all the arrows will be draw with constant width.

Type:

float or None, optional

class rnets.plotter.utils.GraphCfg(opts: Opts | None = {'nodesep': '0.25', 'rankdir': 'TB', 'ranksep': '0.5'}, kind: str = 'digraph', colorscheme: Colorscheme = ((0.267004, 0.004874, 0.329415), (0.26851, 0.009605, 0.335427), (0.269944, 0.014625, 0.341379), (0.271305, 0.019942, 0.347269), (0.272594, 0.025563, 0.353093), (0.273809, 0.031497, 0.358853), (0.274952, 0.037752, 0.364543), (0.276022, 0.044167, 0.370164), (0.277018, 0.050344, 0.375715), (0.277941, 0.056324, 0.381191), (0.278791, 0.062145, 0.386592), (0.279566, 0.067836, 0.391917), (0.280267, 0.073417, 0.397163), (0.280894, 0.078907, 0.402329), (0.281446, 0.08432, 0.407414), (0.281924, 0.089666, 0.412415), (0.282327, 0.094955, 0.417331), (0.282656, 0.100196, 0.42216), (0.28291, 0.105393, 0.426902), (0.283091, 0.110553, 0.431554), (0.283197, 0.11568, 0.436115), (0.283229, 0.120777, 0.440584), (0.283187, 0.125848, 0.44496), (0.283072, 0.130895, 0.449241), (0.282884, 0.13592, 0.453427), (0.282623, 0.140926, 0.457517), (0.28229, 0.145912, 0.46151), (0.281887, 0.150881, 0.465405), (0.281412, 0.155834, 0.469201), (0.280868, 0.160771, 0.472899), (0.280255, 0.165693, 0.476498), (0.279574, 0.170599, 0.479997), (0.278826, 0.17549, 0.483397), (0.278012, 0.180367, 0.486697), (0.277134, 0.185228, 0.489898), (0.276194, 0.190074, 0.493001), (0.275191, 0.194905, 0.496005), (0.274128, 0.199721, 0.498911), (0.273006, 0.20452, 0.501721), (0.271828, 0.209303, 0.504434), (0.270595, 0.214069, 0.507052), (0.269308, 0.218818, 0.509577), (0.267968, 0.223549, 0.512008), (0.26658, 0.228262, 0.514349), (0.265145, 0.232956, 0.516599), (0.263663, 0.237631, 0.518762), (0.262138, 0.242286, 0.520837), (0.260571, 0.246922, 0.522828), (0.258965, 0.251537, 0.524736), (0.257322, 0.25613, 0.526563), (0.255645, 0.260703, 0.528312), (0.253935, 0.265254, 0.529983), (0.252194, 0.269783, 0.531579), (0.250425, 0.27429, 0.533103), (0.248629, 0.278775, 0.534556), (0.246811, 0.283237, 0.535941), (0.244972, 0.287675, 0.53726), (0.243113, 0.292092, 0.538516), (0.241237, 0.296485, 0.539709), (0.239346, 0.300855, 0.540844), (0.237441, 0.305202, 0.541921), (0.235526, 0.309527, 0.542944), (0.233603, 0.313828, 0.543914), (0.231674, 0.318106, 0.544834), (0.229739, 0.322361, 0.545706), (0.227802, 0.326594, 0.546532), (0.225863, 0.330805, 0.547314), (0.223925, 0.334994, 0.548053), (0.221989, 0.339161, 0.548752), (0.220057, 0.343307, 0.549413), (0.21813, 0.347432, 0.550038), (0.21621, 0.351535, 0.550627), (0.214298, 0.355619, 0.551184), (0.212395, 0.359683, 0.55171), (0.210503, 0.363727, 0.552206), (0.208623, 0.367752, 0.552675), (0.206756, 0.371758, 0.553117), (0.204903, 0.375746, 0.553533), (0.203063, 0.379716, 0.553925), (0.201239, 0.38367, 0.554294), (0.19943, 0.387607, 0.554642), (0.197636, 0.391528, 0.554969), (0.19586, 0.395433, 0.555276), (0.1941, 0.399323, 