from pptx import Presentation
from pptx.util import Inches, Pt, Emu
from pptx.dml.color import RGBColor
from pptx.enum.text import PP_ALIGN
from pptx.util import Inches, Pt
import math

prs = Presentation()
prs.slide_width = Inches(16)
prs.slide_height = Inches(9)

# ─── COLOR PALETTE ───────────────────────────────────────────────────────────
BG         = RGBColor(0x0D, 0x1B, 0x2A)   # deep navy
CENTER_BG  = RGBColor(0xFF, 0x6B, 0x35)   # orange
BRANCH1    = RGBColor(0x4E, 0xC9, 0xB0)   # teal
BRANCH2    = RGBColor(0xFF, 0xD1, 0x66)   # yellow
BRANCH3    = RGBColor(0x7E, 0xB8, 0xFF)   # blue
BRANCH4    = RGBColor(0xFF, 0x85, 0xA1)   # pink
BRANCH5    = RGBColor(0xB5, 0xEA, 0xD7)   # mint
BRANCH6    = RGBColor(0xE0, 0xBB, 0xFF)   # lavender
SUBBG      = RGBColor(0x1E, 0x2D, 0x40)   # dark card
WHITE      = RGBColor(0xFF, 0xFF, 0xFF)
DARK       = RGBColor(0x0D, 0x1B, 0x2A)

def add_rounded_box(slide, x, y, w, h, fill_color, text_lines, font_sizes, bold_flags,
                    text_color=WHITE, corner_radius=0.08):
    shape = slide.shapes.add_shape(
        1,  # MSO_SHAPE_TYPE.RECTANGLE -> use freeform instead? No, use 5 = rounded rect
        Inches(x), Inches(y), Inches(w), Inches(h)
    )
    # rounded corners via XML
    from pptx.oxml.ns import qn
    from lxml import etree
    sp = shape.element
    prstGeom = sp.find(qn('p:spPr')).find(qn('a:prstGeom'))
    if prstGeom is not None:
        prstGeom.set('prst', 'roundRect')
        avLst = prstGeom.find(qn('a:avLst'))
        if avLst is None:
            avLst = etree.SubElement(prstGeom, qn('a:avLst'))
        for gd in avLst.findall(qn('a:gd')):
            avLst.remove(gd)
        gd = etree.SubElement(avLst, qn('a:gd'))
        gd.set('name', 'adj')
        gd.set('fmla', 'val 30000')

    fill = shape.fill
    fill.solid()
    fill.fore_color.rgb = fill_color
    shape.line.color.rgb = fill_color

    tf = shape.text_frame
    tf.word_wrap = True
    tf.margin_top = Pt(2)
    tf.margin_bottom = Pt(2)
    tf.margin_left = Pt(4)
    tf.margin_right = Pt(4)

    for i, (line, fsize, bold) in enumerate(zip(text_lines, font_sizes, bold_flags)):
        if i == 0:
            p = tf.paragraphs[0]
        else:
            p = tf.add_paragraph()
        p.alignment = PP_ALIGN.CENTER
        run = p.add_run()
        run.text = line
        run.font.size = Pt(fsize)
        run.font.bold = bold
        run.font.color.rgb = text_color
    return shape


def add_connector(slide, x1, y1, x2, y2, color):
    from pptx.oxml.ns import qn
    from lxml import etree
    spTree = slide.shapes._spTree
    # use a simple line connector
    x1e, y1e = Inches(x1), Inches(y1)
    x2e, y2e = Inches(x2), Inches(y2)
    cx, cy = abs(x2e - x1e), abs(y2e - y1e)
    left = min(x1e, x2e)
    top = min(y1e, y2e)
    sp = slide.shapes.add_connector(1, x1e, y1e, x2e, y2e)
    sp.line.color.rgb = color
    sp.line.width = Pt(1.5)


