id stringlengths 11 11 | smiles stringlengths 2 142 ⌀ | requested listlengths 0 6 | params unknown | category stringclasses 6
values | prompt stringlengths 1.66k 2.25k | completion stringlengths 215 833 | expect_status stringclasses 3
values | expect_reason stringclasses 7
values | writing stringclasses 3
values | family int64 1 8 | source stringclasses 2
values | source_id stringlengths 0 5 | license stringclasses 1
value | shard stringclasses 1
value | graph dict | mutation stringclasses 10
values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
mp-10000000 | FCc1n[nH]cc1N1(C)CCNCC1 | [] | {} | chem_invalid | REQUEST: I have a compound here and I need the element counts including hydrogen, the shortest path between atoms 5 and 3, and the heavy atom count.
STRUCTURE:
SMILES: FCc1n[nH]cc1N1(C)CCNCC1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | overbond_heteroatom | |
mp-10000001 | CCCc1ccn(C(=ONCC)c1 | [] | {} | syntax_invalid | REQUEST: I have a compound here and I need the molecular formula, the element counts including hydrogen, the shortest path between atoms 1 and 4, the bond count, and the heavy atom count.
STRUCTURE:
SMILES: CCCc1ccn(C(=ONCC)c1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen ... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | drop_close_paren | |
mp-10000002 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: For my notebook I need the SMILES string.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 C, 3 O, 4 C, 5 N, 6 N, 7 C, 8 N, 9 C, 10 C, 11 C, 12 C, 13 C, 14 O
BONDS: 0-1 single, 1-2 single, 1-3 single, 3-4 single, 4-5 double, 5-6 single, 6-7 double, 7-8 single, 7-14 single, 8-9 single, 9-10 single, 10-11 single, 11-12 single, 12... | DERIVATION: Walk 0 C H3 1 C H1 2 C H3 3 O H0 4 c H0 5 n H0 6 n H0 7 c H0 8 N H0 9 C H2 10 C H2 11 C H2 12 C H2 13 C H2 14 o H0. Tally C10 H17 N3 O2. Heavy 15. Closures: digit 1 joins 8 to 13, digit 2 joins 4 to 14. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CC(C)O... | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"C"
],
[
3,
"O"
],
[
4,
"C"
],
[
5,
"N"
],
[
6,
"N"
],
[
7,
"C"
],
[
8,
"N"
],
[
9,
... | null | |
mp-10000003 | CCC=C(C1CC1)C(CC(N)#O)C1CCCC1 | [] | {} | chem_invalid | REQUEST: I have a compound here and I need the heavy atom count, the bond count, the molecular formula, the shortest path between atoms 6 and 0, the element counts including hydrogen, and which element sits at index 5.
STRUCTURE:
SMILES: CCC=C(C1CC1)C(CC(N)#O)C1CCCC1
CONVENTIONS: Report the molecular formula in Hill ... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | double_to_triple | |
mp-10000004 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I am checking a supplier record and I need the SMILES string I should store.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 C, 3 C, 4 C, 5 C, 6 Cl, 7 S, 8 S, 9 C, 10 C, 11 C, 12 C, 13 O, 14 P, 15 O, 16 O, 17 O
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 single, 3-7 single, 4-5 single, 5-6 single, 7-8 single, 8-9 single, 9-... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 C H1 4 C H2 5 C H2 6 Cl H0 7 S H0 8 S H0 9 C H1 10 C H2 11 C H1 12 C H3 13 O H1 14 P H0 15 O H0 16 O H1 17 O H1. Tally C10 H22 Cl1 O4 P1 S2. Heavy 18. No ring closures. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CCCC(CCCl)SS... | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"C"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"Cl"
],
[
7,
"S"
],
[
8,
"S"
],
[
9,
... | null | |
mp-10000005 | CC(C)C[C@H](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O | [
"atom_at_index",
"element_counts",
"heavy_atom_count",
"bond_count"
] | {
"atom_at_index": {
"k": 36
}
} | compute | REQUEST: Quick question about this structure. Can you give me what element is at index 36, the element counts with hydrogen included, how many heavy atoms it has, and how many bonds there are?
STRUCTURE:
SMILES: CC(C)C[C@H](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O
CONVENTIONS: Report ... | DERIVATION: Walk 0 C H3 1 C H1 2 C H3 3 C H2 4 C H1 5 N H1 6 C H0 7 O H0 8 O H0 9 C H0 10 C H3 11 C H3 12 C H1 13 C H2 14 C H2 15 C H0 16 F H0 17 F H0 18 C H2 19 C H2 20 C H0 21 O H0 22 N H1 23 C H1 24 C H2 25 C H1 26 C H2 27 C H1 28 N H0 29 C H0 30 O H0 31 C H1 32 O H1 33 S H0 34 O H0 35 O H0 36 O H1. Tally C23 H37 F2... | ok | null | canonical | 2 | wwPDB CCD | YKA | CC0-1.0 | train | null | null |
mp-10000006 | C[N]([Cu])C(=O)c1c[nH]cn1 | [] | {} | out_of_scope | REQUEST: I have a compound here and I need the molecular formula and the heavy atom count.
STRUCTURE:
SMILES: C[N]([Cu])C(=O)c1c[nH]cn1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, or... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000008 | c1cc(-c2cccc(N3CCCC3)n2)nc1 | [] | {} | chem_invalid | REQUEST: For my notebook I need the atom at index 12, the formula, the number of heavy atoms, the bond distance from atom 12 to atom 13, how many of each element there are, and the number of bonds.
STRUCTURE:
SMILES: c1cc(-c2cccc(N3CCCC3)n2)nc1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbo... | DERIVATION: Read the structure. It does not parse as a molecule: kekulization_failure. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "kekulization_failure"}
``` | invalid_structure | kekulization_failure | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | contract_aromatic_ring | |
mp-10000009 | CC(C)c1cc(CO)n(I)c1P(#O)(O)O | [] | {} | chem_invalid | REQUEST: Could you look at this and tell me the number of atoms of each element, how many bonds it has, how many heavy atoms are in it, and the formula for it?
