{"note":{"id":"nte_zznulh7bpt","attempt_id":"att_0bdyoe2bt5","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: SI File 2 parsed by cell geometry: 2052 rows, all pass a GBB template check\nkind: finding\ntags: [ord, gbb, parsing, rdkit]\nmodel: claude-opus-5-5\n---\n- Parser (pdfplumber): row bands = the full-width horizontal rules drawn in S2.pdf; columns = the vertical rules (x ≈ 51/76/147/336/409/450/502/542/599/639/696/736/777 pt). Cell text joined top-to-bottom without spaces, which reassembles the wrapped SMILES. Bands without a number in `#` are section headings carried onto later rows.\n- Result: 2052 rows numbered 1..2052 with no gaps, no empty cells. Sections: \"Preliminary test experiments, TsOH as the catalyst\" rows 1-580 (p.2-47); \"…Sc(OTf)3 as the catalyst\" rows 581-1160 (p.48-95); \"Parallel synthesis of compound library 4, main experiment\" rows 1161-2052 (892 rows, p.96-169). This matches the paper text: 580 members per catalyst in the preliminary screen, 892 in the Sc(OTf)3 library run.\n- 2028 unique product IDs: 24 products appear in both preliminary screens (= the 24 compared in the paper's Figure 2). So 2052 is the right reaction count; the card's \"~700 unique products\" and ORD's \"~2000\" estimates are just approximate.\n- RDKit (2026.09.1): all SMILES parse once CXSMILES extensions (`|c:..|`, `|&1:..,r|`) are stripped from product AND reactant cells. Salts: 210 amines and 18 aldehydes carry `Cl.` (one amine is a dihydrochloride); largest fragment used for the check.\n- GBB template `[NH2]-c:n + [CH](=O)C + [C-]#[N+]R -> 3-(RNH)-imidazo-azine`: 2044/2052 reproduce the listed product exactly; 8 match only after removing stereo (the source's stereo labels differ between the reactant and product cell, e.g. rows 90, 180, 1282, 1412, 1440, 1641, 1906, 1951). Kept as printed, flagged in the README.\n- Yields: mg / MW(product free base) / 0.270 mmol reproduces the printed % (mean difference 0.003 points; 13 rows differ by >3 points, max 6.8), confirming the 0.270 mmol scale of the general procedure in SI File 3 for all three sections.\n","source":"mcp","created_at":"2026-10-14T04:06:07Z","updated_at":"2026-10-14T04:06:07Z","kind":"working"},"header":{"title":"SI File 2 parsed by cell geometry: 2052 rows, all pass a GBB template check","kind":"finding","tags":["ord","gbb","parsing","rdkit"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"- Parser (pdfplumber): row bands = the full-width horizontal rules drawn in S2.pdf; columns = the vertical rules (x ≈ 51/76/147/336/409/450/502/542/599/639/696/736/777 pt). Cell text joined top-to-bottom without spaces, which reassembles the wrapped SMILES. Bands without a number in `#` are section headings carried onto later rows.\n- Result: 2052 rows numbered 1..2052 with no gaps, no empty cells. Sections: \"Preliminary test experiments, TsOH as the catalyst\" rows 1-580 (p.2-47); \"…Sc(OTf)3 as the catalyst\" rows 581-1160 (p.48-95); \"Parallel synthesis of compound library 4, main experiment\" rows 1161-2052 (892 rows, p.96-169). This matches the paper text: 580 members per catalyst in the preliminary screen, 892 in the Sc(OTf)3 library run.\n- 2028 unique product IDs: 24 products appear in both preliminary screens (= the 24 compared in the paper's Figure 2). So 2052 is the right reaction count; the card's \"~700 unique products\" and ORD's \"~2000\" estimates are just approximate.\n- RDKit (2026.09.1): all SMILES parse once CXSMILES extensions (`|c:..|`, `|&1:..,r|`) are stripped from product AND reactant cells. Salts: 210 amines and 18 aldehydes carry `Cl.` (one amine is a dihydrochloride); largest fragment used for the check.\n- GBB template `[NH2]-c:n + [CH](=O)C + [C-]#[N+]R -> 3-(RNH)-imidazo-azine`: 2044/2052 reproduce the listed product exactly; 8 match only after removing stereo (the source's stereo labels differ between the reactant and product cell, e.g. rows 90, 180, 1282, 1412, 1440, 1641, 1906, 1951). Kept as printed, flagged in the README.\n- Yields: mg / MW(product free base) / 0.270 mmol reproduces the printed % (mean difference 0.003 points; 13 rows differ by >3 points, max 6.8), confirming the 0.270 mmol scale of the general procedure in SI File 3 for all three sections.\n","attempt":{"id":"att_0bdyoe2bt5","outcome":"completed","ended_at":"2026-10-14T04:11:27Z","problem_id":"prb_ovvjaeeui7","problem_slug":"ord-govor-2024-gbb-parallel-synthesis","problem_revision_id":"prv_qphdzbn1kp","author_handle":"jordan"}}