# ─── SLIDE 1: MASTER MIND MAP ─────────────────────────────────────────────────
slide_layout = prs.slide_layouts[6]  # blank
slide = prs.slides.add_slide(slide_layout)

# Background
bg = slide.shapes.add_shape(1, 0, 0, prs.slide_width, prs.slide_height)
bg.fill.solid(); bg.fill.fore_color.rgb = BG; bg.line.color.rgb = BG

# Title bar
add_rounded_box(slide, 0.2, 0.1, 15.6, 0.65,
    CENTER_BG,
    ["GENETICS — Robbins Chapter 4 Mind Map", "Robbins Basic Pathology | 4-Hour Study"],
    [18, 10], [True, False])

# Center node
add_rounded_box(slide, 6.2, 3.8, 3.6, 1.2,
    CENTER_BG,
    ["GENETIC DISEASES", "(Ch. 4 Robbins)"],
    [16, 10], [True, False])

# Branch data: (label, color, x, y, sub-items)
branches = [
    {
        "label": "1. MUTATIONS\n& TYPES",
        "color": BRANCH1,
        "x": 0.3, "y": 1.0,
        "sub": [
            "Point mutation (missense/nonsense)",
            "Frameshift (ins/del)",
            "Trinucleotide repeats",
            "Copy number variants (CNV)",
        ]
    },
    {
        "label": "2. MENDELIAN\nDISORDERS",
        "color": BRANCH2,
        "x": 0.3, "y": 4.2,
        "sub": [
            "AD: Marfan, FH, HD, NF",
            "AR: CF, PKU, Sickle cell,\n  Tay-Sachs, Glycogen storage",
            "XR: Duchenne MD,\n  Hemophilia A&B, G6PD",
            "Pleiotropy & Genetic heterogeneity",
        ]
    },
    {
        "label": "3. STRUCT.\nPROTEIN DEFECTS",
        "color": BRANCH3,
        "x": 0.3, "y": 6.8,
        "sub": [
            "Marfan (FBN1 → fibrillin)",
            "EDS subtypes",
            "Osteogenesis imperfecta\n  (COL1A1/2)",
        ]
    },
    {
        "label": "4. ENZYME\nDEFECTS (AR)",
        "color": BRANCH4,
        "x": 11.8, "y": 1.0,
        "sub": [
            "PKU (PAH → ↓Phe → tyrosine def)",
            "Tay-Sachs (HexA → GM2)",
            "Gaucher (glucocerebrosidase)",
            "Glycogen storage (Type I–VI)",
            "Galactosemia",
        ]
    },
    {
        "label": "5. CYTOGENETIC\nDISORDERS",
        "color": BRANCH5,
        "x": 11.8, "y": 4.2,
        "sub": [
            "Trisomy 21 (Down) — 47,+21",
            "Trisomy 18 (Edwards)",
            "Trisomy 13 (Patau)",
            "Turner 45,X",
            "Klinefelter 47,XXY",
            "22q11.2 del (DiGeorge/VCF)",
        ]
    },
    {
        "label": "6. SPECIAL\nMECHANISMS",
        "color": BRANCH6,
        "x": 11.8, "y": 6.8,
        "sub": [
            "Trinucleotide: Fragile X,\n  HD, Myotonic dystrophy",
            "Imprinting: Prader-Willi\n  vs Angelman (Chr 15)",
            "Mitochondrial inheritance\n  (maternal) — Leber",
            "Epigenetics: DNA methylation,\n  histone modification",
        ]
    },
]

branch_colors_map = {b["label"]: b["color"] for b in branches}

# Center coords
cx, cy = 8.0, 4.4

for b in branches:
    bx = b["x"] + 1.9  # center of branch box (box width ~2.6)
    by = b["y"] + 0.4  # center of branch box (box height ~0.8)
    add_connector(slide, cx, cy, bx, by, b["color"])
    add_rounded_box(slide, b["x"], b["y"], 2.6, 0.8,
        b["color"],
        [b["label"]],
        [9], [True], text_color=DARK)

