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Add cation-pi directory with histidine interface files and models
This commit is contained in:
james-m-jordan
parent
866139051a
commit
064d39a163
3
cation-pi/.vscode/settings.json
vendored
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3
cation-pi/.vscode/settings.json
vendored
Normal file
@ -0,0 +1,3 @@
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{
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"git.ignoreLimitWarning": true
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}
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674
cation-pi/cation_pi_aggregate.graphml
Normal file
674
cation-pi/cation_pi_aggregate.graphml
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<?xml version='1.0' encoding='utf-8'?>
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@ -0,0 +1,104 @@
|
||||
<!DOCTYPE html>
|
||||
<html>
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<title>Histidine Interface Visualization - Index</title>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>
|
||||
<script src="https://3dmol.org/build/3Dmol-min.js"></script>
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||||
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||||
body {
|
||||
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|
||||
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|
||||
}
|
||||
.viewer-container {
|
||||
margin-bottom: 30px;
|
||||
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|
||||
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|
||||
border-radius: 5px;
|
||||
}
|
||||
.view-title {
|
||||
font-weight: bold;
|
||||
margin-bottom: 10px;
|
||||
}
|
||||
.viewer {
|
||||
width: 600px;
|
||||
height: 400px;
|
||||
position: relative;
|
||||
}
|
||||
.divider {
|
||||
border-top: 1px solid #ccc;
|
||||
margin: 30px 0;
|
||||
}
|
||||
button {
|
||||
padding: 8px 16px;
|
||||
background-color: #4CAF50;
|
||||
color: white;
|
||||
border: none;
|
||||
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|
||||
cursor: pointer;
|
||||
margin-top: 10px;
|
||||
}
|
||||
button:hover {
|
||||
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|
||||
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|
||||
h2 {
|
||||
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|
||||
}
|
||||
.index-container {
|
||||
display: flex;
|
||||
flex-wrap: wrap;
|
||||
gap: 15px;
|
||||
}
|
||||
.protein-card {
|
||||
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|
||||
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|
||||
padding: 15px;
|
||||
width: 200px;
|
||||
box-shadow: 0 2px 4px rgba(0,0,0,0.1);
|
||||
}
|
||||
.protein-card:hover {
|
||||
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|
||||
}
|
||||
.protein-card h3 {
|
||||
margin-top: 0;
|
||||
color: #2c4e6f;
|
||||
}
|
||||
.protein-card p {
|
||||
color: #666;
|
||||
margin-bottom: 10px;
|
||||
}
|
||||
.protein-card a {
|
||||
display: inline-block;
|
||||
background: #4e79a7;
|
||||
color: white;
|
||||
padding: 8px 12px;
|
||||
text-decoration: none;
|
||||
border-radius: 4px;
|
||||
}
|
||||
.protein-card a:hover {
|
||||
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|
||||
}
|
||||
</style>
|
||||
</head>
|
||||
<body>
|
||||
<h1>Histidine Interface Visualization - Index</h1>
|
||||
<p>Generated on: 2025-04-15 01:40:56</p>
|
||||
<p>This visualization shows histidine-mediated cation-π and π-π interactions in protein structures.</p>
|
||||
<h2>Protein Structures</h2>
|
||||
<div style="margin: 20px 0;">
|
||||
<a href="manuscript.html" style="display: inline-block; background: #4CAF50; color: white;
|
||||
padding: 10px 20px; text-decoration: none; border-radius: 4px;
|
||||
font-weight: bold; font-size: 16px;">
|
||||
Manuscript Figure Builder
|
||||
</a>
|
||||
<p>Create publication-ready figures with optimized layouts and visualization settings</p>