0.555565), (0.192357, 0.403199, 0.555836), (0.190631, 0.407061, 0.556089), (0.188923, 0.41091, 0.556326), (0.187231, 0.414746, 0.556547), (0.185556, 0.41857, 0.556753), (0.183898, 0.422383, 0.556944), (0.182256, 0.426184, 0.55712), (0.180629, 0.429975, 0.557282), (0.179019, 0.433756, 0.55743), (0.177423, 0.437527, 0.557565), (0.175841, 0.44129, 0.557685), (0.174274, 0.445044, 0.557792), (0.172719, 0.448791, 0.557885), (0.171176, 0.45253, 0.557965), (0.169646, 0.456262, 0.55803), (0.168126, 0.459988, 0.558082), (0.166617, 0.463708, 0.558119), (0.165117, 0.467423, 0.558141), (0.163625, 0.471133, 0.558148), (0.162142, 0.474838, 0.55814), (0.160665, 0.47854, 0.558115), (0.159194, 0.482237, 0.558073), (0.157729, 0.485932, 0.558013), (0.15627, 0.489624, 0.557936), (0.154815, 0.493313, 0.55784), (0.153364, 0.497, 0.557724), (0.151918, 0.500685, 0.557587), (0.150476, 0.504369, 0.55743), (0.149039, 0.508051, 0.55725), (0.147607, 0.511733, 0.557049), (0.14618, 0.515413, 0.556823), (0.144759, 0.519093, 0.556572), (0.143343, 0.522773, 0.556295), (0.141935, 0.526453, 0.555991), (0.140536, 0.530132, 0.555659), (0.139147, 0.533812, 0.555298), (0.13777, 0.537492, 0.554906), (0.136408, 0.541173, 0.554483), (0.135066, 0.544853, 0.554029), (0.133743, 0.548535, 0.553541), (0.132444, 0.552216, 0.553018), (0.131172, 0.555899, 0.552459), (0.129933, 0.559582, 0.551864), (0.128729, 0.563265, 0.551229), (0.127568, 0.566949, 0.550556), (0.126453, 0.570633, 0.549841), (0.125394, 0.574318, 0.549086), (0.124395, 0.578002, 0.548287), (0.123463, 0.581687, 0.547445), (0.122606, 0.585371, 0.546557), (0.121831, 0.589055, 0.545623), (0.121148, 0.592739, 0.544641), (0.120565, 0.596422, 0.543611), (0.120092, 0.600104, 0.54253), (0.119738, 0.603785, 0.5414), (0.119512, 0.607464, 0.540218), (0.119423, 0.611141, 0.538982), (0.119483, 0.614817, 0.537692), (0.119699, 0.61849, 0.536347), (0.120081, 0.622161, 0.534946), (0.120638, 0.625828, 0.533488), (0.12138, 0.629492, 0.531973), (0.122312, 0.633153, 0.530398), (0.123444, 0.636809, 0.528763), (0.12478, 0.640461, 0.527068), (0.126326, 0.644107, 0.525311), (0.128087, 0.647749, 0.523491), (0.130067, 0.651384, 0.521608), (0.132268, 0.655014, 0.519661), (0.134692, 0.658636, 0.517649), (0.137339, 0.662252, 0.515571), (0.14021, 0.665859, 0.513427), (0.143303, 0.669459, 0.511215), (0.146616, 0.67305, 0.508936), (0.150148, 0.676631, 0.506589), (0.153894, 0.680203, 0.504172), (0.157851, 0.683765, 0.501686), (0.162016, 0.687316, 0.499129), (0.166383, 0.690856, 0.496502), (0.170948, 0.694384, 0.493803), (0.175707, 0.6979, 0.491033), (0.180653, 0.701402, 0.488189), (0.185783, 0.704891, 0.485273), (0.19109, 0.708366, 0.482284), (0.196571, 0.711827, 0.479221), (0.202219, 0.715272, 0.476084), (0.20803, 0.718701, 0.472873), (0.214, 0.722114, 0.469588), (0.220124, 0.725509, 0.466226), (0.226397, 0.728888, 0.462789), (0.232815, 0.732247, 