Chemical structure drawing & identifiers
Draw molecules and reactions and export correct SMILES/InChI.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- ChemDraw · Ketcher · MarvinSketch
- Class GUI-need label
G3· GUI-only
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.02.01.01-T01 Redraw a drug-like molecule from an image in Ketcher and export SMILES and MOL
Original instruction
Ketcher (standalone web build) is open with an empty canvas. Draw the molecule shown in input/target_01.png (a 24-heavy-atom amide with one wedged stereocenter) using the canvas tools only. Save output/target_01.mol and output/target_01.smi. Do not type or paste SMILES and do not use the Open/Paste dialogs.
- Platforms
web· Any OS (web)- Applications
- Ketcher
- Interfaces
brow· Browser- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
RDKit compares both files to hidden gold: standard InChIKey must match exactly, stereo included. A JS hook detects ketcher.setMolecule, paste and file-open calls (any scores 0), and both files must arrive via Ketcher's Save download in the browser download log. The MOL must carry canvas-drawn 2D coordinates (not all-zero, not an RDKit Compute2DCoords layout).
Proposed partial credit
30% heavy-atom formula matches; 30% connectivity (Morgan Tanimoto ≥0.95); 30% exact InChIKey incl. stereo; 10% both files present and parseable.
R08.02.01.01-T02 Draw three reagents from a supplier sheet in MarvinSketch and save a titled SDF
Original instruction
input/reagents_sheet.pdf page 2 shows three reagents as images with catalog numbers: a boronic acid, a Boc-protected bromoaniline and a biaryl phosphine ligand. In MarvinSketch draw each as a separate molecule and save output/reagents.sdf with one record per reagent in sheet order, record title = catalog number.
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Each SDF record is parsed with RDKit; its InChIKey must match the gold reagent at that position and the title line must equal the catalog number. MOL headers must carry the Marvin program line and non-template 2D coordinates; records written by RDKit/Open Babel are rejected. ChemAxon molconvert/cxcalc are not installed and a file-system audit log flags output/ writes not made by MarvinSketch.
Proposed partial credit
90% reagents with matching InChIKey (30 pts each); 10% titles and order correct.
R08.02.01.01-T03 Draw a two-stereocenter intermediate with wedge bonds in ChemDraw and export InChI
Original instruction
ChemDraw is open with the ACS Document 1996 style. Draw intermediate 14 from input/scheme_p3.png, a (2S,3R) amino alcohol carrying a TBS ether, using hashed and bold wedges only at the two stereocenters. Save output/int14.cdxml and put its standard InChI (Copy As > InChI) in output/int14.inchi.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Standard InChI computed from the .cdxml (RDKit CDXML reader) must equal gold including /t, /m and /s layers and must equal int14.inchi. The .cdxml must carry ChemDraw CreationProgram metadata and wedge Display attributes; an InChI file without a matching drawing scores 0. ChemScript and ChemDraw's COM/AppleScript automation are disabled.
Proposed partial credit
25% connectivity correct; 35% both stereocenters correct; 25% .inchi equals the drawing; 15% wedges placed only at stereocenters.
R08.02.01.01-T04 Edit a lead structure in Ketcher: invert C3, add a C7 methyl, swap phenyl for 3-pyridyl
Original instruction
input/lead_42.ket is open in Ketcher with atom numbers shown. Without redrawing the scaffold, invert the stereocenter at C3, add a methyl at C7, and replace the terminal phenyl with a 3-pyridyl attached through the same carbon. Save output/lead_42b.ket and export output/lead_42b.mol.
- Platforms
web· Any OS (web)- Applications
- Ketcher
- Interfaces
brow· Browser- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
InChIKey of lead_42b.mol must equal gold. Atoms not involved in the edit must keep their input 2D coordinates within 0.05 units, which detects regeneration from SMILES or a re-layout; the JS hook logs setMolecule/layout calls, which score 0.
