USER:PROTEINS CHEMICALREACTIONS.JS

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//<pre>

// Analyze the chemical reactions on a page

//

// To use this script, add "importScript('User:Proteins/chemicalreactions.js');" to your monobook.js subpage 

// under your user page, as you can see at User:Proteins/monobook.js



var isotope_names = { 

"n" : "neutron", 

"H" : "hydrogen", 

"D" : "deuterium", 

"T" : "tritium", 

"He" : "helium", 

"Li" : "lithium", 

"Be" : "beryllium", 

"B" : "boron", 

"C" : "carbon",

"C13" : "carbon-13",  

"N" : "nitrogen", 

"N15" : "nitrogen-15", 

"O" : "oxygen", 

"F" : "fluorine", 

"Ne" : "neon"

};



var isotope_abbreviations = { 

"neutron" : "n", 

"hydrogen" : "H", 

"deuterium" : "D", 

"tritium" : "T", 

"helium" : "He", 

"lithium" : "Li", 

"beryllium" : "Be", 

"boron" : "B", 

"carbon" : "C",

"carbon-13" : "C13",  

"nitrogen" : "N", 

"nitrogen-15" : "N15", 

"oxygen" : "O", 

"fluorine" : "F", 

"neon" : "Ne"

};



var isotope_atomic_numbers = { 

"n" : "0", 

"H" : "1", 

"D" : "1", 

"T" : "1", 

"He" : "2", 

"Li" : "3", 

"Be" : "4", 

"B" : "5", 

"C" : "6",

"C13" : "6",  

"N" : "7", 

"N15" : "7", 

"O" : "8", 

"F" : "9", 

"Ne" : "10"

};



var isotope_weights = { 

"n" : "1.0", 

"H" : "1.0", 

"D" : "2.0", 

"T" : "3.0", 

"He" : "4.0", 

"Li" : "7.0", 

"Be" : "9.0", 

"B" : "11.0", 

"C" : "12.0",

"C13" : "13.0",  

"N" : "14.0", 

"N15" : "15.0", 

"O" : "16.0", 

"F" : "19.0", 

"Ne" : "20.0"

};



var isotope_indices = { 

"n" : "0", 

"H" : "1", 

"D" : "2", 

"T" : "3", 

"He" : "4", 

"Li" : "5", 

"Be" : "6", 

"B" : "7", 

"C" : "8",

"C13" : "9",  

"N" : "10", 

"N15" : "11", 

"O" : "12", 

"F" : "13", 

"Ne" : "14"

};



var isotope_abbreviation_array =  

"n", 

"H", "D", "T", "He", 

"Li", "Be", "B", "C", "C13",  "N", "N15", "O", "F", "Ne"

];



var atomic_element_abbreviation_array =  

"n", // 0 atomic number is also defined

"H", "He", 

"Li", "Be", "B", "C", "N", "O", "F", "Ne"

];



var isotope_name_array =  

"neutron", 

"hydrogen", 

"deuterium", 

"tritium", 

"helium", 

"lithium", 

"beryllium", 

"boron", 

"carbon",

"carbon-13",  

"nitrogen", 

"nitrogen-15", 

"oxygen", 

"fluorine", 

"neon"

];



//*******************

// The Main Function

//*******************



function analyzeChemicalReactions() {

	var alert_string = "";

	var error_string = "";

	var diagnostic_string = "";



	var products_string = "";

	var reactants_string = "";

	var products_Mw_string = "";

	var reactants_Mw_string = "";



	var body_content;



	var span_nodes;

	var temp_span_node;

	var num_span_nodes = 0;

	var span_node_index = 0;



	var temp_chemical_reaction;

	var chemical_reaction_name = ""; 

	var chemical_reaction_list = new Array();



	var num_reactions = 0;

	var reaction_index = 0;



	var reaction_symbol = "";

	var reaction_symbol_node;



	var reaction_products_node; 

	var reaction_reactants_node; 



	var num_product_molecules = 0;

	var num_reactant_molecules = 0;

