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// ==UserScript==
// @name Expasy Data Extract (Auto Submit, Excel Table)
// @namespace http://tampermonkey.net/
// @version 2.2
// @description Collect specific protein data from Expasy ProtParam results, display it in an elegant table with copy functionality and notification, and include a fixed title. Molecular weight is divided by 1000 before displaying.
// @author Faisal Ahmed
// @license MIT
// @match https://web.expasy.org/protparam/*
// @match https://web.expasy.org/cgi-bin/protparam/protparam*
// @grant none
// ==/UserScript==
(function() {
'use strict';
// Log messages to help debugging
console.log("Tampermonkey script started!");
// Function to create and show the table for displaying collected data
function createExcelTable(proteinData) {
console.log("Creating Excel-like table...");
// Create a container div for the table
const tableContainer = document.createElement('div');
tableContainer.style.position = 'fixed';
tableContainer.style.top = '10px';
tableContainer.style.right = '10px';
tableContainer.style.backgroundColor = 'rgba(255, 255, 255, 0.9)';
tableContainer.style.color = '#000';
tableContainer.style.padding = '15px';
tableContainer.style.borderRadius = '8px';
tableContainer.style.zIndex = '9999';
tableContainer.style.width = '450px';
tableContainer.style.fontSize = '12px'; // Smaller font size
tableContainer.style.maxHeight = '400px';
tableContainer.style.overflowY = 'auto';
tableContainer.style.boxShadow = '0 4px 8px rgba(0, 0, 0, 0.2)';
// Create and style the fixed title with blinking rainbow effect
const fixedTitle = document.createElement('div');
fixedTitle.textContent = 'Made By Faisal Ahmed';
fixedTitle.style.fontSize = '14px'; // Slightly smaller title font
fixedTitle.style.fontWeight = 'bold';
fixedTitle.style.marginBottom = '10px';
fixedTitle.style.paddingBottom = '5px';
fixedTitle.style.borderBottom = '1px solid #ddd';
fixedTitle.style.textAlign = 'center';
fixedTitle.style.backgroundClip = 'text';
fixedTitle.style.webkitBackgroundClip = 'text'; // For Safari and Chrome
fixedTitle.style.color = 'transparent'; // Hide the original text color
fixedTitle.style.backgroundImage = 'linear-gradient(to right, violet, indigo, blue, green, yellow, orange, red)';
fixedTitle.style.animation = 'blink 5s linear infinite';
// Add CSS for the blinking rainbow effect
const style = document.createElement('style');
style.innerHTML = `
@keyframes blink {
0% {
background-position: 100%;
}
50% {
background-position: 0%;
}
100% {
background-position: 100%;
}
}
div {
background-size: 200%;
}
`;
document.head.appendChild(style);
tableContainer.appendChild(fixedTitle);
// Create a table element
const table = document.createElement('table');
table.style.width = '100%';
table.style.borderCollapse = 'collapse';
table.style.textAlign = 'left';
table.style.backgroundColor = '#333'; // Darker background color for the table
table.style.borderRadius = '8px'; // Rounded corners for the table
table.style.fontSize = '12px'; // Smaller font size for table
// Create the table header
const headerRow = document.createElement('tr');
const headers = ['Protein Length (aa)', 'Molecular weight (kDa)', 'Theoretical pI', 'Instability index', 'Aliphatic index', 'GRAVY'];
headers.forEach(headerText => {
const th = document.createElement('th');
th.textContent = headerText;
th.style.border = '1px solid #444'; // Darker border for header
th.style.padding = '10px'; // Reduced padding for a more compact look
th.style.backgroundColor = '#555'; // Slightly lighter dark color for header
th.style.color = '#fff'; // White text for better contrast
th.style.borderRadius = '4px';
th.style.fontWeight = 'bold';
headerRow.appendChild(th);
});
table.appendChild(headerRow);
// Create the table row with protein data
const dataRow = document.createElement('tr');
for (const key in proteinData) {
const td = document.createElement('td');
// Add condition for the "Instability index" column
if (key === "Instability index") {
const instabilityValue = parseFloat(proteinData[key]);
if (!isNaN(instabilityValue)) {
if (instabilityValue > 39.9) {
td.textContent = `${instabilityValue} (unstable)`;
} else {
td.textContent = `${instabilityValue} (stable)`;
}
} else {
td.textContent = "Nope";
}
} else if (key === "Molecular weight") {
// Divide molecular weight by 1000 and show in kDa
const molecularWeightValue = parseFloat(proteinData[key]);
td.textContent = !isNaN(molecularWeightValue) ? `${(molecularWeightValue / 1000).toFixed(3)}` : 'Nope';
} else {
td.textContent = proteinData[key] || 'Nope';
}
td.style.border = '1px solid #444'; // Darker border for data cells
td.style.padding = '8px'; // Reduced padding for a more compact look
td.style.borderRadius = '4px';
td.style.color = '#fff'; // White text for better contrast
dataRow.appendChild(td);
}
table.appendChild(dataRow);
// Create the "Copy" button
const copyButton = document.createElement('button');
copyButton.textContent = 'Copy Data';
copyButton.style.marginTop = '15px';