Proposed partial credit
30% C3 inverted; 25% C7 methyl added; 30% 3-pyridyl attached at the right carbon; 15% untouched atoms keep coordinates.
R08.02.01.01-T05 Build a labeled Suzuki coupling scheme in ChemDraw and export RXN
Original instruction
Draw the Suzuki coupling from input/notebook_entry_118.jpg in ChemDraw: aryl bromide + pinacol boronic ester → biaryl. Put 'Pd(PPh3)4, K2CO3' above the arrow and 'dioxane/H2O, 90 °C, 12 h' below it, and bold labels 1–3 under the structures. Save output/suzuki.cdxml and export output/suzuki.rxn.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & droptype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Reactant and product InChIKeys from the .rxn and from the .cdxml reaction step must match gold. The .cdxml must hold one arrow, the two condition texts with bounding boxes above and below it, and bold labels 1–3 centred within 20 pt under each structure. ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
40% reactant/product structures correct; 25% condition text placed above/below arrow; 20% labels; 15% .rxn exported and consistent.
R08.02.01.01-T06 Transcribe a nine-compound SAR table from a paper into MarvinSketch with IC50 fields
Original instruction
input/sar_paper.pdf Table 1 shows a core with R1/R2 positions and nine rows of R-group drawings with IC50 (nM); the PDF has no text layer for the structures. In MarvinSketch draw all nine full compounds (not Markush) and save output/table1.sdf with SD fields 'ID' (e.g., 7a) and 'IC50_nM'.
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch · Adobe Acrobat Reader
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentmulti· Cross-app- Work product
WP02· Records/table- Conditions
multiapp· Multi-app- Proposed difficulty
- 4 / 5
Proposed verifier
For each gold ID, the matching SDF record's InChIKey must equal gold and IC50_nM must equal the table value. Records need Marvin-written 2D coordinates; toolkit SMILES-to-SDF conversions are detected by MOL header program line and idealized template layouts.
Proposed partial credit
70% scaled by fraction of 9 compounds with exact InChIKey; 20% IC50 fields exact; 10% IDs present and unique.
R08.02.01.01-T07 Define a Markush scaffold with R-group definitions in MarvinSketch and save MRV
Original instruction
From input/patent_claim1.png, draw the claimed scaffold in MarvinSketch with R1 at C4 and R2 on N1 as R-group attachment points. Define R1 = {H, F, Cl, OMe} and R2 = {methyl, cyclopropyl} as R-group definitions, not as separate molecules. Save output/claim1.mrv.
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
The MRV is parsed and its R-group definitions enumerated to 8 structures whose InChIKey set must equal gold. The file must contain R-group query definitions with attachment points on the specified atoms; eight separately drawn molecules earn only the scaffold milestone. ChemAxon molconvert/cxcalc, RDKit and Open Babel are not installed on the VM, and a file-system audit log flags output/ writes not made by MarvinSketch.
Proposed partial credit
30% scaffold correct; 20% R1/R2 attachment atoms correct; 40% enumerated set equals gold (scaled); 10% valid MRV with R-group definitions.
R08.02.01.01-T08 Digitize a hand-drawn bicyclic terpene from a notebook photo in ChemDraw
Original instruction
input/notebook_p12.jpg is a phone photo of a hand-drawn bicyclic terpene with three stereocenters and a margin note changing one single bond to a double bond. Draw the corrected structure in ChemDraw, apply Clean Up Structure, save output/np12.cdxml and export output/np12.mol.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 5 / 5
Proposed verifier
InChIKey of np12.mol must equal gold (stereo included; gold applies the margin correction) and match the .cdxml. The .cdxml must carry ChemDraw metadata; structure-recognition tools (OSRA, DECIMER, MolScribe) are absent and their process names are flagged. ChemScript and ChemDraw's COM/AppleScript automation are disabled.
Proposed partial credit
30% ring system and skeleton; 20% margin correction applied; 40% three stereocenters (≈13 pts each); 10% both files exported.