STRUCTURE:
SMILES: CC(C)c1cc(CO)n(I)c1P(#O)(O)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the re... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | double_to_triple | |
mp-10000010 | CC[Si](C)(C)c1ccccc1CC(CC(C)C)C(N1CCOCC1)C2C(F)(F)F | [] | {} | syntax_invalid | REQUEST: I have a compound here and I need the molecular formula, the bond count, the heavy atom count, the element counts including hydrogen, and the shortest path between atoms 15 and 27.
STRUCTURE:
SMILES: CC[Si](C)(C)c1ccccc1CC(CC(C)C)C(N1CCOCC1)C2C(F)(F)F
CONVENTIONS: Report the molecular formula in Hill notatio... | DERIVATION: Read the structure. It does not parse as a molecule: unclosed_ring_bond. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unclosed_ring_bond"}
``` | invalid_structure | unclosed_ring_bond | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | drop_ring_digit | |
mp-10000011 | CCNC1SC(OCC(F)(F)(F)C)C(C(=O)N(C)C)SC1N1CCCC1 | [] | {} | chem_invalid | REQUEST: Working up a sample today. Please report the heavy atom total, the counts of each element, and the path length between atoms 14 and 23.
STRUCTURE:
SMILES: CCNC1SC(OCC(F)(F)(F)C)C(C(=O)N(C)C)SC1N1CCCC1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the ... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | add_fifth_bond | |
mp-10000012 | CNC(=O)c1c(NC2CC2)cc(OC(F)(F)Ee)c2nc([O-])cnc12 | [] | {} | syntax_invalid | REQUEST: Working up a sample today. Please report the path length between atoms 4 and 3, the heavy atom total, the empirical composition, the counts of each element, and which element is at position 6.
STRUCTURE:
SMILES: CNC(=O)c1c(NC2CC2)cc(OC(F)(F)Ee)c2nc([O-])cnc12
CONVENTIONS: Report the molecular formula in Hill... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000013 | C1CN(S(=O)(=O)C)C[C@@H](C(O)=O)C1 | [
"atom_at_index",
"formula",
"path_len"
] | {
"atom_at_index": {
"k": 7
},
"path_len": {
"i": 6,
"j": 11
}
} | compute | REQUEST: I am checking a supplier record and I need the atom at index 7 for the record, the molecular formula as written on a label, and the bond distance between 6 and 11.
STRUCTURE:
SMILES: C1CN(S(=O)(=O)C)C[C@@H](C(O)=O)C1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen s... | DERIVATION: Walk 0 C H2 1 C H2 2 N H0 3 S H0 4 O H0 5 O H0 6 C H3 7 C H2 8 C H1 9 C H0 10 O H1 11 O H0 12 C H2. Tally C7 H13 N1 O4 S1. Heavy 13. Closures: digit 1 joins 0 to 12. index 7 is C. formula C7H13NO4S. path 6 to 11 via 6 3 2 7 8 9 11 is 6 bonds.
```json
{"status": "ok", "atom_at_index": "C", "formula": "C7H13... | ok | null | random | 7 | wwPDB CCD | A1A30 | CC0-1.0 | train | null | null |
mp-10000015 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I have a compound here and I need the SMILES string for this table.
STRUCTURE:
ATOMS: 0 O, 1 B, 2 O, 3 C, 4 C, 5 C, 6 C, 7 C, 8 C, 9 C, 10 C
BONDS: 0-1 single, 1-2 single, 1-3 single, 3-4 single, 4-5 single, 5-6 single, 6-7 single, 7-8 single, 8-9 single, 9-10 single, 10-3 single
CONVENTIONS: Report the mole... | DERIVATION: Walk 0 O H1 1 B H0 2 O H1 3 C H1 4 C H2 5 C H2 6 C H2 7 C H2 8 C H2 9 C H2 10 C H2. Tally C8 H17 B1 O2. Heavy 11. Closures: digit 1 joins 3 to 10. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "OB(O)C1CCCCCCC1"}
``` | ok | null | canonical | 1 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"O"
],
[
1,
"B"
],
[
2,
"O"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000016 | CC[N+](C)(C)c1nnsc1P(=O)(O)O | [
"bond_count",
"formula",
"atom_at_index",
"heavy_atom_count"
] | {
"atom_at_index": {
"k": 9
}
} | near_miss | REQUEST: Quick question about this structure. Can you give me how many bonds there are, its molecular formula, what element is at index 9, and how many heavy atoms it has?
STRUCTURE:
SMILES: CC[N+](C)(C)c1nnsc1P(=O)(O)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second,... | DERIVATION: Walk 0 C H3 1 C H2 2 N H0 3 C H3 4 C H3 5 c H0 6 n H0 7 n H0 8 s H0 9 c H0 10 P H0 11 O H0 12 O H1 13 O H1. Tally C6 H13 N3 O3 P1 S1. Heavy 14. Closures: digit 1 joins 5 to 9. bond_count 14. formula C6H13N3O3PS+. index 9 is C. heavy_atom_count 14.
```json
{"status": "ok", "bond_count": 14, "formula": "C6H1... | ok | null | canonical | 2 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000017 | CCOCC(Cl)O(CC)C | [] | {} | chem_invalid | REQUEST: Working up a sample today. Please report the empirical composition, which element is at position 7, the counts of each element, the path length between atoms 0 and 1, and the heavy atom total.
