Visualization_chemdraw package¶
Submodules¶
Visualization_chemdraw.cdxml_editor¶
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class
Visualization_chemdraw.cdxml_editor.CDXML_Editor(cdxml_files_path=None, output_path=None, BP=None, BP_predicted=None)¶ Bases:
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add_color(fba_value)¶
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add_colortable()¶
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add_product(product, last_id)¶
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add_reactants(reactants, previous_reactions, last_id)¶
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add_transition(promiscuous_reactants, promiscuous_products, misc_products, reaction_proteins='', reaction_solvents='', reaction_catalysts='', reaction_SPRESI_info='')¶
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append(box, arrange='')¶
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generate_file()¶
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get_cpd_cdxml(compound, id_offset=0, color='5')¶
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parse_cdxml(compound)¶
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set_FBA(color_index)¶
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set_output_label(text_string, output, color)¶
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set_products(cdxml_products)¶
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Visualization_chemdraw.cdxml_elements¶
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class
Visualization_chemdraw.cdxml_elements.ARC(el_id='-1', x_0=0, y_0=0, color='3', size=18.75, head=False)¶ -
update_position()¶
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class
Visualization_chemdraw.cdxml_elements.ARROW(el_id='-1', x_0=0, y_0=0, color='3', width=150.0)¶ -
update_position()¶
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class
Visualization_chemdraw.cdxml_elements.BOX(width=0, height=0)¶ -
append(element, arrange='', align='middle')¶ Append elements/boxes to this box
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append_box(box_element)¶
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set_color(new_color)¶
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set_x(new_x)¶
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set_y(new_y)¶
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update_position(dx=0, dy=0)¶
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class
Visualization_chemdraw.cdxml_elements.COMPOUND(cpd_xml, label_xml, id_offset=0, color='0')¶ -
append(xml_element, shift_down=False)¶ Append elements/boxes to this box
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offset_ids(id_offset)¶
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scale()¶
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set_dimensions()¶
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class
Visualization_chemdraw.cdxml_elements.ELEMENT(el_id='-1', x_0=0, y_0=0, color='0')¶ -
append(element)¶
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dump()¶
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get_color()¶
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get_id()¶
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get_x()¶
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get_y()¶
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iter(query)¶
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set_color(new_color)¶
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set_id(new_id)¶
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set_x(new_x)¶
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set_y(new_y)¶
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update_position()¶
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Visualization_chemdraw.reaction_files¶
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class
Visualization_chemdraw.reaction_files.ReactionFiles(output_path, DB, reactions, target, target_organism, incpds, figures, cdxmlfiles=True)¶ Bases:
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alter_name_length(path_to_figure, cpdname)¶ Shorten compound name if it is too long
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generate_cdxml_files(RP=None, fba_fluxes=None, show_rxn_info=True)¶ Produce cdxml files for each pathway
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generate_output_folders(folder)¶ Check to see if output folders are present if not set up new output folder
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get_cdxml(compounds, cdxml_cpds, promiscuous_cpds)¶ Get cdxml files for relevant compounds
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get_target_name()¶
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order_of_paths()¶ Ordered pathway with target as tree root
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