	var num_product_molecule_types = 0;

	var num_reactant_molecule_types = 0;



	var child_nodes;

	var temp_child_node;

	var num_child_nodes = 0;

	var child_node_index = 0;



	var molecule_node; 

	var num_molecules = 0;

	var molecule_index = 0;



	var molecule_title = "";

	var num_molecule_types = 0;

	var molecule_type_index = 0;

	var molecule_type_name = "";



	var atom_node; 

	var num_atoms = 0;

	var atom_index = 0;



	var num_atom_types = 0;

	var atom_type_index = 0;



	var connecting_text = "";

	var prefactor_num_molecules = 1;



	var product_molecule_node;

	var product_molecule_node_list = new Array();

	var product_molecule_name_list = new Array();

	var product_molecule_count_list = new Array();



	var reactant_molecule_node;

	var reactant_molecule_node_list = new Array();

	var reactant_molecule_name_list = new Array();

	var reactant_molecule_count_list = new Array();



	var isotope_index = 0;

	var max_num_isotopes = 0;



	var isotope_name = "";

	var isotope_abbreviation = ""; 

	var atomic_number = 0;

	var molecular_weight = 0.0;

	var total_molecular_weight = 0.0;

	var sum_products_molecular_weights = 0.0;

	var sum_reactants_molecular_weights = 0.0;



	var subscript_node;

	var subscript_nodes;



	var reaction_is_balanced = true;

	var balanced_reaction_string = "";



	var product_num_atoms = new Array();

	var reactant_num_atoms = new Array();





// Initialize the reaction-balancing arrays



	max_num_isotopes = isotope_name_array.length;



	for (isotope_index=0; isotope_index<max_num_isotopes; isotope_index++) { 

		product_num_atomsisotope_index = 0;

		reactant_num_atomsisotope_index = 0;

	}





//****************************************

// Find the chemical reactions on the page

//****************************************



	num_chemical_reactions = 0;



// Get the bodyContent node

	body_content = document.getElementById('bodyContent');

	if (!body_content) { 

		error_string = "ERROR: There is no bodyContent node in this article.";

		window.alert(error_string);

		return;

	}



	span_nodes = body_content.getElementsByTagName("SPAN");

	if (!span_nodes) { 

		error_string = "ERROR: This page has no SPAN nodes.\n";

		window.alert(error_string);

		return; 

	}

	num_span_nodes = span_nodes.length;

	if (num_span_nodes < 1) { 

		error_string = "ERROR: This page has no SPAN nodes.\n";

		window.alert(error_string);

		return; 

	}



	for (span_node_index=0; span_node_index<num_span_nodes; span_node_index++) { 

		temp_span_node = span_nodesspan_node_index];

		if (!temp_span_node) { continue; }



		if (temp_span_node.className == "chemical-reaction") { 

			num_chemical_reactions++;

			chemical_reaction_list.push(temp_span_node);

		}

	} // closes loop over the SPAN nodes in the main article

	if (num_chemical_reactions < 1) { 

		error_string = "No chemical reactions were found on this page.";

		window.alert(error_string);

		return;

	} else if (num_chemical_reactions == 1) {

		alert_string = "This page has one chemical reaction.\n\n"; 

		window.alert(alert_string);

	} else {

		alert_string = "This page has " + num_chemical_reactions + " chemical reactions.\n\n"; 

		alert_string += "These will be analyzed in individual pop-up windows.\n"; 

		window.alert(alert_string);

	}





//*********************************************

// Loop over the chemical reactions on the page

//********************************************* 

	for (reaction_index=1; reaction_index<=num_chemical_reactions; reaction_index++) {

		alert_string = ""; // reset the alert string



		// Reset the reaction-balancing arrays

		for (isotope_index=0; isotope_index<max_num_isotopes; isotope_index++) { 

			product_num_atomsisotope_index = 0;

			reactant_num_atomsisotope_index = 0;

