python -m markitdown /home/daytona/workspace/attachments/6338bf9e-c18c-4f89-805e-6aa68b383fee/"Amino acids and proteins.pptx"

cd /home/daytona/workspace/attachments/6338bf9e-c18c-4f89-805e-6aa68b383fee && python3 -c " from pptx import Presentation prs = Presentation('Amino acids and proteins.pptx') for i, slide in enumerate(prs.slides): print(f'=== Slide {i+1} ===') for shape in slide.shapes: if shape.has_text_frame: for para in shape.text_frame.paragraphs: text = para.text.strip() if text: print(text) print() "

pip install --user python-pptx -q && python3 -c "from pptx import Presentation; print('ok')"

python3 -c " from pptx import Presentation prs = Presentation('/home/daytona/workspace/attachments/6338bf9e-c18c-4f89-805e-6aa68b383fee/Amino acids and proteins.pptx') for i, slide in enumerate(prs.slides): print(f'=== Slide {i+1} ===') for shape in slide.shapes: if shape.has_text_frame: for para in shape.text_frame.paragraphs: text = para.text.strip() if text: print(text) print() "

mkdir -p /home/daytona/workspace/amino-acids-summary && cat > /home/daytona/workspace/amino-acids-summary/build.js << 'EOF' const pptxgen = require("pptxgenjs"); const pres = new pptxgen(); pres.layout = "LAYOUT_WIDE"; // Color palette const BG_DARK = "0D1B2A"; const BG_CARD = "1A2E42"; const BG_CARD2 = "112233"; const ACCENT = "00C2CB"; const ACCENT2 = "F5A623"; const ACCENT3 = "7ED321"; const ACCENT4 = "E84393"; const WHITE = "FFFFFF"; const LIGHT = "B8D4E8"; const SUBTEXT = "8AACCB"; // ───────────────────────────────────────────────────────────── // SLIDE 1 — Title // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); // Accent bar s.addShape(pres.ShapeType.rect, { x: 0, y: 3.1, w: 13.3, h: 0.07, fill: { color: ACCENT } }); s.addText("Amino Acids & Proteins", { x: 1, y: 1.5, w: 11.3, h: 1.4, fontSize: 48, bold: true, color: WHITE, align: "center", fontFace: "Calibri" }); s.addText("Summary Chart", { x: 1, y: 3.2, w: 11.3, h: 0.8, fontSize: 26, color: ACCENT, align: "center", fontFace: "Calibri", italic: true }); s.addText("Dr. Beenish Khalid | Department of Biochemistry", { x: 1, y: 4.4, w: 11.3, h: 0.5, fontSize: 16, color: SUBTEXT, align: "center", fontFace: "Calibri" }); } // ───────────────────────────────────────────────────────────── // SLIDE 2 — What are Amino Acids? // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT } }); s.addText("What Are Amino Acids?", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); const rows = [ ["Term", "Description"], ["Definition", "Derivatives of carboxylic acids where a H atom is replaced by an amino group (–NH₂)"], ["Building Blocks", "Amino acids are the structural units (monomers) of proteins"], ["In Nature", "300+ amino acids occur in nature; only 20 are found in proteins"], ["Configuration", "Proteins use only L-amino acids (enzymes evolved for L-enantiomers)"], ["Zwitterion", "At physiological pH (~7–7.4), amino acids exist as dipolar ions with equal + and – charges"], ["α-Amino Acids", "Amino group is at the α-carbon — the form found in all proteins"], ]; s.addTable(rows, { x: 0.4, y: 0.9, w: 12.5, h: 6.2, fontSize: 14, fontFace: "Calibri", rowH: 0.78, border: { pt: 1, color: ACCENT }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [2.8, 9.7], firstRowFill: ACCENT, firstRowColor: BG_DARK, firstRowBold: true, firstRowFontSize: 15, }); } // ───────────────────────────────────────────────────────────── // SLIDE 3 — Classification by R-group Polarity // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT2 } }); s.addText("Classification by R-Group Polarity", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); const rows = [ ["Category", "Properties", "Examples"], ["Non-polar / Hydrophobic", "Equal amino & carboxyl groups; neutral; buried inside proteins", "Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine, Tryptophan"], ["Polar