    # Sub items below/beside
    sub_start_y = b["y"] + 1.0
    for j, sub in enumerate(b["sub"]):
        sy = sub_start_y + j * 0.42
        if sy > 8.6:
            break
        sx = b["x"]
        box = slide.shapes.add_shape(1, Inches(sx), Inches(sy), Inches(2.6), Inches(0.38))
        box.fill.solid(); box.fill.fore_color.rgb = SUBBG
        box.line.color.rgb = b["color"]
        box.line.width = Pt(0.75)
        tf = box.text_frame; tf.word_wrap = True
        tf.margin_top = Pt(1); tf.margin_bottom = Pt(1)
        tf.margin_left = Pt(3); tf.margin_right = Pt(3)
        p = tf.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
        run = p.add_run(); run.text = "• " + sub
        run.font.size = Pt(6.5); run.font.color.rgb = WHITE


# ─── SLIDE 2: MENDELIAN DISORDERS DEEP DIVE ──────────────────────────────────
slide2 = prs.slides.add_slide(slide_layout)
bg2 = slide2.shapes.add_shape(1, 0, 0, prs.slide_width, prs.slide_height)
bg2.fill.solid(); bg2.fill.fore_color.rgb = BG; bg2.line.color.rgb = BG

add_rounded_box(slide2, 0.2, 0.1, 15.6, 0.65,
    BRANCH2,
    ["MENDELIAN DISORDERS — Key High-Yield Diseases", "Robbins Ch.4 | Marrow High-Yield"],
    [18, 10], [True, False], text_color=DARK)

# Table headers
headers = ["DISEASE", "GENE / DEFECT", "MECHANISM", "KEY FEATURES", "USMLE CLUE"]
col_widths = [2.4, 2.8, 2.8, 4.0, 3.6]
col_x = [0.2]
for w in col_widths[:-1]:
    col_x.append(col_x[-1] + w + 0.05)

for i, (h, w, x) in enumerate(zip(headers, col_widths, col_x)):
    add_rounded_box(slide2, x, 0.9, w, 0.35, BRANCH2, [h], [9], [True], text_color=DARK)

rows = [
    ("Marfan Syndrome", "FBN1 (fibrillin-1)", "AD — struct. protein", "Tall, lens sublux, aortic dissection,\narachnodactyly", "FBN1 → ↓TGF-β signaling"),
    ("Familial Hyperchol.", "LDLR (LDL receptor)", "AD — receptor", "Xanthomas, premature CAD,\ntendon xanthomas", "LDLR loss → ↑LDL"),
    ("Huntington Disease", "HTT (CAG repeat >36)", "AD — toxic gain of function", "Chorea, dementia, age 30-40;\nanticipation", "Striatum degeneration"),
    ("Cystic Fibrosis", "CFTR (ΔF508 most common)", "AR — ion channel", "Thick mucus, chronic lung,\nsteatorrhea, infertility males", "↓Cl⁻ secretion in lungs"),
    ("PKU", "PAH (phenylalanine hydroxylase)", "AR — enzyme", "Intellectual disability if untreated;\nmousy odor, fair skin", "Screen at birth; low Phe diet"),
    ("Sickle Cell", "HBB (β-globin E6V)", "AR — struct protein", "Vaso-occlusion, hemolysis,\nsplenic sequestration, stroke", "HbS → polymerizes with deoxyHb"),
    ("Tay-Sachs", "HEXA (Hex A)", "AR — lysosomal", "Cherry-red macula, progressive\nneurodegeneration, Ashkenazi Jewish", "GM2 accumulation → neurons"),
    ("Duchenne MD", "DMD (dystrophin)", "X-linked recessive", "Progressive proximal weakness,\nGowers sign, calf pseudohypertrophy", "Frameshift → no dystrophin"),
    ("Fragile X", "FMR1 (CGG >200 repeats)", "X-linked; trinucleotide", "Intellectual disability, macroorchidism,\nlarge ears, long face; anticipation", "Premutation in mothers"),
]