		}



		temp_chemical_reaction = chemical_reaction_listreaction_index-1];

		if (!temp_chemical_reaction) { 

			error_string = "ERROR: Chemical reaction " + reaction_index + " is undefined.\n";

			window.alert(error_string);

			continue;

		}

		chemical_reaction_name = temp_chemical_reaction.title;

		if (!chemical_reaction_name) { 

			error_string = "ERROR: No name is defined for chemical reaction " + reaction_index + ".\n";

			window.alert(error_string);

			chemical_reaction_name = "UNNAMED REACTION";

		}

		alert_string += "Reaction " + reaction_index + " represents the " + chemical_reaction_name + "\n\n";

//		window.alert(alert_string);



		child_nodes = temp_chemical_reaction.childNodes;

		if (!child_nodes) { 

			error_string = "ERROR: Chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has no child nodes.\n";

			window.alert(error_string);

			continue;

		} 

		num_child_nodes = child_nodes.length;

		if (num_child_nodes<3) { 

			error_string = "ERROR: Chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has " + num_child_nodes + " child nodes, fewer than the minimum number 3.\n";

			window.alert(error_string);

			continue;

		} 



		reaction_symbol_node = null;

		reaction_products_node = null;

		reaction_reactants_node = null;

		for (child_node_index=0; child_node_index<num_child_nodes; child_node_index++) { 

			temp_child_node = child_nodeschild_node_index];

			if (!temp_child_node) { continue; } 

			if (temp_child_node.nodeType != 1) { continue; } 

			if (!temp_child_node.className) { continue; } 



			if (temp_child_node.className == "reaction-reactants") { 

				reaction_reactants_node = temp_child_node;

			}

			if (temp_child_node.className == "reaction-symbol") { 

				reaction_symbol_node = temp_child_node;

			}

			if (temp_child_node.className == "reaction-products") { 

				reaction_products_node = temp_child_node;

			}

		} // closes loop over the child nodes of the chemical reaction



		if (reaction_reactants_node == null) { 

			error_string = "ERROR: The reactants element of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") is missing.\n";

			window.alert(error_string);

			continue;

		}

		if (reaction_symbol_node == null) { 

			error_string = "ERROR: The symbol element of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") is missing.\n";

			window.alert(error_string);

			continue;

		}

		if (reaction_products_node == null) { 

			error_string = "ERROR: The products element of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") is missing.\n";

			window.alert(error_string);

			continue;

		}

//		alert_string += "Found the reaction reactants, symbol and products elements for chemical reaction " + reaction_index + " (" + chemical_reaction_name + ").\n";

//		window.alert(alert_string);





//**********************

// Analyze the reactants

//**********************

		child_nodes = reaction_reactants_node.childNodes;

		if (!child_nodes) { 

			error_string = "ERROR: The reactants node of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has no child nodes (molecules).\n";

			window.alert(error_string);

			continue;

		} 

		num_child_nodes = child_nodes.length;

		if (num_child_nodes<1) { 

			error_string = "ERROR: The reactants node of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has zero child nodes (molecules).\n";

			window.alert(error_string);

			continue;

		}



		num_reactant_molecules = 0;

		prefactor_num_molecules = 1;

		num_reactant_molecule_types = 0;

		for (child_node_index=0; child_node_index<num_child_nodes; child_node_index++) { 

			temp_child_node = child_nodeschild_node_index];

			if (!temp_child_node) { continue; } 

			if (temp_child_node.nodeType == 1) { // element node

				if (!temp_child_node.className) { continue; }

				

				if (temp_child_node.className == "molecule") {

					num_reactant_molecules += prefactor_num_molecules;

					reactant_molecule_count_listnum_reactant_molecule_types = prefactor_num_molecules;

					reactant_molecule_node_listnum_reactant_molecule_types = temp_child_node;

					molecule_type_name = temp_child_node.title;

					if (!molecule_type_name) { molecule_type_name = "unknown molecule"; }

					reactant_molecule_name_listnum_reactant_molecule_types = molecule_type_name;

					prefactor_num_molecules = 1;

					num_reactant_molecule_types++;