R08.02.01.01-T09 Fix wrong wedge bonds in a ChemDraw drawing to match the stated configuration
Original instruction
input/cmpd_88.cdxml was drawn with incorrect wedges; the compound is the (3R,4S,5S) isomer named in input/spec.txt. In ChemDraw change only wedge/hash bonds so the drawing encodes that configuration; do not move, add or delete atoms. Check with Show Stereochemistry, then save output/cmpd_88_fixed.cdxml.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
InChIKey of the saved file must equal the (3R,4S,5S) gold. Atom coordinates must equal the input within 0.01 pt and atom/bond counts be unchanged, rejecting redraws and SMILES re-imports; only bond Display attributes may differ. ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
90% correct stereocenters (30 pts each); 10% atom set and geometry unchanged.
R08.02.01.01-T10 Apply a journal drawing style and align four structures in a ChemDraw figure
Original instruction
input/fig2_draft.cdxml holds four structures in mixed styles. In ChemDraw apply the ACS Document 1996 style to the document and all structures, align the four on a common horizontal centre line with equal gaps, and keep each structure chemically unchanged. Save output/fig2.cdxml.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickgeom· Precise geometry- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 2 / 5
Proposed verifier
Parse the .cdxml: BondLength 14.4, ChainAngle 120, LineWidth 0.6, BoldWidth 2.0, Arial 10 pt labels on all fragments; structure centroids share y within 1 pt and gaps differ by ≤2 pt; each InChIKey equals the input. ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
40% style applied to all structures; 30% vertical alignment; 20% equal spacing; 10% chemistry unchanged.
R08.02.01.01-T11 Draw a deuterated amino-acid hydrochloride hydrate with correct InChI layers
Original instruction
input/batch_record.png shows a drug substance: a CD3-labelled amino acid isolated as the hydrochloride monohydrate. In MarvinSketch draw it as the salt, ammonium cation with neutral COOH plus a chloride anion and one water, with correct formal charges and isotope labels. Save output/api.mrv and export output/api.inchi (standard InChI).
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
The MRV, parsed with RDKit, must hold the gold components and formal charges (N+ ammonium with neutral COOH, Cl−, water; net charge 0) with Marvin coordinates and mass 2 on the three methyl H. Standard InChI must equal the gold string including the /i layer and multi-component formula; an InChI without a matching MRV scores 0. molconvert/cxcalc are not installed and a file-system audit log flags output/ writes not made by MarvinSketch.
Proposed partial credit
30% parent skeleton; 25% salt form and formal charges; 25% CD3 isotope layer; 20% chloride and water components.
R08.02.01.01-T12 Lay out a three-step synthetic route with intermediates and conditions in ChemDraw
Original instruction
input/route_sketch.pdf is a scanned whiteboard route: SM 1 → 2 (Boc2O, Et3N) → 3 (LiAlH4, THF) → 4 (MsCl, then NaN3). Draw it in ChemDraw as one row with three arrows, conditions above arrows and bold labels 1–4 under structures, ACS 1996 style. Save output/route.cdxml and export output/step1.rxn to step3.rxn.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & droptype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 3 / 5
Proposed verifier
Each .rxn's reactant/product InChIKeys must match gold for that step; the .cdxml must contain three left-to-right arrows with the matching condition strings above each, four labels, and ACS 1996 style settings. Intermediates must be chemically consistent with the reagents (gold). ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
40% four structures correct (10 pts each); 25% three steps exported consistently; 20% conditions placed; 15% labels and style.
R08.02.01.01-T13 Draw a specified 2H-indazole tautomer in Ketcher and preserve it through SMILES export
Original instruction
Medicinal chemistry needs the 2H-indazole tautomer of compound K-17 shown in input/k17_2H.png, not the 1H form. Draw it in Ketcher with the hydrogen explicitly on N2 and substituents as shown, then export output/k17.smi and output/k17.mol. Registration compares tautomer-sensitive canonical SMILES, not standard InChI.