0.459277), (0.239374, 0.735588, 0.455688), (0.24607, 0.73891, 0.452024), (0.252899, 0.742211, 0.448284), (0.259857, 0.745492, 0.444467), (0.266941, 0.748751, 0.440573), (0.274149, 0.751988, 0.436601), (0.281477, 0.755203, 0.432552), (0.288921, 0.758394, 0.428426), (0.296479, 0.761561, 0.424223), (0.304148, 0.764704, 0.419943), (0.311925, 0.767822, 0.415586), (0.319809, 0.770914, 0.411152), (0.327796, 0.77398, 0.40664), (0.335885, 0.777018, 0.402049), (0.344074, 0.780029, 0.397381), (0.35236, 0.783011, 0.392636), (0.360741, 0.785964, 0.387814), (0.369214, 0.788888, 0.382914), (0.377779, 0.791781, 0.377939), (0.386433, 0.794644, 0.372886), (0.395174, 0.797475, 0.367757), (0.404001, 0.800275, 0.362552), (0.412913, 0.803041, 0.357269), (0.421908, 0.805774, 0.35191), (0.430983, 0.808473, 0.346476), (0.440137, 0.811138, 0.340967), (0.449368, 0.813768, 0.335384), (0.458674, 0.816363, 0.329727), (0.468053, 0.818921, 0.323998), (0.477504, 0.821444, 0.318195), (0.487026, 0.823929, 0.312321), (0.496615, 0.826376, 0.306377), (0.506271, 0.828786, 0.300362), (0.515992, 0.831158, 0.294279), (0.525776, 0.833491, 0.288127), (0.535621, 0.835785, 0.281908), (0.545524, 0.838039, 0.275626), (0.555484, 0.840254, 0.269281), (0.565498, 0.84243, 0.262877), (0.575563, 0.844566, 0.256415), (0.585678, 0.846661, 0.249897), (0.595839, 0.848717, 0.243329), (0.606045, 0.850733, 0.236712), (0.616293, 0.852709, 0.230052), (0.626579, 0.854645, 0.223353), (0.636902, 0.856542, 0.21662), (0.647257, 0.8584, 0.209861), (0.657642, 0.860219, 0.203082), (0.668054, 0.861999, 0.196293), (0.678489, 0.863742, 0.189503), (0.688944, 0.865448, 0.182725), (0.699415, 0.867117, 0.175971), (0.709898, 0.868751, 0.169257), (0.720391, 0.87035, 0.162603), (0.730889, 0.871916, 0.156029), (0.741388, 0.873449, 0.149561), (0.751884, 0.874951, 0.143228), (0.762373, 0.876424, 0.137064), (0.772852, 0.877868, 0.131109), (0.783315, 0.879285, 0.125405), (0.79376, 0.880678, 0.120005), (0.804182, 0.882046, 0.114965), (0.814576, 0.883393, 0.110347), (0.82494, 0.88472, 0.106217), (0.83527, 0.886029, 0.102646), (0.845561, 0.887322, 0.099702), (0.85581, 0.888601, 0.097452), (0.866013, 0.889868, 0.095953), (0.876168, 0.891125, 0.09525), (0.886271, 0.892374, 0.095374), (0.89632, 0.893616, 0.096335), (0.906311, 0.894855, 0.098125), (0.916242, 0.896091, 0.100717), (0.926106, 0.89733, 0.104071), (0.935904, 0.89857, 0.108131), (0.945636, 0.899815, 0.112838), (0.9553, 0.901065, 0.118128), (0.964894, 0.902323, 0.123941), (0.974417, 0.90359, 0.130215), (0.983868, 0.904867, 0.136897), (0.993248, 0.906157, 0.143936)), color_offset: tuple[float, float] = (0.0, 0.0), node: NodeCfg = ({'shape': 'plaintext', 'style': 'filled'}, '<\n<TABLE BORDER="0" CELLBORDER="0" CELLSPACING="0" CELLPADDING="0">\n  <TR>\n    <TD>{0}</TD>\n  </TR>\n</TABLE>\n>\n', (0.0, 0.0, 0.0), (1.0, 1.0, 1.0), None), edge: EdgeCfg = ({'weight': '2.'}, None, 1.0, 5.0))