				}

			} else if (temp_child_node.nodeType == 3) { // text node

				connecting_text = temp_child_node.data;

				connecting_text = connecting_text.replace(/[^0-9]/g, "");

				if (!connecting_text) { 

					prefactor_num_molecules = 1; 

				} else { 

					prefactor_num_molecules = connecting_text - 0; 

				}  

			}

		} // closes loop over the child nodes of the reaction_reactants_node



		sum_reactants_molecular_weights = 0.0;

		for (molecule_type_index=0; molecule_type_index<num_reactant_molecule_types; molecule_type_index++) {

			num_molecules = reactant_molecule_count_listmolecule_type_index]; 

			reactant_molecule_node = reactant_molecule_node_listmolecule_type_index];

			if (!reactant_molecule_node) { 

				error_string = "ERROR: Reactant molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") is undefined.\n";

				window.alert(error_string);

				continue;

			}

	

			span_nodes = reactant_molecule_node.getElementsByTagName("SPAN");

			if (!span_nodes) { 

				error_string = "ERROR: Reactant molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has no SPAN nodes (atoms).\n";

				window.alert(error_string);

				continue;

			} 

			num_span_nodes = span_nodes.length;

			if (num_span_nodes<1) { 

				error_string = "ERROR: Reactant molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has zero SPAN nodes (atoms).\n";

				window.alert(error_string);

				continue;

			}



			molecular_weight = 0.0;

			for (span_node_index=0; span_node_index<num_span_nodes; span_node_index++) { 

				temp_span_node = span_nodesspan_node_index];

				if (!temp_span_node) { continue; } 

				if (temp_span_node.className != "atom") { continue; } 



				isotope_name = temp_span_node.title;

				if (!isotope_name) { isotope_name = "hydrogen"; }

				isotope_abbreviation = isotope_abbreviationsisotope_name];

				atomic_number = isotope_atomic_numbersisotope_abbreviation];

				isotope_index = isotope_indicesisotope_abbreviation - 0;



				subscript_nodes = temp_span_node.getElementsByTagName("SUB");

				if (!subscript_nodes) { 

					num_atoms = 1;

				} else {

 					subscript_node = subscript_nodes0];

					if (!subscript_node) { 

						num_atoms = 1;

					} else { 

						num_atoms = subscript_nodes0].innerHTML;

					}

				}

				reactant_num_atomsisotope_index += num_molecules * num_atoms - 0;

				molecular_weight += num_atoms*isotope_weightsisotope_abbreviation - 0;

				total_molecular_weight = num_molecules * molecular_weight;



			} // closes loop over child nodes (atoms) in molecule

			reactant_molecule_name_listmolecule_type_index += " \t " + num_molecules + " x  Mw " + molecular_weight + " = " + total_molecular_weight + " Da";



			sum_reactants_molecular_weights += total_molecular_weight;



		} // closes loop over reactant molecule types 



		reactants_string = "The " + num_reactant_molecules + " reactant molecules are:\n";

		for (molecule_type_index=0; molecule_type_index<num_reactant_molecule_types; molecule_type_index++) { 

			num_molecules = reactant_molecule_count_listmolecule_type_index];

			if (num_molecules != 1) { 

				reactants_string += "\t " + num_molecules + " molecules of ";

			} else { 

				reactants_string += "\t 1 molecule of ";

			} 

			reactants_string += reactant_molecule_name_listmolecule_type_index + "\n";

		}

		reactants_Mw_string = "Molecular weight of reactants = " + sum_reactants_molecular_weights + " Da\n";





//*********************

// Analyze the products

//*********************

		child_nodes = reaction_products_node.childNodes;

		if (!child_nodes) { 

			error_string = "ERROR: The products node of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has no child nodes (molecules).\n";

			window.alert(error_string);

			continue;

		} 

		num_child_nodes = child_nodes.length;

		if (num_child_nodes<1) { 

			error_string = "ERROR: The products node of chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has zero child nodes (molecules).\n";

			window.alert(error_string);

			continue;