STRUCTURE:
SMILES: CCOCC(Cl)O(CC)C
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first,... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | overbond_heteroatom | |
mp-10000018 | CCOc1cc(Br)cc2c1CC([N+](=O)[O-])=C2 | [
"heavy_atom_count",
"bond_count",
"atom_at_index",
"path_len",
"element_counts"
] | {
"atom_at_index": {
"k": 1
},
"path_len": {
"i": 13,
"j": 15
}
} | compute | REQUEST: Setting up a reaction. I need the number of non hydrogen atoms, the total bonds in the structure, which element is at index 1, how far apart 13 and 15 sit, and the element count including hydrogen.
STRUCTURE:
SMILES: CCOc1cc(Br)cc2c1CC([N+](=O)[O-])=C2
CONVENTIONS: Report the molecular formula in Hill notati... | DERIVATION: Walk 0 C H3 1 C H2 2 O H0 3 c H0 4 c H1 5 c H0 6 Br H0 7 c H1 8 c H0 9 c H0 10 C H2 11 C H0 12 N H0 13 O H0 14 O H0 15 C H1. Tally C11 H10 Br1 N1 O3. Heavy 16. Closures: digit 1 joins 3 to 9, digit 2 joins 8 to 15. heavy_atom_count 16. bond_count 17. index 1 is C. path 13 to 15 via 13 12 11 15 is 3 bonds. e... | ok | null | canonical | 8 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000019 | CC(C)(C)c1n[nH]nc1CF | [
"element_counts",
"atom_at_index",
"formula",
"heavy_atom_count",
"bond_count",
"path_len"
] | {
"atom_at_index": {
"k": 10
},
"path_len": {
"i": 1,
"j": 3
}
} | compute | REQUEST: For my notebook I need how many of each element there are, the atom at index 10, the formula, the number of heavy atoms, the number of bonds, and the bond distance from atom 1 to atom 3.
STRUCTURE:
SMILES: CC(C)(C)c1n[nH]nc1CF
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, ... | DERIVATION: Walk 0 C H3 1 C H0 2 C H3 3 C H3 4 c H0 5 n H0 6 n H1 7 n H0 8 c H0 9 C H2 10 F H0. Tally C7 H12 F1 N3. Heavy 11. Closures: digit 1 joins 4 to 8. element_counts from the tally. index 10 is F. formula C7H12FN3. heavy_atom_count 11. bond_count 11. path 1 to 3 via 1 3 is 1 bonds.
```json
{"status": "ok", "ele... | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000021 | Ic(1ccccc1 | [] | {} | syntax_invalid | REQUEST: Quick question about this structure. Can you give me how many heavy atoms it has, the element counts with hydrogen included, how far apart atoms 1 and 2 are, what element is at index 3, and how many bonds there are?
STRUCTURE:
SMILES: Ic(1ccccc1
CONVENTIONS: Report the molecular formula in Hill notation, mea... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 2 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000022 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I am checking a supplier record and I need the SMILES string I should store.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 N, 3 C, 4 C, 5 C, 6 C, 7 C, 8 C, 9 C, 10 C, 11 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 2-5 single, 3-4 single, 5-6 single, 6-7 single, 6-8 single, 8-9 single, 9-10 single, 9-11 single
CONVENTIONS: ... | DERIVATION: Walk 0 C H3 1 C H2 2 N H0 3 C H2 4 C H3 5 C H2 6 C H1 7 C H3 8 C H2 9 C H1 10 C H3 11 C H3. Tally C11 H25 N1. Heavy 12. No ring closures. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CCN(CC)CC(C)CC(C)C"}
``` | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"N"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000024 | CCNCCC(=O)(N(I)CC)C | [] | {} | chem_invalid | REQUEST: For my notebook I need the formula, the bond distance from atom 6 to atom 0, how many of each element there are, the number of heavy atoms, the atom at index 4, and the number of bonds.
STRUCTURE:
SMILES: CCNCCC(=O)(N(I)CC)C
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hy... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | add_fifth_bond | |
mp-10000025 | CCC(=O)OC1CNC(n2nc([O-])c(C(C)=O)n2)CO1 | [
"atom_at_index",
"element_counts",
"formula"
] | {
"atom_at_index": {
"k": 10
}
} | compute | REQUEST: Before I weigh this out I want what element sits at index 10, a per element breakdown, and the molecular formula in Hill order.
STRUCTURE:
SMILES: CCC(=O)OC1CNC(n2nc([O-])c(C(C)=O)n2)CO1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elem... | DERIVATION: Walk 0 C H3 1 C H2 2 C H0 3 O H0 4 O H0 5 C H1 6 C H2 7 N H1 8 C H1 9 n H0 10 n H0 11 c H0 12 O H0 13 c H0 14 C H0 15 C H3 16 O H0 17 n H0 18 C H2 19 O H0. Tally C11 H15 N4 O5. Heavy 20. Closures: digit 1 joins 9 to 17, digit 2 joins 5 to 19. index 10 is N. element_counts from the tally. formula C11H15N4O5-... | ok | null | canonical | 5 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000026 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: For my notebook I need the SMILES string.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 N, 3 C, 4 O, 5 C, 6 C, 7 N, 8 C, 9 C, 10 C, 11 C, 12 O, 13 C, 14 C, 15 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 double, 3-5 single, 5-6 single, 6-7 single, 7-8 single, 7-10 single, 8-9 single, 10-11 single, 11-12 single, 12-13 sin... | DERIVATION: Walk 0 C H3 1 C H2 2 N H1 3 C H0 4 O H0 5 C H2 6 C H2 7 N H0 8 C H2 9 C H3 10 C H2 11 C H2 12 O H0 13 C H1 14 C H2 15 C H2. Tally C12 H24 N2 O2. Heavy 16. Closures: digit 1 joins 13 to 15. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CCNC(=O)CCN(CC)CCOC1... | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"N"
],
[
3,
"C"
],
[
4,
"O"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"N"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000027 | CC[Si](C)(C)c1ccon1 | [
"bond_count",
"atom_at_index",
"formula",
"path_len"
] | {
"atom_at_index": {
"k": 1
},
"path_len": {
"i": 9,
"j": 1
}
} | near_miss | REQUEST: I am checking a supplier record and I need the number of bonds in the skeleton, the atom at index 1 for the record, the molecular formula as written on a label, and the bond distance between 9 and 1.
