File size: 6,990 Bytes
b075954 | 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 | """Downloadable candidate and variant reports."""
from io import BytesIO
from datetime import datetime
from reportlab.lib import colors
from reportlab.lib.enums import TA_CENTER, TA_LEFT
from reportlab.lib.pagesizes import A4
from reportlab.lib.styles import ParagraphStyle
from reportlab.lib.units import cm
from reportlab.platypus import (
HRFlowable,
Paragraph,
SimpleDocTemplate,
Spacer,
Table,
TableStyle,
)
NAVY = colors.HexColor("#1B365D")
TEAL = colors.HexColor("#0E7C7B")
LIGHT = colors.HexColor("#F4F7FB")
WHITE = colors.white
TEXT = colors.HexColor("#111827")
MUTED = colors.HexColor("#4A5568")
GREEN = colors.HexColor("#2F855A")
RED = colors.HexColor("#C53030")
ORANGE = colors.HexColor("#C45C26")
def _styles():
return {
"title": ParagraphStyle("t", fontName="Helvetica-Bold", fontSize=16, textColor=NAVY, alignment=TA_CENTER),
"sub": ParagraphStyle("s", fontName="Helvetica", fontSize=9, textColor=colors.HexColor("#D6E0F0"), alignment=TA_CENTER),
"h": ParagraphStyle("h", fontName="Helvetica-Bold", fontSize=11, textColor=NAVY, spaceBefore=10, spaceAfter=4),
"b": ParagraphStyle("b", fontName="Helvetica", fontSize=9, textColor=TEXT, leading=12),
"small": ParagraphStyle("sm", fontName="Helvetica", fontSize=8, textColor=MUTED, leading=11),
}
def _header_footer(canvas, doc):
canvas.saveState()
canvas.setFillColor(NAVY)
canvas.rect(0, A4[1] - 52, A4[0], 52, fill=1, stroke=0)
canvas.setFillColor(TEAL)
canvas.rect(0, 0, A4[0], 22, fill=1, stroke=0)
canvas.setFillColor(WHITE)
canvas.setFont("Helvetica", 8)
canvas.drawString(1.6 * cm, 8, "TP53 Mutant Discovery Platform | Computational prioritization, not clinical proof")
canvas.restoreState()
def generate_variant_report(variant_row, candidates, structure_row=None, pocket_row=None) -> bytes:
styles = _styles()
buf = BytesIO()
doc = SimpleDocTemplate(
buf,
pagesize=A4,
leftMargin=1.6 * cm,
rightMargin=1.6 * cm,
topMargin=2.4 * cm,
bottomMargin=1.4 * cm,
)
hgvs = variant_row.get("hgvs_p", "")
story = [
Spacer(1, 6),
Paragraph("TP53 Variant-to-Compound Discovery Report", styles["title"]),
Paragraph(f"Project: Lung Cancer · Variant {hgvs} · {datetime.utcnow():%Y-%m-%d}", styles["sub"]),
Spacer(1, 28),
Paragraph("Mutation analysis", styles["h"]),
Paragraph(
f"<b>{hgvs}</b> | Exon {variant_row.get('exon','')} | "
f"{variant_row.get('domain','')} | Inferred type: {variant_row.get('type_inferred','')}<br/>"
f"Source type: {variant_row.get('type_source','')} | Effect: {variant_row.get('effect_source','')}<br/>"
f"Allele frequency (observation): {variant_row.get('allele_frequency','')} | "
f"QC: {variant_row.get('qc_flags','')} | Route: {variant_row.get('route','')}<br/>"
f"Priority score: {variant_row.get('priority_score','')} | "
f"Hotspot: {variant_row.get('hotspot','')}",
styles["b"],
),
]
if structure_row is not None:
story += [
Paragraph("Wild-type versus mutant structure", styles["h"]),
Paragraph(
f"ΔΔG proxy: {structure_row.get('ddg_kcal','')} kcal/mol | "
f"Cα RMSD: {structure_row.get('ca_rmsd_A','')} Å | "
f"Local RMSD: {structure_row.get('local_rmsd_A','')} Å<br/>"
f"Pocket volume WT→mut: {structure_row.get('pocket_vol_wt','')} → {structure_row.get('pocket_vol_mut','')} ų | "
f"Structure quality: {structure_row.get('structure_quality','')}",
styles["b"],
),
]
if pocket_row is not None:
story += [
Paragraph("Primary pocket", styles["h"]),
Paragraph(
f"{pocket_row.get('pocket_name','')} ({pocket_row.get('pocket_id','')}) | "
f"Druggability {pocket_row.get('druggability','')} | "
f"Docking gate: {pocket_row.get('docking_gate','')} | "
f"Volume Δ {pocket_row.get('volume_delta','')} ų",
styles["b"],
),
]
story.append(Paragraph("Top ranked candidates", styles["h"]))
header = ["Rank", "Compound", "Status", "Dock mut", "Dock WT", "Sel.", "MD", "ADMET", "Score", "Rec."]
data = [header]
use = candidates.sort_values("rank").head(10)
for _, r in use.iterrows():
data.append(
[
str(int(r["rank"])),
str(r["name"])[:18],
str(r["status"])[:10],
f"{r['dock_mut']:.1f}",
f"{r['dock_wt']:.1f}",
f"{r['Sselectivity']:.2f}",
f"{r['MDstability']:.2f}",
f"{r['ADMET']:.2f}",
f"{r['rescue_score']:.2f}",
str(r["recommendation"]),
]
)
tbl = Table(data, repeatRows=1)
tbl.setStyle(
TableStyle(
[
("BACKGROUND", (0, 0), (-1, 0), NAVY),
("TEXTCOLOR", (0, 0), (-1, 0), WHITE),
("FONTNAME", (0, 0), (-1, 0), "Helvetica-Bold"),
("FONTSIZE", (0, 0), (-1, -1), 7),
("BACKGROUND", (0, 1), (-1, -1), LIGHT),
("GRID", (0, 0), (-1, -1), 0.3, colors.HexColor("#D1D5DB")),
("ALIGN", (0, 0), (-1, -1), "CENTER"),
("VALIGN", (0, 0), (-1, -1), "MIDDLE"),
("TOPPADDING", (0, 0), (-1, -1), 4),
("BOTTOMPADDING", (0, 0), (-1, -1), 4),
]
)
)
story += [tbl, Spacer(1, 8)]
if len(use):
top = use.iloc[0]
story += [
Paragraph("AI recommendation", styles["h"]),
Paragraph(
f"Top candidate <b>{top['name']}</b> | Rescue/Opportunity Score {top['rescue_score']:.2f} "
f" | Confidence {top['confidence']:.2f}<br/>"
f"Recommendation: <b>{top['recommendation']}</b> | Next: {top['next_experiment']}<br/>"
f"Reason codes: {top['reason_codes']}",
styles["b"],
),
]
story += [
Paragraph("Disclaimer", styles["h"]),
Paragraph(
"Scores are multi-objective computational estimates for prioritization. "
"They are not proof of binding, rescue, or clinical efficacy. Experimental assays remain the validation layer.",
styles["small"],
),
]
# dummy title overlay: we already drew header bar in canvas; put title into flow with white space
doc.build(story, onFirstPage=_header_footer, onLaterPages=_header_footer)
return buf.getvalue()
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