		}

		num_product_molecules = 0;

		prefactor_num_molecules = 1;

		num_product_molecule_types = 0;

		for (child_node_index=0; child_node_index<num_child_nodes; child_node_index++) { 

			temp_child_node = child_nodeschild_node_index];

			if (!temp_child_node) { continue; } 

			if (temp_child_node.nodeType == 1) { // element node

				if (!temp_child_node.className) { continue; }

				

				if (temp_child_node.className == "molecule") {

					num_product_molecules += prefactor_num_molecules;

					product_molecule_count_listnum_product_molecule_types = prefactor_num_molecules;

					product_molecule_node_listnum_product_molecule_types = temp_child_node;

					molecule_type_name = temp_child_node.title;

					if (!molecule_type_name) { molecule_type_name = "unknown molecule"; }

					product_molecule_name_listnum_product_molecule_types = molecule_type_name;

					prefactor_num_molecules = 1;

					num_product_molecule_types++;

				}

			} else if (temp_child_node.nodeType == 3) { // text node

				connecting_text = temp_child_node.data;

				connecting_text = connecting_text.replace(/[^0-9]/g, "");

				if (!connecting_text) { 

					prefactor_num_molecules = 1; 

				} else { 

					prefactor_num_molecules = connecting_text - 0; 

				}  

			}

		} // closes loop over the child nodes of the reaction_products_node



		sum_products_molecular_weights = 0.0;

		for (molecule_type_index=0; molecule_type_index<num_product_molecule_types; molecule_type_index++) {

			num_molecules = product_molecule_count_listmolecule_type_index];  

			product_molecule_node = product_molecule_node_listmolecule_type_index];

			if (!product_molecule_node) { 

				error_string = "ERROR: Product molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") is undefined.\n";

				window.alert(error_string);

				continue;

			}

	

			span_nodes = product_molecule_node.getElementsByTagName("SPAN");

			if (!span_nodes) { 

				error_string = "ERROR: Product molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has no SPAN nodes (atoms).\n";

				window.alert(error_string);

				continue;

			} 

			num_span_nodes = span_nodes.length;

			if (num_span_nodes<1) { 

				error_string = "ERROR: Product molecule type " + molecule_type_index + " in chemical reaction " + reaction_index + " (" + chemical_reaction_name + ") has zero SPAN nodes (atoms).\n";

				window.alert(error_string);

				continue;

			}



			molecular_weight = 0.0;

			for (span_node_index=0; span_node_index<num_span_nodes; span_node_index++) { 

				temp_span_node = span_nodesspan_node_index];

				if (!temp_span_node) { continue; } 

				if (temp_span_node.className != "atom") { continue; } 



				isotope_name = temp_span_node.title;

				if (!isotope_name) { isotope_name = "hydrogen"; }

				isotope_abbreviation = isotope_abbreviationsisotope_name];

				atomic_number = isotope_atomic_numbersisotope_abbreviation];

				isotope_index = isotope_indicesisotope_abbreviation - 0;



				subscript_nodes = temp_span_node.getElementsByTagName("SUB");

				if (!subscript_nodes) { 

					num_atoms = 1;

				} else {

 					subscript_node = subscript_nodes0];

					if (!subscript_node) { 

						num_atoms = 1;

					} else { 

						num_atoms = subscript_nodes0].innerHTML;

					}

				}

				product_num_atomsisotope_index += num_molecules * num_atoms - 0;

				molecular_weight += num_atoms*isotope_weightsisotope_abbreviation - 0;

				total_molecular_weight = num_molecules * molecular_weight;



			} // closes loop over child nodes (atoms) in molecule

			product_molecule_name_listmolecule_type_index += " \t " + num_molecules + " x  Mw " + molecular_weight + " = " + total_molecular_weight + " Da";



			sum_products_molecular_weights += total_molecular_weight;



		} // closes loop over product molecule types 



		products_string = "The " + num_product_molecules + " product molecules are:\n";

		for (molecule_type_index=0; molecule_type_index<num_product_molecule_types; molecule_type_index++) { 

			num_molecules = product_molecule_count_listmolecule_type_index];

			if (num_molecules != 1) { 

				products_string += "\t " + num_molecules + " molecules of ";