STRUCTURE:
SMILES: CC[Si](C)(C)c1ccon1
CONVENTIONS: Report the molecular formula in Hill notation, meaning ca... | DERIVATION: Walk 0 C H3 1 C H2 2 Si H0 3 C H3 4 C H3 5 c H0 6 c H1 7 c H1 8 o H0 9 n H0. Tally C7 H13 N1 O1 Si1. Heavy 10. Closures: digit 1 joins 5 to 9. bond_count 10. index 1 is C. formula C7H13NOSi. path 9 to 1 via 9 5 2 1 is 3 bonds.
```json
{"status": "ok", "bond_count": 10, "atom_at_index": "C", "formula": "C7H... | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000028 | CCNc1ccc2c(CF)nncc2c1 | [
"bond_count",
"heavy_atom_count",
"atom_at_index",
"element_counts",
"path_len"
] | {
"atom_at_index": {
"k": 3
},
"path_len": {
"i": 4,
"j": 5
}
} | compute | REQUEST: Setting up a reaction. I need the total bonds in the structure, the number of non hydrogen atoms, which element is at index 3, the element count including hydrogen, and how far apart 4 and 5 sit.
STRUCTURE:
SMILES: CCNc1ccc2c(CF)nncc2c1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carb... | DERIVATION: Walk 0 C H3 1 C H2 2 N H1 3 c H0 4 c H1 5 c H1 6 c H0 7 c H0 8 C H2 9 F H0 10 n H0 11 n H0 12 c H1 13 c H0 14 c H1. Tally C11 H12 F1 N3. Heavy 15. Closures: digit 1 joins 6 to 13, digit 2 joins 3 to 14. bond_count 16. heavy_atom_count 15. index 3 is C. element_counts from the tally. path 4 to 5 via 4 5 is 1... | ok | null | canonical | 8 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000032 | [CH3][Cu][O]c1c[nH]cn1 | [] | {} | out_of_scope | REQUEST: Could you look at this and tell me the formula for it and how many heavy atoms are in it?
STRUCTURE:
SMILES: [CH3][Cu][O]c1c[nH]cn1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbo... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000033 | OCCCCCCNCCCCCCCNCCCNCCCCCCONNOCCCNNOCCNCCCCCOO | [] | {} | out_of_scope | REQUEST: For my notebook I need the formula and the number of heavy atoms.
STRUCTURE:
SMILES: OCCCCCCNCCCCCCCNCCCNCCCCCCONNOCCCNNOCCNCCCCCOO
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbo... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000034 | CCCCCCCC[O-] | [
"bond_count",
"heavy_atom_count",
"formula",
"atom_at_index"
] | {
"atom_at_index": {
"k": 6
}
} | compute | REQUEST: Quick question about this structure. Can you give me how many bonds there are, how many heavy atoms it has, its molecular formula, and what element is at index 6?
STRUCTURE:
SMILES: CCCCCCCC[O-]
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remain... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 C H2 4 C H2 5 C H2 6 C H2 7 C H2 8 O H0. Tally C8 H17 O1. Heavy 9. No ring closures. bond_count 8. heavy_atom_count 9. formula C8H17O-. index 6 is C.
```json
{"status": "ok", "bond_count": 8, "heavy_atom_count": 9, "formula": "C8H17O-", "atom_at_index": "C"}
``` | ok | null | canonical | 2 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000035 | CC(C#CC(C[Si](C)(C)C)[N+](C)(C)C)P(C)(C)=O | [
"path_len",
"bond_count",
"element_counts",
"formula",
"atom_at_index",
"heavy_atom_count"
] | {
"atom_at_index": {
"k": 4
},
"path_len": {
"i": 0,
"j": 2
}
} | near_miss | REQUEST: Working up a sample today. Please report the path length between atoms 0 and 2, the total bonds, the counts of each element, the empirical composition, which element is at position 4, and the heavy atom total.
STRUCTURE:
SMILES: CC(C#CC(C[Si](C)(C)C)[N+](C)(C)C)P(C)(C)=O
CONVENTIONS: Report the molecular for... | DERIVATION: Walk 0 C H3 1 C H1 2 C H0 3 C H0 4 C H1 5 C H2 6 Si H0 7 C H3 8 C H3 9 C H3 10 N H0 11 C H3 12 C H3 13 C H3 14 P H0 15 C H3 16 C H3 17 O H0. Tally C14 H31 N1 O1 P1 Si1. Heavy 18. No ring closures. path 0 to 2 via 0 1 2 is 2 bonds. bond_count 17. element_counts from the tally. formula C14H31NOPSi+. index 4 i... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000036 | CCQCC1CNCC(N=[N+]=[N-])C(C2CCC2)O1 | [] | {} | syntax_invalid | REQUEST: Could you look at this and tell me how many heavy atoms are in it, the shortest path from atom 16 to atom 7, and which element occupies index 6?
STRUCTURE:
SMILES: CCQCC1CNCC(N=[N+]=[N-])C(C2CCC2)O1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the re... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000037 | c1nc(N2(C)CCCCC2)n[nH]1 | [] | {} | chem_invalid | REQUEST: I am checking a supplier record and I need the heavy atoms total, the number of bonds in the skeleton, the atom at index 1 for the record, and the bond distance between 4 and 0.
STRUCTURE:
SMILES: c1nc(N2(C)CCCCC2)n[nH]1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrog... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | overbond_heteroatom | |
mp-10000038 | CCCC1NC(N(C)C)CC(C(#O)N(C)C)CC1CC(C)(C)C | [] | {} | chem_invalid | REQUEST: Working up a sample today. Please report the counts of each element, which element is at position 10, the total bonds, and the path length between atoms 17 and 7.