|
||||
</div>
|
||||
<p>Click on a protein to view its histidine interfaces:</p><div class='index-container'>
|
||||
<div class='protein-card'>
|
||||
<h3>ACOT9</h3>
|
||||
<p>1 structure</p>
|
||||
<a href='histidine_acot9_20250415_014056.html'>View Structures</a>
|
||||
</div>
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
@ -0,0 +1,441 @@
|
||||
<!DOCTYPE html>
|
||||
<html>
|
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
.figure-cell {
|
||||
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|
||||
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|
||||
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||||
}
|
||||
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|
||||
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|
||||
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height: 450px;
|
||||
position: relative;
|
||||
}
|
||||
.viewer-large {
|
||||
width: 600px;
|
||||
height: 500px;
|
||||
position: relative;
|
||||
}
|
||||
h2, h3 {
|
||||
margin-top: 20px;
|
||||
}
|
||||
button {
|
||||
padding: 8px 16px;
|
||||
background-color: #4CAF50;
|
||||
color: white;
|
||||
border: none;
|
||||
border-radius: 4px;
|
||||
cursor: pointer;
|
||||
margin-top: 10px;
|
||||
margin-right: 5px;
|
||||
}
|
||||
button:hover {
|
||||
background-color: #45a049;
|
||||
}
|
||||
.controls {
|
||||
margin: 20px 0;
|
||||
padding: 15px;
|
||||
background-color: #f5f5f5;
|
||||
border-radius: 5px;
|
||||
}
|
||||
.inset-controls {
|
||||
display: flex;
|
||||
flex-wrap: wrap;
|
||||
gap: 10px;
|
||||
margin-top: 10px;
|
||||
}
|
||||
.inset-controls label {
|
||||
margin-right: 5px;
|
||||
}
|
||||
.panel-label {
|
||||
position: absolute;
|
||||
top: 0;
|
||||
left: 0;
|
||||
background: rgba(0,0,0,0.7);
|
||||
color: white;
|
||||
padding: 2px 6px;
|
||||
font-weight: bold;
|
||||
border-bottom-right-radius: 5px;
|
||||
z-index: 100;
|
||||
}
|
||||
.figure-title {
|
||||
font-weight: bold;
|
||||
margin-bottom: 10px;
|
||||
}
|
||||
.label-settings {
|
||||
margin-top: 15px;
|
||||
border-top: 1px solid #ddd;
|
||||
padding-top: 15px;
|
||||
}
|
||||
.color-picker {
|
||||
display: inline-block;
|
||||
width: 30px;
|
||||
height: 20px;
|
||||
border: 1px solid #ccc;
|
||||
margin-right: 5px;
|
||||
vertical-align: middle;
|
||||
}
|
||||
</style>
|
||||
</head>
|
||||
<body>
|
||||
<h1>Manuscript Figure Builder</h1>
|
||||
<p>Create optimized views for manuscript figures. Group structures, create insets, and export ready-to-use figures.</p>
|
||||
<p><a href="index.html">← Back to Main Index</a></p>
|
||||
|
||||
<div class="controls">
|
||||
<h3>Figure Settings</h3>
|
||||
<div>
|
||||
<button id="add-row-btn">Add Row</button>
|
||||
<button id="add-2col-btn">Add 2-Column Row</button>
|
||||
<button id="add-3col-btn">Add 3-Column Row</button>
|
||||
<button id="capture-figure-btn">Export Figure as PNG</button>
|
||||
</div>
|
||||
|
||||
<div class="label-settings">
|
||||
<h4>Global Label Settings</h4>
|
||||
<div>
|
||||
<label>Font Size:</label>
|
||||
<select id="global-font-size">
|
||||
<option value="20">Small (20px)</option>
|
||||
<option value="28" selected>Medium (28px)</option>
|
||||
<option value="36">Large (36px)</option>
|
||||
</select>
|
||||
|
||||
<label style="margin-left:15px">Font Weight:</label>
|
||||
<select id="global-font-weight">
|
||||
<option value="normal">Normal</option>
|
||||
<option value="bold" selected>Bold</option>
|
||||
</select>
|
||||
|
||||
<label style="margin-left:15px">Background:</label>
|
||||
<select id="global-background">
|
||||
<option value="false">None</option>
|
||||
<option value="true" selected>Show</option>
|
||||
</select>
|
||||
</div>
|
||||
<div style="margin-top:10px">
|
||||
<label>Chain A Label Color:</label>
|
||||
<input type="color" id="chain-a-color" value="#2c4e6f" class="color-picker">
|
||||
|
||||