copyButton.style.padding = '8px 15px';
copyButton.style.backgroundColor = '#007bff';
copyButton.style.color = '#fff';
copyButton.style.border = 'none';
copyButton.style.borderRadius = '5px';
copyButton.style.cursor = 'pointer';
copyButton.style.fontSize = '12px'; // Smaller font size for the button
copyButton.addEventListener('click', copyTableData);
tableContainer.appendChild(copyButton);
// Append the table to the container
tableContainer.appendChild(table);
// Add the table container to the webpage
document.body.appendChild(tableContainer);
console.log("Excel-like table created and data added.");
}
// Function to extract data from the plain text result
function extractProteinDataFromText() {
let proteinData = {};
// Get the entire text content of the page
const resultText = document.body.textContent;
console.log("Result text found on the page.");
// Use regular expressions to extract the specific data points
const aminoAcidsMatch = resultText.match(/Number of amino acids:\s*(\d+)/);
const molecularWeightMatch = resultText.match(/Molecular weight:\s*([\d.]+)/);
const piMatch = resultText.match(/Theoretical pI:\s*([\d.]+)/);
const instabilityIndexMatch = resultText.match(/The instability index \(II\) is computed to be\s*([\d.]+)/);
const aliphaticIndexMatch = resultText.match(/Aliphatic index:\s*([\d.]+)/);
const gravyMatch = resultText.match(/Grand average of hydropathicity \(GRAVY\):\s*([\d.-]+)/);
// Save the matched results in the proteinData object
proteinData["Number of amino acids"] = aminoAcidsMatch ? aminoAcidsMatch[1] : "Nope";
proteinData["Molecular weight"] = molecularWeightMatch ? molecularWeightMatch[1] : "Nope";
proteinData["Theoretical pI"] = piMatch ? piMatch[1] : "Nope";
proteinData["Instability index"] = instabilityIndexMatch ? instabilityIndexMatch[1] : "Nope";
proteinData["Aliphatic index"] = aliphaticIndexMatch ? aliphaticIndexMatch[1] : "Nope";
proteinData["GRAVY"] = gravyMatch ? gravyMatch[1] : "Nope";
console.log("Protein data extracted:", proteinData);
// Create and display the table with the extracted data
createExcelTable(proteinData);
}
// On the form page (https://web.expasy.org/protparam/), listen for paste event and submit the form automatically
if (window.location.href.includes("web.expasy.org/protparam/")) {
const sequenceInput = document.querySelector('textarea');
const form = document.querySelector('form');
if (sequenceInput && form) {
console.log("Form detected on the protparam page.");
// Listen for paste event in the sequence input
sequenceInput.addEventListener('paste', function(event) {
setTimeout(function() {
if (sequenceInput.value.trim().length > 0) {
// Create a form data object
const formData = new FormData(form);
// Construct the URL for the new tab with form data as query params
const urlParams = new URLSearchParams(formData).toString();
const targetURL = `${form.action}?${urlParams}`;
// Open the new tab with the constructed URL
console.log("Opening results in a new tab...");
window.open(targetURL, '_blank');
// Reset the form in the original tab
console.log("Resetting the form in the original tab...");
form.reset();
}
}, 100); // Delay to ensure paste is completed
});
}
}
// Function to display a temporary notification
function showCopyNotification() {
const notification = document.createElement('div');
notification.textContent = 'Table data copied to clipboard!';
notification.style.position = 'fixed';
notification.style.top = '20px'; // Changed from bottom to top
notification.style.right = '20px';
notification.style.backgroundColor = '#28a745';
notification.style.color = '#fff';
notification.style.padding = '10px 20px';
notification.style.borderRadius = '5px';
notification.style.boxShadow = '0 4px 8px rgba(0, 0, 0, 0.1)';
notification.style.zIndex = '9999';
document.body.appendChild(notification);
// Remove notification after 1 second
setTimeout(() => {
notification.remove();
}, 1000);
}
// Function to copy the table data to the clipboard
function copyTableData() {
const table = document.querySelector('table');
// Create a temporary textarea to store table data for copying
const tempTextArea = document.createElement('textarea');
tempTextArea.style.position = 'fixed'; // Prevent it from appearing in the view
tempTextArea.style.opacity = '0';
document.body.appendChild(tempTextArea);
// Collect data from each table cell, excluding the title row
let tableData = '';
table.querySelectorAll('tr').forEach((row, rowIndex) => {
if (rowIndex > 0) { // Skip the header row (rowIndex 0)
row.querySelectorAll('td').forEach(cell => {
tableData += cell.textContent.trim() + '\t'; // Tab-separated values
});
tableData += '\n'; // New line for each row
}
});
// Set the collected table data into the textarea
tempTextArea.value = tableData;
tempTextArea.select();
document.execCommand('copy');
document.body.removeChild(tempTextArea); // Remove the temporary textarea
// Show the copy notification
showCopyNotification();
}
// Wait for the page to load and then extract the data
window.addEventListener('load', extractProteinDataFromText);
})();