Uncharged", "Carry –OH, –SH, or amide groups; hydrogen bonding; no charge on R", "Serine, Threonine, Cysteine, Glutamine, Asparagine, Tyrosine"], ["Polar (+) Charged\n(Basic)", "Diaminomonocarboxylic; hydrophilic; positive charge at pH 7", "Arginine, Lysine, Histidine"], ["Polar (–) Charged\n(Acidic)", "Monoaminodicarboxylic; hydrophilic; negative charge at pH 7", "Aspartic Acid, Glutamic Acid"], ]; s.addTable(rows, { x: 0.3, y: 0.85, w: 12.7, h: 6.3, fontSize: 13, fontFace: "Calibri", rowH: 1.3, border: { pt: 1, color: ACCENT2 }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [3.0, 4.5, 5.2], firstRowFill: ACCENT2, firstRowColor: BG_DARK, firstRowBold: true, firstRowFontSize: 15, }); } // ───────────────────────────────────────────────────────────── // SLIDE 4 — Classification by Acid/Base Behavior // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT3 } }); s.addText("Classification by Acid / Base Behavior", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); const rows = [ ["Type", "Examples"], ["Acidic (negative charge)", "Glutamic Acid, Aspartic Acid"], ["Basic (positive charge)", "Arginine, Lysine, Histidine"], ["Neutral", "Glycine, Alanine, Leucine, Isoleucine, Valine, Serine, Threonine, Methionine, Cysteine"], ]; s.addTable(rows, { x: 0.4, y: 0.9, w: 12.5, h: 3.2, fontSize: 15, fontFace: "Calibri", rowH: 0.7, border: { pt: 1, color: ACCENT3 }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [4.5, 8.0], firstRowFill: ACCENT3, firstRowColor: BG_DARK, firstRowBold: true, firstRowFontSize: 16, }); // Isomerism box below s.addShape(pres.ShapeType.rect, { x: 0.4, y: 4.3, w: 12.5, h: 2.9, fill: { color: BG_CARD2 }, line: { color: ACCENT3, pt: 1 } }); s.addText("Isomerism in Amino Acids", { x: 0.6, y: 4.4, w: 12, h: 0.45, fontSize: 16, bold: true, color: ACCENT3, fontFace: "Calibri" }); s.addText([ { text: "D/L Isomerism: ", options: { bold: true, color: ACCENT, breakLine: false } }, { text: "L-amino acids are natural (used in protein biosynthesis); D-amino acids are unnatural (found in bacterial cell walls & some insects).\n", options: { color: WHITE, breakLine: true } }, { text: "Optical Isomerism: ", options: { bold: true, color: ACCENT, breakLine: false } }, { text: "Due to asymmetric carbon; rotate plane of polarized light as dextrorotatory [d] or levorotatory [l].\n", options: { color: WHITE, breakLine: true } }, { text: "Exception: ", options: { bold: true, color: ACCENT2, breakLine: false } }, { text: "Glycine has no asymmetric C atom — shows no isomerism.", options: { color: WHITE } }, ], { x: 0.6, y: 4.85, w: 12, h: 2.2, fontSize: 13, fontFace: "Calibri" }); } // ───────────────────────────────────────────────────────────── // SLIDE 5 — Metabolic Fate // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT4 } }); s.addText("Metabolic Fate of Amino Acids", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: WHITE, fontFace: "Calibri" }); const rows = [ ["Fate", "Conversion Product", "Examples"], ["Ketogenic", "Acetyl-CoA / Acetoacetate → Ketone bodies / Fats", "Leucine, Isoleucine, Tryptophan, Tyrosine, Phenylalanine, Lysine"], ["Glucogenic", "Pyruvate / Oxaloacetate → Glucose", "Glycine, Alanine, Serine, Cysteine, Glutamic Acid, Aspartic Acid, Arginine"], ["Mixed (Both)", "Both ketone bodies AND glucose", "Isoleucine, Phenylalanine, Tryptophan, Tyrosine"], ]; s.addTable(rows, { x: 0.3, y: 0.85, w: 12.7, h: 4.0, fontSize: 13, fontFace: "Calibri", rowH: 0.87, border: { pt: 1, color: ACCENT4 }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [2.5, 4.8, 5.4], firstRowFill: ACCENT4, firstRowColor: WHITE, firstRowBold: true, firstRowFontSize: 15, }); // Derived amino acids note s.addShape(pres.ShapeType.rect, { x: 0.3, y: 5.1, w: 12.7, h: 2.1, fill: { color: BG_CARD2 }, line: { color: ACCENT4, pt: 1 } }); s.addText("Derived (Non-Standard) Amino Acids", { x: 0.6, y: 5.2, w: 12, h: 0.4, fontSize: 15, bold: true, color: ACCENT4, fontFace: "Calibri" }); s.addText([ { text: "Cysteine ", options: { bold: true, color: ACCENT } }, { text: "← Cystine ", options: { color: WHITE } }, { text: "Hydroxylysine ", options: { bold: true, color: ACCENT } }, { text: "← Lysine ", options: { color: WHITE } }, { text: "Hydroxyproline ", options: { bold: true, color: ACCENT } }, { text: "← Proline ", options: { color: WHITE } }, { text: "Histamine ", options: { bold: true, color: ACCENT } }, { text: "← Histidine", options: { color: WHITE } }, ], { x: 0.6, y: 5.65, w: 12, h: 1.3, fontSize: 14, fontFace: "Calibri" }); } // ───────────────────────────────────────────────────────────── // SLIDE 6 — Nutritional Classification // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT } }); s.addText("Classification by Nutritional Requirement", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); const rows = [ ["Type", "Definition", "Examples"], ["Essential (9)", "Cannot be synthesized by the body; must come from diet", "PVT TIM HALL:\nPhenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine"], ["Non-Essential (11)", "Synthesized by human cells; not required in diet", "Glycine, Alanine, Serine, Cysteine, Aspartate, Glutamate, Asparagine, Glutamine, Tyrosine, Proline, Arginine"], ["Conditionally Essential", "Synthesis limited in premature infants, illness, catabolic stress", "Glutamine, Arginine, Tyrosine, Cysteine"], ]; s.addTable(rows, { x: 0.3, y: 0.85, w: 12.7, h: 5.0, fontSize: 13, fontFace: "Calibri", rowH: 1.1, border: { pt: 1, color: ACCENT }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [2.8, 4.5, 5.4], firstRowFill: ACCENT, firstRowColor: BG_DARK, firstRowBold: true, firstRowFontSize: 15, }); // Complete vs incomplete s.addShape(pres.ShapeType.rect, { x: 0.3, y: 6.0, w: 6.0, h: 1.2, fill: { color: BG_CARD2 }, line: { color: ACCENT, pt: 1 } }); s.addText("Complete Protein: Contains ALL 9 essential AAs\n(meat, fish, eggs, dairy, soy)", { x: 0.5, y: 6.1, w: 5.6, h: 1.0, fontSize: 12, color: WHITE, fontFace: "Calibri" }); s.addShape(pres.ShapeType.rect, { x: 7.0, y: 6.0, w: 6.0, h: 1.2, fill: { color: BG_CARD2 }, line: { color: ACCENT2, pt: 1 } }); s.addText("Incomplete Protein: Lacks one or more essential AAs\n(most plant sources)", { x: 7.2, y: 6.1, w: 5.6, h: 1.0, fontSize: 12, color: WHITE, fontFace: "Calibri" }); } // ───────────────────────────────────────────────────────────── // SLIDE 7 — Individual Amino Acid Functions // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT2 } }); s.addText("Functions of Individual Amino Acids", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); const rows = [ ["Amino Acid", "Key Function(s)"], ["Glycine", "Cell growth; synthesis of glutathione (antioxidant) and hemoglobin"], ["Valine", "Converts to succinyl-CoA via transamination → enters TCA cycle"], ["Leucine", "Muscle protein biosynthesis; cell growth"], ["Isoleucine", "Fat & protein metabolism; carbohydrate transportation"], ["Serine", "Synthesis of sphingolipids, phospholipids, and nucleotides"], ["Threonine", "Porphyrin & fat metabolism; prevents hepatic fat buildup; component of collagen & elastin"], ["Aspartic Acid", "Urea cycle; donates N for biosynthesis of purines (inosine)"], ["Alanine", "Glucose-alanine cycle: shuttles glucose & N between liver and muscle; gluconeogenesis precursor"], ["Glutamic Acid", "Precursor for GABA (inhibitory neurotransmitter); ammonia detoxification via deamination"], ["Arginine", "Intermediate of urea cycle; polyamine & structural protein synthesis"], ["Histidine", "Converts to histamine (allergic response); binds heme in hemoglobin synthesis"], ["Lysine", "Collagen formation"], ["Tryptophan", "Precursor to serotonin and niacin"], ["Tyrosine", "Precursor to