<label style="margin-left:15px">Chain B Label Color:</label>
|
||||
<input type="color" id="chain-b-color" value="#8B4513" class="color-picker">
|
||||
|
||||
<label style="margin-left:15px">Stroke Width:</label>
|
||||
<select id="global-stroke-width">
|
||||
<option value="2">Thin (2px)</option>
|
||||
<option value="3" selected>Medium (3px)</option>
|
||||
<option value="4">Thick (4px)</option>
|
||||
</select>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="manuscript-container" class="manuscript-container">
|
||||
<!-- Rows and viewers will be added here -->
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
<script>
|
||||
// Available protein structures
|
||||
const availableProteins = [
|
||||
{ id: 'ACOT9', name: 'ACOT9 (1 structures)', url: 'histidine_acot9_20250415_014056.html' },
|
||||
];
|
||||
|
||||
|
||||
// Global settings that will be applied to new viewers
|
||||
const globalSettings = {
|
||||
fontSize: 28,
|
||||
fontWeight: 'bold',
|
||||
showBackground: true,
|
||||
chainAColor: '#2c4e6f',
|
||||
chainBColor: '#8B4513',
|
||||
strokeWidth: 3
|
||||
};
|
||||
|
||||
// Load and display a protein structure with specified options
|
||||
function loadStructure(proteinId, viewerId, viewType) {
|
||||
if (!proteinId) return;
|
||||
|
||||
// Find the protein in our available list
|
||||
const protein = availableProteins.find(p => p.id === proteinId);
|
||||
if (!protein) return;
|
||||
|
||||
// Open the protein's HTML file in a hidden iframe to extract the structure data
|
||||
const iframe = document.createElement('iframe');
|
||||
iframe.style.display = 'none';
|
||||
iframe.src = protein.url;
|
||||
document.body.appendChild(iframe);
|
||||
|
||||
// Wait for iframe to load
|
||||
iframe.onload = function() {
|
||||
try {
|
||||
// Find a 3DMol viewer in the iframe that matches our viewType
|
||||
const iframeDoc = iframe.contentDocument || iframe.contentWindow.document;
|
||||
|
||||
// Create a new viewer in our current document
|
||||
let viewer = $3Dmol.createViewer($(`#${viewerId}`), {
|
||||
backgroundColor: "white"
|
||||
});
|
||||
|
||||
// Based on viewType, try to extract either ribbon or labeled view HTML
|
||||
let scriptContent;
|
||||
let modelData;
|
||||
|
||||
// Find all scripts in the iframe
|
||||
const scripts = iframeDoc.querySelectorAll('script');
|
||||
for (let script of scripts) {
|
||||
// Look for scripts that contain our viewer type
|
||||
if ((viewType === 'ribbon' && script.textContent.includes('cartoon')) ||
|
||||
(viewType === 'label' && script.textContent.includes('addLabel'))) {
|
||||
|
||||
scriptContent = script.textContent;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
// If we found a script with the right content
|
||||
if (scriptContent) {
|
||||
// Extract the PDB data from the script
|
||||
const pdbMatch = scriptContent.match(/let pdbData = `([^`]+)`/);
|
||||
if (pdbMatch && pdbMatch[1]) {
|
||||
modelData = pdbMatch[1];
|
||||
|
||||
// Configure the viewer with the extracted data
|
||||
viewer.addModel(modelData, "pdb");
|
||||
|
||||
// Set basic view style
|
||||
viewer.setViewStyle({
|
||||
style: 'outline',
|
||||
color: 'gray',
|
||||
width: 0.01
|
||||
});
|
||||
|
||||
// Add surfaces
|
||||
viewer.addSurface($3Dmol.SAS, {opacity: 0.6, color: '#4e79a7'}, {chain: 'A'});
|
||||
viewer.addSurface($3Dmol.SAS, {opacity: 0.6, color: '#f2be2b'}, {chain: 'B'});
|
||||
|
||||
if (viewType === 'ribbon') {
|
||||
// Add ribbons
|
||||
viewer.setStyle({chain: 'A'}, {cartoon: {color: '#4e79a7', opacity: 1.0}});
|
||||
viewer.setStyle({chain: 'B'}, {cartoon: {color: '#f2be2b', opacity: 1.0}});
|
||||
} else {
|
||||
// Hide cartoon for label view
|
||||
viewer.setStyle({model: -1}, {cartoon: {hidden: true}});
|
||||
|
||||
// Add sticks and labels by extracting this data from the script
|
||||
const stickMatch = scriptContent.match(/viewer.setStyle\(\{\s*chain:.*?\},\s*\{\s*stick:.*?\}\)/g);
