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b47954d | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 | """Interactive sequence viewer with per-residue displacement heatmap."""
import streamlit as st
import numpy as np
# Amino acid property classification
AA_PROPS = {
"A": "hydrophobic", "I": "hydrophobic", "L": "hydrophobic", "M": "hydrophobic",
"F": "hydrophobic", "W": "hydrophobic", "V": "hydrophobic", "P": "hydrophobic",
"D": "charged", "E": "charged", "K": "charged", "R": "charged", "H": "charged",
"S": "polar", "T": "polar", "N": "polar", "Q": "polar", "C": "polar", "Y": "polar",
"G": "special", "X": "unknown",
}
PROP_COLORS = {
"hydrophobic": "#f59e0b",
"charged": "#ef4444",
"polar": "#10b981",
"special": "#94a3b8",
"unknown": "#64748b",
}
def render_sequence_viewer(
seq: str,
displacements: np.ndarray,
coverage: np.ndarray = None,
mode_label: str = "Mode 0",
max_chars_per_row: int = 80,
):
"""Render interactive HTML sequence viewer with displacement coloring.
Each residue is displayed as a colored cell where:
- Background: displacement magnitude (white → red gradient)
- Border: coverage (thick = low coverage)
- Tooltip: residue info
Args:
seq: Amino acid sequence (1-letter codes)
displacements: Per-residue displacement magnitudes (N,)
coverage: Per-residue coverage (N,) in [0, 1]
mode_label: Label for the current mode
max_chars_per_row: Characters per row before wrapping
"""
n = len(seq)
if coverage is None:
coverage = np.ones(n)
max_d = displacements.max() + 1e-8
html = f"""
<style>
.seq-container {{
font-family: 'Consolas', 'Monaco', monospace;
background: #1e1b4b;
border-radius: 8px;
padding: 12px;
margin: 8px 0;
}}
.seq-header {{
color: #a5b4fc;
font-size: 13px;
margin-bottom: 8px;
font-weight: bold;
}}
.seq-row {{
display: flex;
flex-wrap: wrap;
gap: 1px;
margin-bottom: 2px;
}}
.res {{
display: inline-flex;
align-items: center;
justify-content: center;
width: 14px;
height: 22px;
font-size: 10px;
font-weight: bold;
border-radius: 2px;
cursor: pointer;
transition: transform 0.1s;
position: relative;
}}
.res:hover {{
transform: scale(1.8);
z-index: 10;
box-shadow: 0 0 8px rgba(99, 102, 241, 0.8);
}}
.res:hover::after {{
content: attr(data-tooltip);
position: absolute;
top: -38px;
left: 50%;
transform: translateX(-50%);
background: #312e81;
color: white;
padding: 4px 8px;
border-radius: 4px;
font-size: 10px;
white-space: nowrap;
z-index: 100;
border: 1px solid #6366f1;
}}
.seq-ruler {{
display: flex;
gap: 1px;
margin-bottom: 1px;
}}
.ruler-mark {{
width: 14px;
font-size: 7px;
color: #64748b;
text-align: center;
}}
.legend {{
display: flex;
gap: 16px;
margin-top: 8px;
font-size: 11px;
color: #94a3b8;
}}
.legend-item {{
display: flex;
align-items: center;
gap: 4px;
}}
.legend-swatch {{
width: 12px;
height: 12px;
border-radius: 2px;
}}
</style>
<div class="seq-container">
<div class="seq-header">{mode_label} — Per-residue displacement ({n} residues)</div>
"""
# Build rows
for row_start in range(0, n, max_chars_per_row):
row_end = min(row_start + max_chars_per_row, n)
# Ruler
html += '<div class="seq-ruler">'
for i in range(row_start, row_end):
if (i + 1) % 10 == 0:
html += f'<div class="ruler-mark">{i + 1}</div>'
elif (i + 1) % 5 == 0:
html += '<div class="ruler-mark">·</div>'
else:
html += '<div class="ruler-mark"></div>'
html += "</div>"