for r_i, row in enumerate(rows):
    y = 1.35 + r_i * 0.82
    bg_c = SUBBG if r_i % 2 == 0 else RGBColor(0x16, 0x25, 0x38)
    for val, w, x in zip(row, col_widths, col_x):
        box = slide2.shapes.add_shape(1, Inches(x), Inches(y), Inches(w), Inches(0.75))
        box.fill.solid(); box.fill.fore_color.rgb = bg_c
        box.line.color.rgb = RGBColor(0x2A, 0x4A, 0x6A)
        box.line.width = Pt(0.5)
        tf = box.text_frame; tf.word_wrap = True
        tf.margin_top = Pt(2); tf.margin_bottom = Pt(2)
        tf.margin_left = Pt(3); tf.margin_right = Pt(3)
        p = tf.paragraphs[0]; p.alignment = PP_ALIGN.LEFT
        run = p.add_run(); run.text = val
        run.font.size = Pt(7); run.font.color.rgb = WHITE
        run.font.bold = (val in [r[0] for r in rows])  # bold disease names


# ─── SLIDE 3: CYTOGENETIC DISORDERS ──────────────────────────────────────────
slide3 = prs.slides.add_slide(slide_layout)
bg3 = slide3.shapes.add_shape(1, 0, 0, prs.slide_width, prs.slide_height)
bg3.fill.solid(); bg3.fill.fore_color.rgb = BG; bg3.line.color.rgb = BG

add_rounded_box(slide3, 0.2, 0.1, 15.6, 0.65,
    BRANCH5,
    ["CYTOGENETIC DISORDERS — Key Syndromes", "Numeric + Structural Abnormalities"],
    [18, 10], [True, False], text_color=DARK)

cyto_data = [
    {
        "title": "DOWN SYNDROME (Trisomy 21)",
        "color": BRANCH1,
        "details": [
            "Karyotype: 47, XX/XY +21",
            "Cause: Nondisjunction (95%), Robertsonian translocation (4%), Mosaicism (1%)",
            "Features: Flat facies, epicanthal folds, Brushfield spots, single palmar crease,",
            "  sandal-gap toe, hypotonia, intellectual disability",
            "Complications: ASD/VSD (40-50%), ALL/AML, early Alzheimer (APP gene on Chr 21),",
            "  Hirschsprung, duodenal atresia",
            "Risk: ↑ with maternal age (nondisjunction); translocation risk = NOT age-related",
        ]
    },
    {
        "title": "TURNER SYNDROME (45,X)",
        "color": BRANCH4,
        "details": [
            "Karyotype: 45,X (most common), mosaics 45,X/46,XX",
            "Cause: Paternal nondisjunction (lost paternal X in ~75%)",
            "Features: Short stature, webbed neck, shield chest, lymphedema at birth,",
            "  streak gonads, primary amenorrhea, coarctation of aorta",
            "Labs: ↑FSH, ↓estrogen, ↑LH",
            "Rx: GH for height; estrogen for secondary sex characters",
        ]
    },
    {
        "title": "KLINEFELTER SYNDROME (47,XXY)",
        "color": BRANCH3,
        "details": [
            "Karyotype: 47,XXY (most common); 15% mosaics (46XY/47XXY)",
            "Cause: Maternal or paternal nondisjunction (equal contribution)",
            "Features: Tall, elongated limbs, hypogonadism, gynecomastia,",
            "  small testes (<2 cm), ↓testosterone, ↑FSH",
            "Complications: Infertility (azoospermia), breast cancer risk ↑, cognitive difficulties",
            "Note: X inactivation (Lyon hypothesis) applies; one active X remains",
        ]
    },
    {
        "title": "22q11.2 DELETION (DiGeorge/VCF)",
        "color": BRANCH2,
        "details": [
            "Mechanism: Microdeletion of Chr 22q11.2 (CATCH-22 mnemonic)",
            "CATCH: Cardiac defects (conotruncal), Abnormal facies, Thymic aplasia,",
            "  Cleft palate, Hypocalcemia (parathyroid aplasia)",
            "Spectrum: DiGeorge (thymus/parathyroid) + Velocardiofacial syndrome (palate/cardiac)",
            "Immune: T-cell deficiency (thymic aplasia → no T-cell maturation)",
            "Dx: FISH or chromosomal microarray",
        ]
    },
]