|
||||
if (stickMatch) {
|
||||
for (let stick of stickMatch) {
|
||||
eval('viewer.' + stick.substring(7));
|
||||
}
|
||||
}
|
||||
|
||||
const labelMatch = scriptContent.match(/viewer.addLabel\(.*?\)/g);
|
||||
if (labelMatch) {
|
||||
for (let label of labelMatch) {
|
||||
// Apply global label settings
|
||||
let modifiedLabel = label.replace(/fontSize: \d+/, `fontSize: ${globalSettings.fontSize}`);
|
||||
modifiedLabel = modifiedLabel.replace(/fontWeight: ['"].*?['"]/, `fontWeight: '${globalSettings.fontWeight}'`);
|
||||
modifiedLabel = modifiedLabel.replace(/strokeWidth: \d+/, `strokeWidth: ${globalSettings.strokeWidth}`);
|
||||
|
||||
// Font colors
|
||||
if (label.includes("chain: 'A'")) {
|
||||
modifiedLabel = modifiedLabel.replace(/fontColor: ['"].*?['"]/, `fontColor: '${globalSettings.chainAColor}'`);
|
||||
} else {
|
||||
modifiedLabel = modifiedLabel.replace(/fontColor: ['"].*?['"]/, `fontColor: '${globalSettings.chainBColor}'`);
|
||||
}
|
||||
|
||||
// Background
|
||||
if (globalSettings.showBackground) {
|
||||
modifiedLabel = modifiedLabel.replace(/showBackground: \w+/, `showBackground: true`);
|
||||
} else {
|
||||
modifiedLabel = modifiedLabel.replace(/showBackground: \w+/, `showBackground: false`);
|
||||
}
|
||||
|
||||
eval('viewer.' + modifiedLabel.substring(7));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
viewer.zoomTo();
|
||||
viewer.render();
|
||||
}
|
||||
}
|
||||
} catch (e) {
|
||||
console.error("Error loading structure:", e);
|
||||
} finally {
|
||||
// Clean up
|
||||
document.body.removeChild(iframe);
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
// Add a new row to the figure
|
||||
function addRow(numCols = 1) {
|
||||
const container = document.getElementById('manuscript-container');
|
||||
const rowIndex = container.children.length + 1;
|
||||
|
||||
const row = document.createElement('div');
|
||||
row.className = 'figure-row';
|
||||
row.id = `row-${rowIndex}`;
|
||||
|
||||
for (let i = 1; i <= numCols; i++) {
|
||||
const cell = document.createElement('div');
|
||||
cell.className = 'figure-cell';
|
||||
|
||||
const cellControls = document.createElement('div');
|
||||
cellControls.innerHTML = `
|
||||
<div style="margin-bottom:10px">
|
||||
<select class="protein-select" data-row="${rowIndex}" data-col="${i}">
|
||||
<option value="">Select protein...</option>
|
||||
${availableProteins.map(p => `<option value="${p.id}">${p.name}</option>`).join('')}
|
||||
</select>
|
||||
|
||||
<select class="view-type" data-row="${rowIndex}" data-col="${i}">
|
||||
<option value="ribbon">Ribbon view</option>
|
||||
<option value="label">Labeled view</option>
|
||||
</select>
|
||||
|
||||
<select class="viewer-size" data-row="${rowIndex}" data-col="${i}">
|
||||
<option value="small">Small</option>
|
||||
<option value="medium" selected>Medium</option>
|
||||
<option value="large">Large</option>
|
||||
</select>
|
||||
</div>
|
||||
<div class="viewer-container">
|
||||
<div class="panel-label">${String.fromCharCode(64 + rowIndex)}${i}</div>
|
||||
<div id="viewer-${rowIndex}-${i}" class="viewer-medium"></div>
|
||||
</div>
|
||||
`;
|
||||
|
||||
cell.appendChild(cellControls);
|
||||
row.appendChild(cell);
|
||||
}
|
||||
|
||||
container.appendChild(row);
|
||||
|
||||
// Add event listeners to the new selects
|
||||
row.querySelectorAll('.protein-select').forEach(select => {
|
||||
select.addEventListener('change', function() {
|
||||
const row = this.dataset.row;
|
||||
const col = this.dataset.col;
|
||||
const viewType = document.querySelector(`.view-type[data-row="${row}"][data-col="${col}"]`).value;
|
||||
const viewerId = `viewer-${row}-${col}`;
|
||||
loadStructure(this.value, viewerId, viewType);
|
||||
});
|
||||
});
|
||||
|
||||
row.querySelectorAll('.view-type').forEach(select => {
|
||||
select.addEventListener('change', function() {