# Residues
html += '<div class="seq-row">'
for i in range(row_start, row_end):
aa = seq[i] if i < len(seq) else "X"
d = displacements[i]
c = coverage[i] if i < len(coverage) else 1.0
t = d / max_d # Normalized displacement
# Background: displacement heatmap (dark purple → bright red)
r = int(30 + 225 * t)
g = int(27 + 20 * (1 - t))
b = int(75 - 50 * t)
bg = f"rgb({r},{g},{b})"
# Text color: white for high displacement, light for low
txt_color = "white" if t > 0.3 else "#a5b4fc"
# Border: thicker = lower coverage
border_w = max(0, int(3 * (1 - c)))
border = f"{border_w}px solid #ef4444" if border_w > 0 else "none"
prop = AA_PROPS.get(aa, "unknown")
tooltip = f"{aa}{i+1} | {d:.3f}Å | cov={c:.2f} | {prop}"
html += (
f'<div class="res" style="background:{bg};color:{txt_color};'
f'border:{border}" data-tooltip="{tooltip}">{aa}</div>'
)
html += "</div>"
# Legend
html += """
<div class="legend">
<div class="legend-item">
<div class="legend-swatch" style="background:linear-gradient(90deg,#1e1b4b,#ff3030)"></div>
Low → High displacement
</div>
<div class="legend-item">
<div class="legend-swatch" style="border:2px solid #ef4444;background:none"></div>
Red border = low coverage
</div>
</div>
</div>
"""
st.markdown(html, unsafe_allow_html=True)
def render_displacement_chart(
displacements: dict,
seq: str = "",
coverage: np.ndarray = None,
):
"""Render interactive displacement profile chart using Plotly.
Args:
displacements: {mode_idx: np.ndarray of per-residue magnitudes}
seq: Amino acid sequence
coverage: Per-residue coverage
"""
import plotly.graph_objects as go
from plotly.subplots import make_subplots
n_modes = len(displacements)
n_res = len(list(displacements.values())[0])
residues = np.arange(1, n_res + 1)
# Hover text with AA identity
hover_text = [f"{seq[i] if i < len(seq) else '?'}{i+1}" for i in range(n_res)]
fig = make_subplots(
rows=2, cols=1, row_heights=[0.75, 0.25],
shared_xaxes=True, vertical_spacing=0.08,
subplot_titles=["Displacement by Mode", "Coverage"]
)
colors = ["#6366f1", "#ef4444", "#10b981", "#f59e0b", "#ec4899", "#8b5cf6"]
for k, d in displacements.items():
mags = np.linalg.norm(d, axis=1) if d.ndim == 2 else d
fig.add_trace(go.Scatter(
x=residues, y=mags,
mode="lines",
name=f"Mode {k} (μ={mags.mean():.3f}Å)",
line=dict(color=colors[k % len(colors)], width=1.5),
fill="tozeroy",
fillcolor=colors[k % len(colors)].replace(")", ",0.1)").replace("rgb", "rgba"),
text=hover_text,
hovertemplate="%{text}<br>Displacement: %{y:.3f}Å<extra>Mode " + str(k) + "</extra>",
), row=1, col=1)
# Coverage
if coverage is not None:
fig.add_trace(go.Scatter(
x=residues, y=coverage[:n_res],
mode="lines",
name="Coverage",
line=dict(color="#94a3b8", width=1.5),
fill="tozeroy",
fillcolor="rgba(148,163,184,0.15)",
hovertemplate="%{x}<br>Coverage: %{y:.3f}<extra></extra>",
), row=2, col=1)
fig.update_layout(
template="plotly_dark",
height=400,
paper_bgcolor="rgba(0,0,0,0)",
plot_bgcolor="rgba(30,27,75,0.5)",
legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
margin=dict(l=50, r=20, t=40, b=30),
)
fig.update_xaxes(title_text="Residue", row=2, col=1)
fig.update_yaxes(title_text="Displacement (Å)", row=1, col=1)
fig.update_yaxes(title_text="Coverage", range=[0, 1.1], row=2, col=1)
st.plotly_chart(fig, use_container_width=True, key=f"disp_chart")
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