box_w, box_h = 7.5, 3.5
positions = [(0.2, 0.9), (8.3, 0.9), (0.2, 4.6), (8.3, 4.6)]
for data, (bx, by) in zip(cyto_data, positions):
    # Header
    add_rounded_box(slide3, bx, by, box_w, 0.38, data["color"],
        [data["title"]], [10], [True], text_color=DARK)
    # Content box
    content_box = slide3.shapes.add_shape(1,
        Inches(bx), Inches(by + 0.4), Inches(box_w), Inches(box_h - 0.42))
    content_box.fill.solid(); content_box.fill.fore_color.rgb = SUBBG
    content_box.line.color.rgb = data["color"]; content_box.line.width = Pt(1)
    tf = content_box.text_frame; tf.word_wrap = True
    tf.margin_top = Pt(4); tf.margin_bottom = Pt(4)
    tf.margin_left = Pt(6); tf.margin_right = Pt(6)
    for k, det in enumerate(data["details"]):
        p = tf.paragraphs[0] if k == 0 else tf.add_paragraph()
        p.alignment = PP_ALIGN.LEFT
        run = p.add_run(); run.text = det
        run.font.size = Pt(7.5); run.font.color.rgb = WHITE


# ─── SLIDE 4: SPECIAL MECHANISMS (Trinucleotide, Imprinting, Mito) ───────────
slide4 = prs.slides.add_slide(slide_layout)
bg4 = slide4.shapes.add_shape(1, 0, 0, prs.slide_width, prs.slide_height)
bg4.fill.solid(); bg4.fill.fore_color.rgb = BG; bg4.line.color.rgb = BG

add_rounded_box(slide4, 0.2, 0.1, 15.6, 0.65,
    BRANCH6,
    ["SPECIAL GENETIC MECHANISMS", "Trinucleotide Repeats | Imprinting | Mitochondrial | Epigenetics"],
    [18, 10], [True, False], text_color=DARK)

# Trinucleotide box
add_rounded_box(slide4, 0.2, 0.9, 5.0, 0.4, BRANCH1, ["TRINUCLEOTIDE REPEAT DISORDERS"], [11], [True], text_color=DARK)
tri_box = slide4.shapes.add_shape(1, Inches(0.2), Inches(1.35), Inches(5.0), Inches(4.0))
tri_box.fill.solid(); tri_box.fill.fore_color.rgb = SUBBG
tri_box.line.color.rgb = BRANCH1; tri_box.line.width = Pt(1)
tf = tri_box.text_frame; tf.word_wrap = True
tf.margin_top = Pt(4); tf.margin_bottom = Pt(4); tf.margin_left = Pt(6); tf.margin_right = Pt(4)
tri_content = [
    "Disease        | Repeat | Location    | Inheritance",
    "─────────────────────────────────────────────────",
    "Fragile X (FXS)| CGG    | FMR1 5'UTR  | X-linked",
    "Huntington     | CAG    | HTT exon 1  | AD",
    "Myotonic Dyst. | CTG    | DMPK 3'UTR  | AD",
    "Friedreich Atx | GAA    | FXN intron  | AR",
    "SCA (type 1)   | CAG    | ATXN1       | AD",
    "",
    "KEY CONCEPT: ANTICIPATION — repeat expands each",
    "generation → earlier/worse disease",
    "",
    "Fragile X specifics:",
    "• Normal: 6-54 CGG repeats",
    "• Premutation: 55-200 (carrier males/females)",
    "• Full mutation: >200 → methylation → FMR1 silenced",
    "• Macroorchidism, intellectual disability, autism",
    "• Normal transmitting males (premutation carriers)",
    "• 20% carrier females affected",
]
for k, line in enumerate(tri_content):
    p = tf.paragraphs[0] if k == 0 else tf.add_paragraph()
    p.alignment = PP_ALIGN.LEFT
    run = p.add_run(); run.text = line
    run.font.size = Pt(7.2); run.font.color.rgb = WHITE
    if k == 0: run.font.bold = True