|
||||
const row = this.dataset.row;
|
||||
const col = this.dataset.col;
|
||||
const proteinId = document.querySelector(`.protein-select[data-row="${row}"][data-col="${col}"]`).value;
|
||||
const viewerId = `viewer-${row}-${col}`;
|
||||
if (proteinId) {
|
||||
loadStructure(proteinId, viewerId, this.value);
|
||||
}
|
||||
});
|
||||
});
|
||||
|
||||
row.querySelectorAll('.viewer-size').forEach(select => {
|
||||
select.addEventListener('change', function() {
|
||||
const row = this.dataset.row;
|
||||
const col = this.dataset.col;
|
||||
const viewerId = document.getElementById(`viewer-${row}-${col}`);
|
||||
|
||||
// Remove existing size classes
|
||||
viewerId.classList.remove('viewer-small', 'viewer-medium', 'viewer-large');
|
||||
|
||||
// Add the new size class
|
||||
viewerId.classList.add(`viewer-${this.value}`);
|
||||
|
||||
// Reload the viewer to update the size
|
||||
setTimeout(() => {
|
||||
const proteinId = document.querySelector(`.protein-select[data-row="${row}"][data-col="${col}"]`).value;
|
||||
if (proteinId) {
|
||||
const viewType = document.querySelector(`.view-type[data-row="${row}"][data-col="${col}"]`).value;
|
||||
loadStructure(proteinId, `viewer-${row}-${col}`, viewType);
|
||||
}
|
||||
}, 100);
|
||||
});
|
||||
});
|
||||
}
|
||||
|
||||
// Capture the figure as an image
|
||||
function captureFigure() {
|
||||
html2canvas(document.getElementById('manuscript-container')).then(canvas => {
|
||||
const link = document.createElement('a');
|
||||
link.download = 'manuscript-figure.png';
|
||||
link.href = canvas.toDataURL('image/png');
|
||||
link.click();
|
||||
});
|
||||
}
|
||||
|
||||
// Event listeners for the control buttons
|
||||
document.getElementById('add-row-btn').addEventListener('click', () => addRow(1));
|
||||
document.getElementById('add-2col-btn').addEventListener('click', () => addRow(2));
|
||||
document.getElementById('add-3col-btn').addEventListener('click', () => addRow(3));
|
||||
document.getElementById('capture-figure-btn').addEventListener('click', captureFigure);
|
||||
|
||||
// Update global settings when controls change
|
||||
document.getElementById('global-font-size').addEventListener('change', function() {
|
||||
globalSettings.fontSize = parseInt(this.value);
|
||||
});
|
||||
|
||||
document.getElementById('global-font-weight').addEventListener('change', function() {
|
||||
globalSettings.fontWeight = this.value;
|
||||
});
|
||||
|
||||
document.getElementById('global-background').addEventListener('change', function() {
|
||||
globalSettings.showBackground = this.value === 'true';
|
||||
});
|
||||
|
||||
document.getElementById('chain-a-color').addEventListener('change', function() {
|
||||
globalSettings.chainAColor = this.value;
|
||||
});
|
||||
|
||||
document.getElementById('chain-b-color').addEventListener('change', function() {
|
||||
globalSettings.chainBColor = this.value;
|
||||
});
|
||||
|
||||
document.getElementById('global-stroke-width').addEventListener('change', function() {
|
||||
globalSettings.strokeWidth = parseInt(this.value);
|
||||
});
|
||||
|
||||
// Add an initial row to get started
|
||||
addRow(2);
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
1689
cation-pi/his-interface-visualization.py
Normal file
1689
cation-pi/his-interface-visualization.py
Normal file
File diff suppressed because it is too large
Load Diff
89
cation-pi/histidine_interface_progress_log.md
Normal file
89
cation-pi/histidine_interface_progress_log.md
Normal file
@ -0,0 +1,89 @@
|
||||
# Histidine Interface Visualization Project - Progress Log
|
||||
|
||||
Date: April 15, 2024
|
||||
|
||||
## Project Overview
|
||||
|
||||
We've been adapting a Jupyter notebook script for visualizing histidine-mediated cation-π and π-π interactions into a standalone Python script (his-interface-visualization.py) that works in VS Code with py3Dmol visualization.