STRUCTURE:
SMILES: CCCC1NC(N(C)C)CC(C(#O)N(C)C)CC1CC(C)(C)C
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydr... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | double_to_triple | |
mp-10000039 | CCOC(=O)CCC(=O)C(=O)C(CCC(C)C)CC(=O()N(C)C | [] | {} | syntax_invalid | REQUEST: Setting up a reaction. I need the total bonds in the structure, how far apart 3 and 11 sit, the formula I should put on the vial, the number of non hydrogen atoms, and the element count including hydrogen.
STRUCTURE:
SMILES: CCOC(=O)CCC(=O)C(=O)C(CCC(C)C)CC(=O()N(C)C
CONVENTIONS: Report the molecular formula... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 8 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000040 | CC(I)NC(#O)CC(CCl)c1ccns1 | [] | {} | chem_invalid | REQUEST: Before I weigh this out I want the bond count for the skeleton, the steps between atom 3 and atom 12, the count of non hydrogen atoms, a per element breakdown, and what element sits at index 7.
STRUCTURE:
SMILES: CC(I)NC(#O)CC(CCl)c1ccns1
CONVENTIONS: Report the molecular formula in Hill notation, meaning ca... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | double_to_triple | |
mp-10000041 | CCCCCCCNOOCNCCOCCCCOCNCOCOOONNCCNNCNCCOCCCCCNNCNCCCCCOCOCCNCCN | [] | {} | out_of_scope | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label and the heavy atoms total.
STRUCTURE:
SMILES: CCCCCCCNOOCNCCOCCCCOCNCOCOOONNCCNNCNCCOCCCCCNNCNCCCCCOCOCCNCCN
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remai... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000042 | CCCNN1CC(C2(N3CCCC3)(C)SCC([Si](C)(C)CC)SC2CCC)CN1 | [] | {} | chem_invalid | REQUEST: Quick question about this structure. Can you give me its molecular formula, the element counts with hydrogen included, how far apart atoms 17 and 0 are, how many bonds there are, and what element is at index 12?
STRUCTURE:
SMILES: CCCNN1CC(C2(N3CCCC3)(C)SCC([Si](C)(C)CC)SC2CCC)CN1
CONVENTIONS: Report the mol... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 2 | scaffold_enumerator | CC0-1.0 | train | null | add_fifth_bond | |
mp-10000043 | CC((C)CCC1CCCNCC1 | [] | {} | syntax_invalid | REQUEST: Working up a sample today. Please report the heavy atom total, the path length between atoms 7 and 4, and which element is at position 2.
STRUCTURE:
SMILES: CC((C)CCC1CCCNCC1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabe... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000044 | S1CC(SC(C1[B-](F)(F)F)[B-](F)(F)F)[Si](C)(C)C | [
"atom_at_index",
"path_len",
"bond_count",
"heavy_atom_count",
"formula",
"element_counts"
] | {
"atom_at_index": {
"k": 9
},
"path_len": {
"i": 4,
"j": 17
}
} | near_miss | REQUEST: I have a compound here and I need which element sits at index 9, the shortest path between atoms 4 and 17, the bond count, the heavy atom count, the molecular formula, and the element counts including hydrogen.
STRUCTURE:
SMILES: S1CC(SC(C1[B-](F)(F)F)[B-](F)(F)F)[Si](C)(C)C
CONVENTIONS: Report the molecular... | DERIVATION: Walk 0 S H0 1 C H2 2 C H1 3 S H0 4 C H1 5 C H1 6 B H0 7 F H0 8 F H0 9 F H0 10 B H0 11 F H0 12 F H0 13 F H0 14 Si H0 15 C H3 16 C H3 17 C H3. Tally C7 H14 B2 F6 S2 Si1. Heavy 18. Closures: digit 1 joins 0 to 5. index 9 is F. path 4 to 17 via 4 3 2 14 17 is 4 bonds. bond_count 18. heavy_atom_count 18. formula... | ok | null | random | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000045 | CCC(CCC[N+](C)(C)C)P(=O)(O)O | [
"formula",
"element_counts",
"atom_at_index",
"path_len",
"bond_count",
"heavy_atom_count"
] | {
"atom_at_index": {
"k": 10
},
"path_len": {
"i": 10,
"j": 11
}
} | near_miss | REQUEST: Working up a sample today. Please report the empirical composition, the counts of each element, which element is at position 10, the path length between atoms 10 and 11, the total bonds, and the heavy atom total.
STRUCTURE:
SMILES: CCC(CCC[N+](C)(C)C)P(=O)(O)O
CONVENTIONS: Report the molecular formula in Hil... | DERIVATION: Walk 0 C H3 1 C H2 2 C H1 3 C H2 4 C H2 5 C H2 6 N H0 7 C H3 8 C H3 9 C H3 10 P H0 11 O H0 12 O H1 13 O H1. Tally C9 H23 N1 O3 P1. Heavy 14. No ring closures. formula C9H23NO3P+. element_counts from the tally. index 10 is P. path 10 to 11 via 10 11 is 1 bonds. bond_count 13. heavy_atom_count 14.
```json
{"... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000046 | CCOC(=O)C(C)CCl | [
"bond_count",
"path_len",
"element_counts"
] | {
"path_len": {
"i": 1,
"j": 8
}
} | compute | REQUEST: Working up a sample today. Please report the total bonds, the path length between atoms 1 and 8, and the counts of each element.
STRUCTURE:
SMILES: CCOC(=O)C(C)CCl
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if... | DERIVATION: Walk 0 C H3 1 C H2 2 O H0 3 C H0 4 O H0 5 C H1 6 C H3 7 C H2 8 Cl H0. Tally C6 H11 Cl1 O2. Heavy 9. No ring closures. bond_count 8. path 1 to 8 via 1 2 3 5 7 8 is 5 bonds. element_counts from the tally.