# Imprinting box
add_rounded_box(slide4, 5.5, 0.9, 5.0, 0.4, BRANCH2, ["GENOMIC IMPRINTING"], [11], [True], text_color=DARK)
imp_box = slide4.shapes.add_shape(1, Inches(5.5), Inches(1.35), Inches(5.0), Inches(4.0))
imp_box.fill.solid(); imp_box.fill.fore_color.rgb = SUBBG
imp_box.line.color.rgb = BRANCH2; imp_box.line.width = Pt(1)
tf2 = imp_box.text_frame; tf2.word_wrap = True
tf2.margin_top = Pt(4); tf2.margin_bottom = Pt(4); tf2.margin_left = Pt(6); tf2.margin_right = Pt(4)
imp_content = [
    "Concept: Differential silencing of maternal vs paternal",
    "allele via DNA methylation + histone modification",
    "",
    "CHROMOSOME 15q11-q13 DELETION:",
    "",
    "PRADER-WILLI SYNDROME:",
    "• Del of PATERNAL Chr 15 (or maternal UPD)",
    "• Features: Hypotonia at birth, obesity, short stature,",
    "  hypogonadism, intellectual disability, hyperphagia",
    "• Mnemonic: Paternal PWS = 'Fat, Floppy, Funny'",
    "",
    "ANGELMAN SYNDROME:",
    "• Del of MATERNAL Chr 15 (or paternal UPD)",
    "• Features: Intellectual disability, seizures,",
    "  ataxic gait, inappropriate laughter ('happy puppet')",
    "• UBE3A gene (ubiquitin ligase) — maternal allele lost",
    "",
    "Memory trick: Angelman = mAtErnal deletion",
    "Prader-Willi = PAtErnal deletion",
]
for k, line in enumerate(imp_content):
    p = tf2.paragraphs[0] if k == 0 else tf2.add_paragraph()
    p.alignment = PP_ALIGN.LEFT
    run = p.add_run(); run.text = line
    run.font.size = Pt(7.2); run.font.color.rgb = WHITE
    if k in [3, 5, 11]: run.font.bold = True

# Mitochondrial + Epigenetics box
add_rounded_box(slide4, 10.8, 0.9, 5.0, 0.4, BRANCH4, ["MITOCHONDRIAL + EPIGENETICS"], [11], [True], text_color=DARK)
mito_box = slide4.shapes.add_shape(1, Inches(10.8), Inches(1.35), Inches(5.0), Inches(4.0))
mito_box.fill.solid(); mito_box.fill.fore_color.rgb = SUBBG
mito_box.line.color.rgb = BRANCH4; mito_box.line.width = Pt(1)
tf3 = mito_box.text_frame; tf3.word_wrap = True
tf3.margin_top = Pt(4); tf3.margin_bottom = Pt(4); tf3.margin_left = Pt(6); tf3.margin_right = Pt(4)
mito_content = [
    "MITOCHONDRIAL INHERITANCE:",
    "• Exclusively MATERNAL transmission",
    "• Affects high-energy tissues: CNS, skeletal/cardiac",
    "  muscle, liver, kidney",
    "• Heteroplasmy: mix of mutant + normal mtDNA",
    "• Example: LEBER HEREDITARY OPTIC NEUROPATHY",
    "  (bilateral loss of central vision → blindness)",
    "• MELAS, MERRF syndromes",
    "",
    "EPIGENETICS:",
    "• DNA methylation: CpG islands → gene silencing",
    "  (adds methyl group to cytosine)",
    "• Histone acetylation → chromatin opening → active",
    "• Histone methylation → silencing (in most contexts)",
    "• XIST gene → X inactivation (Lyon hypothesis)",
    "• ~30% of Xp genes ESCAPE inactivation",
    "  → explains Turner syndrome features",
    "",
    "Clinical relevance: Epigenetic changes in cancer",
    "Promoter hypermethylation → tumor suppressor silencing",
]
for k, line in enumerate(mito_content):
    p = tf3.paragraphs[0] if k == 0 else tf3.add_paragraph()
    p.alignment = PP_ALIGN.LEFT
    run = p.add_run(); run.text = line
    run.font.size = Pt(7.2); run.font.color.rgb = WHITE
    if k in [0, 9]: run.font.bold = True