dopamine, epinephrine, norepinephrine, melanin, thyroxin"], ["Phenylalanine", "Precursor to norepinephrine"], ["Proline", "Synthesis of arginine, polyamines, collagen & elastin; imino acid (–NH not –NH₂)"], ["Cysteine", "Found in β-keratin (nails, skin, hair); important for collagen synthesis"], ]; s.addTable(rows, { x: 0.3, y: 0.8, w: 12.7, h: 6.5, fontSize: 11, fontFace: "Calibri", rowH: 0.33, border: { pt: 0.5, color: "2A4A6A" }, fill: BG_CARD, color: WHITE, align: "left", valign: "middle", colW: [2.6, 10.1], firstRowFill: ACCENT2, firstRowColor: BG_DARK, firstRowBold: true, firstRowFontSize: 14, autoPage: false, }); } // ───────────────────────────────────────────────────────────── // SLIDE 8 — Biomedical Importance & Deficiency // ───────────────────────────────────────────────────────────── { const s = pres.addSlide(); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 7.5, fill: { color: BG_DARK } }); s.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 13.3, h: 0.7, fill: { color: ACCENT3 } }); s.addText("Biomedical Importance & Deficiency Effects", { x: 0.3, y: 0.08, w: 12.7, h: 0.55, fontSize: 22, bold: true, color: BG_DARK, fontFace: "Calibri" }); // Left — functions of proteins s.addShape(pres.ShapeType.rect, { x: 0.3, y: 0.85, w: 6.1, h: 6.3, fill: { color: BG_CARD }, line: { color: ACCENT3, pt: 1 } }); s.addText("Protein Functions in the Body", { x: 0.4, y: 0.95, w: 5.9, h: 0.45, fontSize: 15, bold: true, color: ACCENT3, fontFace: "Calibri" }); s.addText([ { text: "• Cell & tissue structure: ", options: { bold: true, color: ACCENT, breakLine: false } }, { text: "skin, hair, muscle, organs, glands\n", options: { color: WHITE, breakLine: true } }, { text: "• New cell production\n", options: { color: WHITE, breakLine: true } }, { text: "• Hormone synthesis\n", options: { color: WHITE, breakLine: true } }, { text: "• Immune system strengthening\n", options: { color: WHITE, breakLine: true } }, { text: "• Muscle growth & maintenance\n", options: { color: WHITE, breakLine: true } }, { text: "• Enzyme catalysis\n", options: { color: WHITE, breakLine: true } }, { text: "• Nutrient transport\n", options: { color: WHITE, breakLine: true } }, { text: "• Neurotransmitter precursors", options: { color: WHITE } }, ], { x: 0.5, y: 1.45, w: 5.7, h: 5.3, fontSize: 13, fontFace: "Calibri" }); // Right — deficiency effects s.addShape(pres.ShapeType.rect, { x: 6.9, y: 0.85, w: 6.1, h: 6.3, fill: { color: BG_CARD }, line: { color: ACCENT4, pt: 1 } }); s.addText("Effects of Essential AA Deficiency", { x: 7.0, y: 0.95, w: 5.9, h: 0.45, fontSize: 15, bold: true, color: ACCENT4, fontFace: "Calibri" }); s.addText([ { text: "• Decreased immunity\n", options: { color: WHITE, breakLine: true } }, { text: "• Digestive problems\n", options: { color: WHITE, breakLine: true } }, { text: "• Depression\n", options: { color: WHITE, breakLine: true } }, { text: "• Fertility issues\n", options: { color: WHITE, breakLine: true } }, { text: "• Lower mental alertness\n", options: { color: WHITE, breakLine: true } }, { text: "• Slowed growth in children\n", options: { color: WHITE, breakLine: true } }, { text: "• Muscle wasting\n", options: { color: WHITE, breakLine: true } }, { text: "• Metabolic disorders", options: { color: WHITE } }, ], { x: 7.1, y: 1.45, w: 5.7, h: 5.3, fontSize: 13, fontFace: "Calibri" }); } // ───────────────────────────────────────────────────────────── // Write // ───────────────────────────────────────────────────────────── pres.writeFile({ fileName: "/home/daytona/workspace/amino-acids-summary/Amino_Acids_Summary_Charts.pptx" }) .then(() => console.log("Done!")) .catch(e => { console.error(e); process.exit(1); }); EOF node /home/daytona/workspace/amino-acids-summary/build.js

~/amino-acids-summary/build.js

node /home/daytona/workspace/amino-acids-summary/build.js