```json
{"status": "ok", "bond_count": 8, "path_len": 5, "element_counts": {"C": 6, "Cl": 1, "H": 11, "O... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000047 | O=C(O)[C@@H]1CCCN1S(=O)(=O)c1cccc2c1NSN2 | [
"heavy_atom_count",
"path_len",
"atom_at_index"
] | {
"atom_at_index": {
"k": 15
},
"path_len": {
"i": 11,
"j": 13
}
} | compute | REQUEST: Could you look at this and tell me how many heavy atoms are in it, the shortest path from atom 11 to atom 13, and which element occupies index 15?
STRUCTURE:
SMILES: O=C(O)[C@@H]1CCCN1S(=O)(=O)c1cccc2c1NSN2
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, the... | DERIVATION: Walk 0 O H0 1 C H0 2 O H1 3 C H1 4 C H2 5 C H2 6 C H2 7 N H0 8 S H0 9 O H0 10 O H0 11 c H0 12 c H1 13 c H1 14 c H1 15 c H0 16 c H0 17 N H1 18 S H0 19 N H1. Tally C11 H13 N3 O4 S2. Heavy 20. Closures: digit 1 joins 3 to 7, digit 2 joins 11 to 16, digit 3 joins 15 to 19. heavy_atom_count 20. path 11 to 13 via... | ok | null | canonical | 6 | wwPDB CCD | A1A47 | CC0-1.0 | train | null | null |
mp-10000048 | CNC(=O)c1cccc2c1[nH]c1ccc(OCC(F)(F)Ee)c(NC3CC3)c12 | [] | {} | syntax_invalid | REQUEST: For my notebook I need the bond distance from atom 7 to atom 25, the atom at index 18, and the number of heavy atoms.
STRUCTURE:
SMILES: CNC(=O)c1cccc2c1[nH]c1ccc(OCC(F)(F)Ee)c(NC3CC3)c12
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining ele... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000049 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: For my notebook I need the SMILES string.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 O, 3 C, 4 C, 5 C, 6 C, 7 N, 8 C
BONDS: 0-1 single, 1-2 double, 1-3 single, 3-4 double, 4-5 single, 5-6 double, 6-7 single, 7-8 double, 8-3 single
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen ... | DERIVATION: Walk 0 C H3 1 C H0 2 O H0 3 c H0 4 c H1 5 c H1 6 c H1 7 n H0 8 c H1. Tally C7 H7 N1 O1. Heavy 9. Closures: digit 1 joins 3 to 8. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CC(=O)c1cccnc1"}
``` | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"O"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"N"
],
[
8,
"C"
]
],
"bonds": [
... | null | |
mp-10000050 | CCCCc1coc(C2CC2c1NC1CC1 | [] | {} | syntax_invalid | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label, the atom at index 13 for the record, the number of bonds in the skeleton, the heavy atoms total, the bond distance between 1 and 7, and the count of each element on the label.
STRUCTURE:
SMILES: CCCCc1coc(C2CC2c1NC1CC1
CO... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | drop_close_paren | |
mp-10000051 | CN(C)C(=O)(C1CC(P(C)(C)=O)N1)C | [] | {} | chem_invalid | REQUEST: For my notebook I need the number of heavy atoms, the formula, how many of each element there are, the bond distance from atom 9 to atom 1, and the number of bonds.
STRUCTURE:
SMILES: CN(C)C(=O)(C1CC(P(C)(C)=O)N1)C
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen sec... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | add_fifth_bond | |
mp-10000052 | CCC(=O)OC(C)NC(C)#O | [] | {} | chem_invalid | REQUEST: Working up a sample today. Please report the total bonds, the heavy atom total, and which element is at position 9.
STRUCTURE:
SMILES: CCC(=O)OC(C)NC(C)#O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the stru... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | double_to_triple | |
mp-10000054 | [CH3][Ni][CH2]Nc1nc2c(C(F)F)cc(P(=O)(O)O)cc2cc1I | [] | {} | out_of_scope | REQUEST: For my notebook I need the formula and the number of heavy atoms.
STRUCTURE:
SMILES: [CH3][Ni][CH2]Nc1nc2c(C(F)F)cc(P(=O)(O)O)cc2cc1I
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no car... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000055 | [N-]=[N+]=NC1Cc2occcc2CC1N=[N+]=[N-] | [] | {} | chem_invalid | REQUEST: Before I weigh this out I want the bond count for the skeleton, the count of non hydrogen atoms, and what element sits at index 8.
STRUCTURE:
SMILES: [N-]=[N+]=NC1Cc2occcc2CC1N=[N+]=[N-]
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elem... | DERIVATION: Read the structure. It does not parse as a molecule: kekulization_failure. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "kekulization_failure"}
``` | invalid_structure | kekulization_failure | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | carbon_to_chalcogen_aromatic | |
mp-10000056 | ONCCCOOCOCCCOONOCCCNCCCCCOCNCNCNOCCNCCCCCCOCCNCCCN | [] | {} | out_of_scope | REQUEST: Before I weigh this out I want the molecular formula in Hill order and the count of non hydrogen atoms.
STRUCTURE:
SMILES: ONCCCOOCOCCCOONOCCCNCCCCCOCNCNCNOCCNCCCCCCOCCNCCCN
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabet... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000057 | CCN(C(=O)CC(=O)[O-])P(C)(C)=O | [
"heavy_atom_count",
"element_counts",
"formula",
"atom_at_index"
] | {
"atom_at_index": {
"k": 1
}
} | near_miss | REQUEST: Setting up a reaction. I need the number of non hydrogen atoms, the element count including hydrogen, the formula I should put on the vial, and which element is at index 1.