# Bottom strip: Molecular diagnosis methods
add_rounded_box(slide4, 0.2, 5.55, 15.6, 0.38,
    CENTER_BG,
    ["MOLECULAR DIAGNOSIS TOOLS: Karyotype | FISH | Chromosomal Microarray | PCR/Southern Blot | NGS/WES"],
    [9], [True])

# ─── SLIDE 5: 4-HOUR STUDY PLAN ──────────────────────────────────────────────
slide5 = prs.slides.add_slide(slide_layout)
bg5 = slide5.shapes.add_shape(1, 0, 0, prs.slide_width, prs.slide_height)
bg5.fill.solid(); bg5.fill.fore_color.rgb = BG; bg5.line.color.rgb = BG

add_rounded_box(slide5, 0.2, 0.1, 15.6, 0.65,
    CENTER_BG,
    ["4-HOUR GENETICS STUDY PLAN — Robbins + Marrow", "Exam-Focused | High-Yield Strategy"],
    [18, 10], [True, False])

plan = [
    {
        "time": "Hour 1\n(0:00-1:00)",
        "color": BRANCH1,
        "title": "FOUNDATIONS\n+ MUTATIONS",
        "robbins": "Robbins Ch.4 pp.84-92\nNature of genetic abnormalities\nMutation types (point, frameshift, CNV)\nMendelian inheritance patterns (Tables 4.1 & 4.2)\nKey vocabulary: hereditary vs congenital vs familial",
        "marrow": "Marrow: Genetics intro module\nPatterns of inheritance (AD/AR/XLR)\nMutation mnemonics\nQuick MCQ revision on basic genetics",
    },
    {
        "time": "Hour 2\n(1:00-2:00)",
        "color": BRANCH2,
        "title": "MENDELIAN\nDISORDERS",
        "robbins": "Robbins Ch.4 pp.92-109\nStructural proteins: Marfan, OI, EDS\nReceptor/channel defects: FH, CF\nEnzyme defects: PKU, Tay-Sachs, Gaucher,\n  Glycogen storage diseases (esp. Type I, II, V)\nNiemann-Pick, Mucopolysaccharidoses",
        "marrow": "Marrow: Each disease — focus on pathogenesis\nStorage diseases comparison table\nCF: CFTR mutations, sweat chloride test\nHigh-yield: Enzyme involved in each storage disease",
    },
    {
        "time": "Hour 3\n(2:00-3:00)",
        "color": BRANCH3,
        "title": "CYTOGENETIC\nDISORDERS",
        "robbins": "Robbins Ch.4 pp.110-122\nNumeric vs structural abnormalities\nNondisjunction mechanism\nDown syndrome (Trisomy 21)\nEdwards, Patau syndromes\nTurner, Klinefelter syndromes\n22q11.2 deletion (DiGeorge)",
        "marrow": "Marrow: Chromosome disorders\nKaryotype interpretation\nLyon hypothesis / X inactivation\nSex chromosome anomalies comparison\nMCQ practice on cytogenetics",
    },
    {
        "time": "Hour 4\n(3:00-4:00)",
        "color": BRANCH6,
        "title": "SPECIAL MECH.\n+ REVISION",
        "robbins": "Robbins Ch.4 pp.122-129\nTrinucleotide repeats (Fragile X, HD)\nGenomic imprinting (PWS vs Angelman)\nMitochondrial inheritance (Leber)\nEpigenetics, CRISPR overview\nMolecular diagnosis tools",
        "marrow": "Marrow: Anticipation, imprinting\nFragile X pedigree analysis\nFull Chapter 4 summary video\nPrevious year MCQ blitz (30-40 Qs)\nWeakness areas — targeted re-read",
    },
]