- Platforms
web· Any OS (web)- Applications
- Ketcher
- Interfaces
brow· Browser- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
RDKit canonical SMILES of both files must equal the gold 2H form; the 1H tautomer fails even though its standard InChI matches. The JS hook detects and rejects setMolecule/paste calls and files must arrive via Ketcher's Save download; MOL coordinates must be canvas-drawn (template-layout check).
Proposed partial credit
40% skeleton and substituents correct; 40% H on N2 (2H tautomer); 20% SMILES and MOL consistent.
R08.02.01.01-T14 Build a cyclic RGD pentapeptide with a D-residue in Ketcher macromolecules mode
Original instruction
Switch Ketcher to Macromolecules mode and build cyclo-[D-Phe-Pro-Arg-Gly-Asp] from the peptide monomer library, closing the ring head-to-tail with a backbone bond. Export output/crgd.helm and output/crgd.mol. Do not draw the peptide atom by atom in small-molecule mode.
- Platforms
web· Any OS (web)- Applications
- Ketcher
- Interfaces
brow· Browser- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & drop- Work product
WP03· Visual layout- Conditions
tutorial· Follow docs/tutorial- Proposed difficulty
- 4 / 5
Proposed verifier
Normalized HELM must equal gold (monomer IDs incl. D-Phe, cyclic R2–R1 connection). InChIKey of the MOL must match gold with correct D/L configuration. A JS hook detects programmatic monomer insertion or HELM import; such calls score 0.
Proposed partial credit
30% five correct monomers in order; 20% D-Phe configuration; 30% head-to-tail cyclization; 20% HELM and MOL valid and consistent.
R08.02.01.01-T15 Atom-map an SNAr reaction in ChemDraw and export a mapped RXN
Original instruction
input/snar.cdxml contains 2,4-difluoronitrobenzene + morpholine → 4-(5-fluoro-2-nitrophenyl)morpholine + HF. Using ChemDraw's reaction-mapping tools, map every reactant heavy atom that appears in a product, correcting wrong automatic maps so the morpholine N maps onto the new C–N bond at C2. Save output/snar_mapped.cdxml and export output/snar_mapped.rxn.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
Map numbers parsed from the RXN must give a product-to-reactant correspondence equal to gold for every heavy atom, including the ortho fluorine as leaving group. The .cdxml must hold ChemDraw mapping objects; RXNs produced by RXNMapper/RDKit without a matching .cdxml fail. ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
30% all product heavy atoms mapped; 40% reacting centre (new C–N, leaving F) correct; 20% remaining atoms correct; 10% files consistent.
R08.02.01.01-T16 Draw twenty example compounds from a scanned patent into a registration SDF
Original instruction
input/patent_examples.pdf (image-only scan, 6 pages) shows Examples 12–31 with structures and names; two names are wrong, so drawings are authoritative. Draw each compound in ChemDraw, save output/ex_<n>.cdxml, and list EX, SMILES (Copy As SMILES) and ChemDraw MW (2 decimals) in output/examples.csv. List in output/notes.txt each example whose name disagrees with its drawing.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw · Adobe Acrobat Reader
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentmulti· Cross-app- Work product
WP02· Records/table- Conditions
licensed· Licensed pro applong· Long-horizonmultiapp· Multi-app- Proposed difficulty
- 5 / 5
Proposed verifier
Per example, the .cdxml InChIKey must match gold drawn from the image, the CSV SMILES must match the .cdxml and MW be within 0.01. notes.txt must list exactly the two conflicting examples; converting the names instead of the images reproduces the two wrong structures and fails them. ChemScript and ChemDraw's COM/AppleScript automation are disabled.
Proposed partial credit
70% scaled by fraction of 20 InChIKey matches; 15% MW fields; 15% both name conflicts found with no false positives.