STRUCTURE:
SMILES: CCN(C(=O)CC(=O)[O-])P(C)(C)=O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydro... | DERIVATION: Walk 0 C H3 1 C H2 2 N H0 3 C H0 4 O H0 5 C H2 6 C H0 7 O H0 8 O H0 9 P H0 10 C H3 11 C H3 12 O H0. Tally C7 H13 N1 O4 P1. Heavy 13. No ring closures. heavy_atom_count 13. element_counts from the tally. formula C7H13NO4P-. index 1 is C.
```json
{"status": "ok", "heavy_atom_count": 13, "element_counts": {"C... | ok | null | canonical | 8 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000058 | CCCC1Cc2cc(CC(=O)(O)C)cc(C(=O)OCC)c2CC1[Si](C)(C)CC | [] | {} | chem_invalid | REQUEST: Working up a sample today. Please report the path length between atoms 0 and 23, which element is at position 15, and the counts of each element.
STRUCTURE:
SMILES: CCCC1Cc2cc(CC(=O)(O)C)cc(C(=O)OCC)c2CC1[Si](C)(C)CC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen s... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | add_fifth_bond | |
mp-10000060 | CC(C)(C)CCC(=O)C(=O)CCC(=O)[O-] | [
"formula",
"heavy_atom_count",
"path_len",
"atom_at_index"
] | {
"atom_at_index": {
"k": 4
},
"path_len": {
"i": 10,
"j": 13
}
} | compute | REQUEST: Could you look at this and tell me the formula for it, how many heavy atoms are in it, the shortest path from atom 10 to atom 13, and which element occupies index 4?
STRUCTURE:
SMILES: CC(C)(C)CCC(=O)C(=O)CCC(=O)[O-]
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen s... | DERIVATION: Walk 0 C H3 1 C H0 2 C H3 3 C H3 4 C H2 5 C H2 6 C H0 7 O H0 8 C H0 9 O H0 10 C H2 11 C H2 12 C H0 13 O H0 14 O H0. Tally C11 H17 O4. Heavy 15. No ring closures. formula C11H17O4-. heavy_atom_count 15. path 10 to 13 via 10 11 12 13 is 3 bonds. index 4 is C.
```json
{"status": "ok", "formula": "C11H17O4-", ... | ok | null | canonical | 6 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000061 | O=C([O-])C1C(I)CC(CC2CC2)(c2ccc3nc4ccccc4nc3c2)N1Cl | [
"path_len",
"heavy_atom_count",
"bond_count",
"atom_at_index",
"formula",
"element_counts"
] | {
"atom_at_index": {
"k": 13
},
"path_len": {
"i": 2,
"j": 8
}
} | compute | REQUEST: Quick question about this structure. Can you give me how far apart atoms 2 and 8 are, how many heavy atoms it has, how many bonds there are, what element is at index 13, its molecular formula, and the element counts with hydrogen included?
STRUCTURE:
SMILES: O=C([O-])C1C(I)CC(CC2CC2)(c2ccc3nc4ccccc4nc3c2)N1Cl... | DERIVATION: Walk 0 O H0 1 C H0 2 O H0 3 C H1 4 C H1 5 I H0 6 C H2 7 C H0 8 C H2 9 C H1 10 C H2 11 C H2 12 c H0 13 c H1 14 c H1 15 c H0 16 n H0 17 c H0 18 c H1 19 c H1 20 c H1 21 c H1 22 c H0 23 n H0 24 c H0 25 c H1 26 N H0 27 Cl H0. Tally C21 H18 Cl1 I1 N3 O2. Heavy 28. Closures: digit 1 joins 9 to 11, digit 2 joins 17... | ok | null | canonical | 2 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000062 | O[CH2][Pt][c]1cc(N2CCCC2)c2c(C3CCCCC3)cccc2c1 | [] | {} | out_of_scope | REQUEST: Could you look at this and tell me the formula for it and how many heavy atoms are in it?
STRUCTURE:
SMILES: O[CH2][Pt][c]1cc(N2CCCC2)c2c(C3CCCCC3)cccc2c1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the stru... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000063 | CCCc1c(F)noc1[CH](C)[Mn] | [] | {} | out_of_scope | REQUEST: I have a compound here and I need the molecular formula and the heavy atom count.
STRUCTURE:
SMILES: CCCc1c(F)noc1[CH](C)[Mn]
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, ord... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000064 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: Before I weigh this out I want the SMILES string for the record.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 C, 3 O, 4 C, 5 C, 6 C, 7 N, 8 N, 9 C, 10 C, 11 C, 12 C, 13 C, 14 C, 15 C, 16 C, 17 C, 18 C, 19 C, 20 C, 21 C, 22 C, 23 C, 24 C, 25 C, 26 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 single, 4-5 double, 5-6 singl... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 O H0 4 c H0 5 c H1 6 c H0 7 n H0 8 n H0 9 c H0 10 C H2 11 C H1 12 C H3 13 C H3 14 c H1 15 c H0 16 c H0 17 C H2 18 C H1 19 C H2 20 C H2 21 C H2 22 c H0 23 C H1 24 C H2 25 C H2 26 C H2. Tally C24 H34 N2 O1. Heavy 27. Closures: digit 1 joins 6 to 15, digit 2 joins 18 to 21, digit 3 ... | ok | null | canonical | 5 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"C"
],
[
3,
"O"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"N"
],
[
8,
"N"
],
[
9,
... | null | |
mp-10000065 | CC((=O)C1CNCC(C2CCC2)N1C(=O)O | [] | {} | syntax_invalid | REQUEST: Before I weigh this out I want what element sits at index 3, the count of non hydrogen atoms, the molecular formula in Hill order, the steps between atom 13 and atom 6, the bond count for the skeleton, and a per element breakdown.
STRUCTURE:
SMILES: CC((=O)C1CNCC(C2CCC2)N1C(=O)O
CONVENTIONS: Report the molec... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000066 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I am checking a supplier record and I need the SMILES string I should store.