Dot graph general configuration.

opts

Dot additional global graph options. Defauts to None. Defaults to GRAPH_ATTR_DEF.

Type:

dict of str as keys and str as values or None, optional

kind

Kind of the dotgraph. Defaults to digraph.

Type:

str, optional

colorscheme

Sequence of colors that will be interpolate to set the colors of the graph. See interp_cs. Defaults to COLORSCH.

Type:

sequence of floats

color_offset

When using the energy of a node to decide its color, the offset to apply to norm. Should be a value between 0. and 1. Useful to avoid falling on the extremes of a predefined colorscheme. Defaults to (0., 0.)

Type:

tuple of two floats, optional

class rnets.plotter.utils.HTMLFormat(value, names=_not_given, *values, module=None, qualname=None, type=None, start=1, boundary=None)

HTML format for strings.

class rnets.plotter.utils.NodeCfg(opts: Opts | None = {'shape': 'plaintext', 'style': 'filled'}, box_tmp: str = '<\n<TABLE BORDER="0" CELLBORDER="0" CELLSPACING="0" CELLPADDING="0">\n  <TR>\n    <TD>{0}</TD>\n  </TR>\n</TABLE>\n>\n', font_color: Color = (0.0, 0.0, 0.0), font_color_alt: Color | None = (1.0, 1.0, 1.0), font_lum_threshold: float | None = None)

Dot node general configuration.

opts

Dot additional global node options. Defauts to None.

Type:

dict of str as keys and str as values or None, optional

box_tmp

Box template. Should have two format modificators, the first consisting on the label and the second consisting on the background color. Defaults to BOX_TMP

Type:

str, optional

font_color

Font color of the node. Defaults to C_BLACK

Type:

Color, optional

font_color_alt

Alternative font color. If not None, would be used as the font color for dark background colors (see calc_relative_luminance)

Type:

Color or None, optional

font_lum_threshold

If font_color_alt is defined, the luminance threshold to use it instead of font_color.

Type:

float on None, optional

rnets.plotter.utils.apply_html_format(s: str, fs: set[FFlags]) → str

Given a set of FFlags apply it as HTML format labels to a string.

Parameters:

• s (str) -- String to apply the format.

• fs (set of FFlags) -- Set with the formats to apply.

Returns:

with the applied HTML formats.

Return type:

str

rnets.plotter.utils.build_dotedge(o: str, t: str, opts: Opts | None = None, c: Color | None = None, w: float | None = None) → Edge

Build a dot Edge.

Parameters:

• o (str) -- Origin node.

• t (str) -- Target node.

• opts (Opts or None, optional) -- Graphviz attributes of the edge. Defaults to None.

• c (Color or None, optional) -- Color of edge. Defaults to None.

• w (float or None, optional) -- Edge width. Defaults to None.

Return type:

Edge

Note

None values will not be defined in the generated file and default Graphviz values will be used. Opts overrides color and width definitions.

rnets.plotter.utils.build_dotedges(r: Reaction, width: float, color: Color | None = C_BLACK, reverse: bool = False) → Iterator[Edge]

Converts a Reaction into one or more dot Edge.

Parameters:

• r (Reaction) -- Reaction to convert.

• width (float) -- Width of the reaction arrow.

• color (Color, optional) -- Color of the arrow. Defaults to C_BLACK.

• reverse (bool, optional) -- If True, invert the order of the reactants and the products.

Returns:

Iterator with the generated dot Edge corresponding to the Reaction with the given width and color.

Return type:

Iterator[Edge]

rnets.plotter.utils.build_dotnode(c: Compound, bc: Color = C_WHITE, fc: Color = C_BLACK) → Node

Creates a Node from a Compound.

Parameters:

• c (Compound) -- Compound to be coverted.

• bc (Color, optional) -- RGB color of the background. Defaults to white.

• fc (Color, optional) -- RGB color of the text. Defaults to black (C_BLACK).

Returns:

Dot node with the given font and background colors. Inherits applies the format flags and the dot opts in Compound.

Return type:

Node

Note

To allow custom labels, this function will check for "label" in

Compound.opts, if found, it will use it instead of the layer.

rnets.plotter.utils.build_glob_opt(cfg: GraphCfg) → OptsGlob | None

Given a certain GraphCfg, build a dictionary containing the dot options for the graph, the node and the edges.

