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import matplotlib.pyplot as plt # type: ignore
import pandas as pd
import re
def create_design_plot(fasta_file_path):
"""
Parses the MPNN fasta file and returns a Matplotlib figure.
"""
data = []
with open(fasta_file_path, 'r') as f:
content = f.read()
# Extract score (local score, not global_score) and recovery from headers
# Example: >T=0.1, sample=1, score=0.7880, global_score=1.3897, seq_recovery=0.4295
# We want to capture the local "score=" value, not "global_score="
pattern = r"score=([\d\.]+)(?:,\s+global_score=[\d\.]+)?,\s+seq_recovery=([\d\.]+)"
for line in content.split('\n'):
if line.startswith(">") and "score=" in line and "seq_recovery" in line:
# Make sure we're not matching global_score by checking the pattern order
match = re.search(pattern, line)
if match:
# Verify we got the local score (should be before global_score if present)
score_val = float(match.group(1))
recovery_val = float(match.group(2))
data.append({
"Score": score_val,
"Recovery": recovery_val
})
df = pd.DataFrame(data)
# Create the Plot
fig, ax = plt.subplots(figsize=(8, 5))
ax.scatter(df['Score'], df['Recovery'], color='black', alpha=0.6, s=80, edgecolors='white')
# Highlight the Lead Candidate (Lowest Score) with a gold star
best = df.loc[df['Score'].idxmin()]
ax.scatter(best['Score'], best['Recovery'], marker='*', color='gold', s=400, edgecolors='black', linewidths=1.5, label="Lead Candidate", zorder=10)
ax.set_title("BroteinShake: Design Evolution (N=20)", fontsize=14)
ax.set_xlabel("ProteinMPNN Score (Lower = More Stable)", fontsize=10)
ax.set_ylabel("Sequence Recovery (%)", fontsize=10)
ax.legend()
ax.grid(True, linestyle='--', alpha=0.5)
return fig
def create_protein_viewer(pdb_file_path):
"""
Generates HTML/JS for a 3D protein viewer using 3Dmol.js.
"""
with open(pdb_file_path, 'r') as f:
pdb_content = f.read().replace('\n', '\\n')
html_content = f"""
<div id="container-3d" style="height: 500px; width: 100%; position: relative;"></div>
<script>
(function() {{
// Wait for 3Dmol to be loaded (from head)
function initViewer() {{
if (typeof $3Dmol === 'undefined') {{
setTimeout(initViewer, 100);
return;
}}
let element = document.getElementById('container-3d');
if (!element) return;
let config = {{ backgroundColor: 'white' }};
let viewer = $3Dmol.createViewer(element, config);
let pdbData = `{pdb_content}`;
viewer.addModel(pdbData, "pdb");
viewer.setStyle({{}}, {{cartoon: {{color: 'spectrum'}}}});
viewer.zoomTo();
viewer.render();
}}
if (document.readyState === 'loading') {{
document.addEventListener('DOMContentLoaded', initViewer);
}} else {{
initViewer();
}}
}})();
</script>
"""
return html_content |