col_w_plan = [1.4, 1.4, 5.6, 5.6]
col_x_plan = [0.2, 1.65, 3.1, 8.75]
plan_headers = ["TIME", "TOPIC", "ROBBINS (READ)", "MARROW (REVISE)"]
for h, w, x in zip(plan_headers, col_w_plan, col_x_plan):
    add_rounded_box(slide5, x, 0.9, w, 0.35, CENTER_BG, [h], [9], [True])

for r_i, row in enumerate(plan):
    y = 1.32 + r_i * 1.82
    bg_c = SUBBG if r_i % 2 == 0 else RGBColor(0x16, 0x25, 0x38)

    # Time
    add_rounded_box(slide5, col_x_plan[0], y, col_w_plan[0], 1.72,
        row["color"], [row["time"]], [8], [True], text_color=DARK)
    # Topic
    add_rounded_box(slide5, col_x_plan[1], y, col_w_plan[1], 1.72,
        RGBColor(row["color"].red//2, row["color"].green//2, row["color"].blue//2),
        [row["title"]], [8], [True])
    # Robbins
    rbox = slide5.shapes.add_shape(1, Inches(col_x_plan[2]), Inches(y), Inches(col_w_plan[2]), Inches(1.72))
    rbox.fill.solid(); rbox.fill.fore_color.rgb = bg_c
    rbox.line.color.rgb = row["color"]; rbox.line.width = Pt(0.75)
    tf = rbox.text_frame; tf.word_wrap = True
    tf.margin_top = Pt(3); tf.margin_bottom = Pt(3); tf.margin_left = Pt(5); tf.margin_right = Pt(5)
    for k, line in enumerate(row["robbins"].split("\n")):
        p = tf.paragraphs[0] if k == 0 else tf.add_paragraph()
        run = p.add_run(); run.text = line
        run.font.size = Pt(7.2); run.font.color.rgb = WHITE
        run.font.bold = (k == 0)
    # Marrow
    mbox = slide5.shapes.add_shape(1, Inches(col_x_plan[3]), Inches(y), Inches(col_w_plan[3]), Inches(1.72))
    mbox.fill.solid(); mbox.fill.fore_color.rgb = bg_c
    mbox.line.color.rgb = row["color"]; mbox.line.width = Pt(0.75)
    tf2 = mbox.text_frame; tf2.word_wrap = True
    tf2.margin_top = Pt(3); tf2.margin_bottom = Pt(3); tf2.margin_left = Pt(5); tf2.margin_right = Pt(5)
    for k, line in enumerate(row["marrow"].split("\n")):
        p = tf2.paragraphs[0] if k == 0 else tf2.add_paragraph()
        run = p.add_run(); run.text = line
        run.font.size = Pt(7.2); run.font.color.rgb = WHITE
        run.font.bold = (k == 0)


out_path = "/tmp/workspace/genetics-mindmap/Genetics_Robbins_Mindmap.pptx"
prs.save(out_path)
print(f"Saved to {out_path}")

Successfully replaced 1 instance(s) of the string in '/tmp/workspace/genetics-mindmap/create_mindmap.py'