Parameters:

cfg (GraphCfg) -- Configuration to use to generate the dictionary.

Returns:

With the given dictionary. Using graph, node and edge as keys and their corresponding Opts as values. None: If no Opts are found.

Return type:

OptsGlob

rnets.plotter.utils.build_node_box(s: str, fc: Color = C_BLACK, box_tmp: str = BOX_TMP) → str

Creates an string describing a colored-background HTML with a text label in the middle. This is the typical node representation of this code.

Parameters:

• s (str) -- String that will be used as a label.

• fc (Color, optional) -- Text color for the label. Defaults to black (C_BLACK).

• box_tmp (str, optional) -- Box template. Should have a format modificator for the text label. Defaults to BOX_TMP

Returns:

HTML table with the given label, background color and text color.

Return type:

str

Note

Note that Color follows the colorsys representation, meaning

that it consists of 3 float values ranging from [0, 1].

rnets.plotter.utils.color_interp(norm_fn: Callable[[float], float], cs: Sequence[Color], offset: tuple[float, float] = (0., 0.), cspace: ColorSpace = 'lab') → Callable[[float], Color]

Given a reaction network and a sequence of colors, build a color interpolation function that converts the energy of a component inside the network to the corresponding color in the color sequence.

Parameters:

• n (Network) -- Reaction network.

• cs (sequence of Color) -- Sequence of colors to interpolate.

• offset (tuple of 2 float, optional) -- Minimum and maximum energy offsets to add to the minimum and maximum detected energies.

• c_space (str) -- Colorspace in which the interpolation will be perform. Check ColorSpace for available values.

Returns:

A function that takes a float as input an returns a Color as output.

Return type:

Callable[[float], Color]

Notes

The normalizer is set for the input network and thus, if an energy

value that it is out of range is used as input, the normalization will follow the (under)overflow rules of normalizer.

I found that the offset is extremely useful to avoid very dark and very

bright zones of certain colorschemes.

rnets.plotter.utils.fformat_to_html(f: FFlags) → HTMLFormat

Convert FFlags to HTMLFormat.

Parameters:

f (FFlags) -- FFlags to convert.

Returns:

HTML format conversion.

Return type:

HTMLFormat

rnets.plotter.utils.gen_react_arrows(rt: Sequence[Compound], pt: Sequence[Compound]) → Iterator[tuple[Compound, Compound]]

Given a set of reactants and a set of products, generate an iterator that returns every react->product combination, skipping the ones containing a not visible Compound.

Parameters:

• rt (sequence of Compound) -- Compounds acting as reactants.

• pt (sequence of Compound) -- Compounds acting as products.

Returns:

A consumable iterator with all the (react, product) combinations excluding the ones with non visible compounds.

Return type:

Iterator[tuple[Compound, Compound]]

Note

To avoid duplicated edges due to duplicated compounds, e.g. 2H + 2O -> 2H2O ((H,H,O,O), (H2O,H2O)), only the unique reactants and products will be taken into account.

rnets.plotter.utils.nodecolor_sel(c_norm: Callable[[float], Color], fg_c: Color = C_BLACK, fg_alt: Color | None = None, lum_threshold: float | None = None) → Callable[[float, Visibility], tuple[Color, Color]]

Creates a function that takes an energy as input and returns the assigned color for the background of the node and the foreground.

Parameters:

• c_norm (Function taking a float as input and returns a Color) -- Color normalizer that will be used to compute the color of the node background. See network_color_enery_interp.

• fg_c (Color, optional) -- Color of the text. Defaults to C_BLACK.

• fg_alt (Color, optional) -- If set, alternative Color for the text if the luminance is below the a certain threshold. Defaults to None.

• lum_threshold (float, optional) -- If set, threshold of the luminance. If None, the default value in color_sel_lum will be used. This argument has no effect if fg_alt is not defined. Ideally, a value between 0. and 1. Defaults to None.

Returns:

A function that given a Compound returns a tuple of two Color s, the first being the background color and the second one being the color of the font.

Return type:

Callable(Compound) -> tuple[Color, Color]