R08.02.01.01-T17 Audit an inventory sheet whose SMILES disagree with embedded structure images
Original instruction
fixtures/inventory.xlsx has 12 rows, each with an embedded structure image and a SMILES cell; some SMILES are wrong. For each row redraw the image in MarvinSketch, compare with the SMILES, and overwrite wrong cells with Marvin's exported canonical SMILES. Add column 'Fixed' (Y/N) and save output/inventory_fixed.xlsx.
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch · Microsoft Excel
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentmulti· Cross-app- Work product
WP02· Records/table- Conditions
multiapp· Multi-app- Proposed difficulty
- 3 / 5
Proposed verifier
Each row's final SMILES must give the gold InChIKey of its image; 'Fixed' must be Y exactly for rows whose original SMILES were wrong. Other cells and images must be unchanged (openpyxl diff). Images carry no alt text or metadata containing SMILES. molconvert/cxcalc, RDKit and Open Babel are absent, Excel macros are disabled, and a file-system audit flags writes not made by MarvinSketch or Excel.
Proposed partial credit
50% scaled by rows with correct final SMILES; 30% Fixed flags exact; 20% no collateral changes.
R08.02.01.01-T18 Convert a Fischer projection of a hexose into a stereo-correct pyranose drawing
Original instruction
input/fischer.png shows the open-chain Fischer projection of an aldohexose. In ChemDraw draw the β-pyranose form of that sugar as a flat skeletal ring with wedges at all five stereocenters, save output/sugar.cdxml, and write its name (e.g., β-D-glucopyranose) to output/sugar.txt.
- Platforms
mac· macOSwin· Windows- Applications
- ChemDraw
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
InChIKey of the drawing must equal gold for all five stereocenters including the anomeric carbon; sugar.txt must equal the gold name (case-insensitive). Wedge/hash bond Display attributes must be present at all five stereocenters in the .cdxml. ChemScript and ChemDraw's COM/AppleScript automation are disabled, and a file-system audit flags output/ writes not made by ChemDraw.
Proposed partial credit
20% ring form and connectivity; 50% four ring stereocenters (12.5 pts each); 20% anomeric β; 10% name correct.
R08.02.01.01-T19 Control: generate intermediate 14's InChI from its IUPAC name on the command line
Original instruction
Control pair of T03. Given the IUPAC name of intermediate 14 in input/int14_name.txt, produce output/int14.inchi and output/int14.mol using command-line tools only (OPSIN, RDKit and Open Babel are installed). No structure editor is available.
- Platforms
mac· macOSlin· Linux- Applications
- OPSIN · RDKit
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Same checker as T03: standard InChI must equal gold including /t, /m, /s layers, and the MOL must parse to the same InChIKey. Scored as the CLI control for T03.
Proposed partial credit
50% InChI exact; 30% MOL parses with matching InChIKey; 20% stereo layers present.
R08.02.01.01-T20 Encode mixed absolute and relative stereo with enhanced stereo groups and export V3000
Original instruction
input/mixture_note.pdf states batch B-77 is racemic at C2 with fixed relative configuration (2R*,5S*) to C5, while C8 is absolute R. In MarvinSketch draw the compound from input/b77.png, assign enhanced stereo groups (abs for C8, and1 for C2/C5), save output/b77.mrv and export output/b77.mol as V3000.
- Platforms
mac· macOSwin· Windows- Applications
- MarvinSketch
- Interfaces
desk· Desktop GUI- GUI need · task setting
G3· GUI-only- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
tutorial· Follow docs/tutorial- Proposed difficulty
- 5 / 5
Proposed verifier
Parse the V3000 COLLECTION block: STEABS holds C8, STERAC1 holds exactly C2 and C5, and atom parities match gold; skeleton InChIKey matches. The MRV must carry Marvin enhanced-stereo labels; V2000 exports or groups lost in conversion fail. ChemAxon molconvert/cxcalc, RDKit and Open Babel are absent from the VM, and a file-system audit flags output/ writes not made by MarvinSketch.
Proposed partial credit
30% skeleton correct; 30% three stereocenter parities; 30% stereo groups exact; 10% valid V3000 export.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.