|
||||
|
||||
## Completed Improvements
|
||||
|
||||
1. **Separate HTML Files for Different Proteins**
|
||||
- Created individual HTML files for each anchor protein (Chain A) to prevent browser crashes
|
||||
- Added an index page with links to each protein's visualization page
|
||||
- Added manuscript figure builder tool for publication-ready figures
|
||||
|
||||
2. **CIF Filename Parsing**
|
||||
- Fixed the extraction of anchor protein names from CIF filenames
|
||||
- Added logic to parse patterns like `fold_2025_03_16_23_33_acad_acat1_model_0.cif` to extract "ACAD"
|
||||
- Added safeguards to prevent returning "FOLD" as an anchor protein name
|
||||
- Still seeing some files grouped under "FOLD" that need better parsing
|
||||
|
||||
3. **Label Visibility Improvements**
|
||||
- Increased font size from 20px to 28px for better readability
|
||||
- Changed Chain B label color from gold to dark brown (#8B4513) for better contrast against gold surface
|
||||
- Added semi-transparent white backgrounds behind labels
|
||||
- Increased stroke width around text from 2px to 3px
|
||||
- Changed Chain B stroke color from white to black for better visibility
|
||||
- Added comments in code to document these styling improvements
|
||||
|
||||
4. **Manuscript Figure Builder**
|
||||
- Created a new tool for building publication figures with multiple panels
|
||||
- Added ability to select different proteins and view types for each panel
|
||||
- Implemented global label settings for customizing appearance
|
||||
- Added size control for individual viewers (small, medium, large)
|
||||
- Added export to PNG functionality
|
||||
- Uses iframe approach to extract data from individual protein pages
|
||||
|
||||
5. **Code Organization**
|
||||
- Moved from Jupyter notebook to standalone Python script
|
||||
- Added proper command-line argument handling
|
||||
- Added documentation and docstrings
|
||||
- Improved error handling and messaging
|
||||
|
||||
## Remaining Issues
|
||||
|
||||
1. **Regex Pattern Escaping**
|
||||
- SyntaxWarning: invalid escape sequence '\(' in JavaScript regex
|
||||
- Need to properly escape backslashes in JavaScript regex patterns
|
||||
|
||||
2. **Some CIF Files Still Under "FOLD"**
|
||||
- Some CIF files are still being grouped under a "FOLD" category
|
||||
- Need to improve filename parsing for more variants
|
||||
|
||||
3. **Browser Stability**
|
||||
- While greatly improved, very large files might still cause slowness
|
||||
- Consider adding pagination for proteins with many structures
|
||||
|
||||
4. **JavaScript Integration**
|
||||
- The manuscript figure builder's dynamic loading of protein structures could be enhanced
|
||||
- Consider adding a loading indicator while structures load
|
||||
|
||||
## Usage Instructions
|
||||
|
||||
```bash
|
||||
# Basic usage
|
||||
python his-interface-visualization.py path/to/pdb/folder
|
||||
|
||||
# With output directory specified
|
||||
python his-interface-visualization.py path/to/pdb/folder --output output_dir
|
||||
|
||||
# Auto-open in browser
|
||||
python his-interface-visualization.py path/to/pdb/folder --open
|
||||
```
|
||||
|
||||
## Next Steps
|
||||
|
||||
1. Fix the JavaScript regex escape warnings
|
||||
2. Further refine the CIF filename parsing to reduce "FOLD" grouping
|
||||
3. Enhance the manuscript figure builder UI for easier use
|
||||
4. Add configuration options for colors and styling
|
||||
5. Consider adding more export formats beyond PNG
|
||||
6. Add option to modify distance cutoff via command line
|
||||
|
||||
## Dependencies
|
||||
|
||||
- py3Dmol
|
||||
- Biopython
|
||||
- jQuery (web interface)
|
||||
- html2canvas (for PNG export)
|
||||
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Reference in New Issue
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