			} else { 

				products_string += "\t 1 molecule of ";

			} 

			products_string += product_molecule_name_listmolecule_type_index + "\n";

		}

		products_Mw_string = "Molecular weight of products = " + sum_products_molecular_weights + " Da\n";





//****************************

// Analyze the reaction symbol

//****************************

		reaction_symbol = reaction_symbol_node.title;

		if (!reaction_symbol) { 

			error_string = "ERROR: The reaction symbol is undefined.\n";

			window.alert(error_string);

			continue;

		}

		switch (reaction_symbol) { 

			case "equilibrium":

				alert_string += "This reaction is an equilibrium between " + num_reactant_molecules + " reactant and " + num_product_molecules + " product molecules.\n\n";

				break;

			case "forward":

			case "forwards":

			case "forward_reaction":

				alert_string += "This is the forward reaction from " + num_reactant_molecules + " reactant molecules to " + num_product_molecules + " product molecules.\n\n";

				break;

			case "backward":

			case "backwards":

			case "back_reaction":

			case "backward_reaction":

				alert_string += "This is the backward reaction from " + num_product_molecules + " product molecules to " + num_reactant_molecules + " reactant molecules.\n\n";

				break;

			case "forward_equilibrium":

				alert_string += "This reaction is an equilibrium between " + num_reactant_molecules + " reactant and " + num_product_molecules + " product molecules that is strongly biased towards the products.\n\n";

				break;

			case "backward_equilibrium":

				alert_string += "This reaction is an equilibrium between " + num_reactant_molecules + " reactant and " + num_product_molecules + " product molecules that is strongly biased towards the reactants.\n\n";

				break;

			default: 

				error_string = "ERROR: The reaction symbol \"" + reaction_symbol + "\" is not recognized.\n";

				window.alert(error_string);

				continue;

		} // closes switch over the reaction_symbol





// ********************************

// Report analysis of this reaction

// ********************************

		alert_string += reactants_string + "\n";

		alert_string += products_string + "\n";



		if (sum_reactants_molecular_weights == sum_products_molecular_weights) { 

			alert_string += "Mass is conserved in the reaction\n";

		} else { 

			alert_string += "Mass is NOT conserved in the reaction\n";

		}

		alert_string += "\t" + reactants_Mw_string;

		alert_string += "\t" + products_Mw_string;

		alert_string += "\n";



		reaction_is_balanced = true;

		balanced_reaction_string = "";

		for (isotope_index=1; isotope_index<max_num_isotopes; isotope_index++) { 

			if (product_num_atomsisotope_index != reactant_num_atomsisotope_index]) { 

				reaction_is_balanced = false;

				balanced_reaction_string += "\t Unbalanced " + isotope_name_arrayisotope_index + " atoms: Reactants " + reactant_num_atomsisotope_index + ", Products " + product_num_atomsisotope_index + "\n";

			} else if (reactant_num_atomsisotope_index>0){ 

				balanced_reaction_string += "\t Balanced " + isotope_name_arrayisotope_index + " atoms: Reactants " + reactant_num_atomsisotope_index + ", Products " + product_num_atomsisotope_index + "\n";

			}

		}

		if (reaction_is_balanced == true) { 

			alert_string += "Reaction is balanced in all atoms:\n";

			alert_string += balanced_reaction_string + "\n";

		} else { 

			alert_string += "Reaction is UNBALANCED as follows:\n";

			alert_string += balanced_reaction_string + "\n";

		}

		window.alert(alert_string);



	} // closes loop over the chemical reactions



} // closes function analyzeChemicalReactions()



addOnloadHook(function () {

mw.util.addPortletLink('p-navigation', 'javascript:analyzeChemicalReactions()', 'Chemical reactions', 'ca-reactions', 'Analyze the chemical reactions on a page', '!', '');

});



//</pre>
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