STRUCTURE:
ATOMS: 0 F, 1 C, 2 F, 3 C, 4 C, 5 C, 6 Cl, 7 C, 8 C, 9 C, 10 N, 11 C, 12 N, 13 C, 14 C, 15 C, 16 C, 17 C, 18 N, 19 C
BONDS: 0-1 single, 1-2 single, 1-3 single, 3-4 single, 4-5 single, 4-7 double, 5-6 single, 7-8 single, 8-... | DERIVATION: Walk 0 F H0 1 C H1 2 F H0 3 c H0 4 c H0 5 C H2 6 Cl H0 7 c H1 8 c H1 9 c H0 10 n H0 11 c H0 12 N H1 13 C H1 14 C H2 15 C H2 16 C H2 17 c H1 18 n H0 19 c H0. Tally C14 H14 Cl1 F2 N3. Heavy 20. Closures: digit 1 joins 13 to 16, digit 2 joins 3 to 19, digit 3 joins 9 to 19. read the table in index order and cl... | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"F"
],
[
1,
"C"
],
[
2,
"F"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"Cl"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000067 | [O-]C1NC(C(C(=O)[O-])C1[N+]([O-])=O)[O-] | [
"formula",
"element_counts",
"atom_at_index"
] | {
"atom_at_index": {
"k": 6
}
} | near_miss | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label, the count of each element on the label, and the atom at index 6 for the record.
STRUCTURE:
SMILES: [O-]C1NC(C(C(=O)[O-])C1[N+]([O-])=O)[O-]
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first,... | DERIVATION: Walk 0 O H0 1 C H1 2 N H1 3 C H1 4 C H1 5 C H0 6 O H0 7 O H0 8 C H1 9 N H0 10 O H0 11 O H0 12 O H0. Tally C5 H5 N2 O6. Heavy 13. Closures: digit 1 joins 1 to 8. formula C5H5N2O6-3. element_counts from the tally. index 6 is O.
```json
{"status": "ok", "formula": "C5H5N2O6-3", "element_counts": {"C": 5, "H":... | ok | null | random | 7 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000068 | [N-]=[N+]=Nc1ncc2nc(OP(=O)(O)O)ccc2c1P(=O)(O)O | [
"heavy_atom_count",
"atom_at_index",
"formula"
] | {
"atom_at_index": {
"k": 18
}
} | near_miss | REQUEST: Working up a sample today. Please report the heavy atom total, which element is at position 18, and the empirical composition.
STRUCTURE:
SMILES: [N-]=[N+]=Nc1ncc2nc(OP(=O)(O)O)ccc2c1P(=O)(O)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remainin... | DERIVATION: Walk 0 N H0 1 N H0 2 N H0 3 c H0 4 n H0 5 c H1 6 c H0 7 n H0 8 c H0 9 O H0 10 P H0 11 O H0 12 O H1 13 O H1 14 c H1 15 c H1 16 c H0 17 c H0 18 P H0 19 O H0 20 O H1 21 O H1. Tally C8 H7 N5 O7 P2. Heavy 22. Closures: digit 1 joins 6 to 16, digit 2 joins 3 to 17. heavy_atom_count 22. index 18 is P. formula C8H7... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000069 | C1CC(C(C(C(=O)O)CC(CC(C)C)C1)C1CCCCC1)OCCC | [
"path_len",
"bond_count",
"atom_at_index",
"element_counts"
] | {
"atom_at_index": {
"k": 14
},
"path_len": {
"i": 22,
"j": 24
}
} | compute | REQUEST: For my notebook I need the bond distance from atom 22 to atom 24, the number of bonds, the atom at index 14, and how many of each element there are.
STRUCTURE:
SMILES: C1CC(C(C(C(=O)O)CC(CC(C)C)C1)C1CCCCC1)OCCC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second,... | DERIVATION: Walk 0 C H2 1 C H2 2 C H1 3 C H1 4 C H1 5 C H0 6 O H0 7 O H1 8 C H2 9 C H1 10 C H2 11 C H1 12 C H3 13 C H3 14 C H2 15 C H1 16 C H2 17 C H2 18 C H2 19 C H2 20 C H2 21 O H0 22 C H2 23 C H2 24 C H3. Tally C22 H40 O3. Heavy 25. Closures: digit 1 joins 0 to 14, digit 2 joins 15 to 20. path 22 to 24 via 22 23 24 ... | ok | null | random | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000070 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I am checking a supplier record and I need the SMILES string I should store.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 O, 3 N, 4 C, 5 C, 6 Si, 7 C, 8 C, 9 C, 10 C, 11 N, 12 C, 13 C, 14 C, 15 C, 16 O, 17 C, 18 C, 19 N
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 single, 4-5 double, 5-6 single, 5-11 single, 6-7 single, 6... | DERIVATION: Walk 0 C H3 1 C H2 2 O H0 3 n H0 4 c H1 5 c H0 6 Si H0 7 C H3 8 C H3 9 C H2 10 C H3 11 n H0 12 c H0 13 C H1 14 C H2 15 C H2 16 O H0 17 C H2 18 C H2 19 N H1. Tally C14 H27 N3 O2 Si1. Heavy 20. Closures: digit 1 joins 3 to 12, digit 2 joins 13 to 19. read the table in index order and close the rings.
```json... | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"O"
],
[
3,
"N"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"Si"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000071 | CCCOC(=OCC | [] | {} | syntax_invalid | REQUEST: I am checking a supplier record and I need the atom at index 4 for the record, the molecular formula as written on a label, the number of bonds in the skeleton, the bond distance between 2 and 6, and the count of each element on the label.
STRUCTURE:
SMILES: CCCOC(=OCC
CONVENTIONS: Report the molecular formu... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | drop_close_paren | |
mp-10000072 | CC[N+](C)(C)c1cc2c(c1)CCC2 | [] | {} | chem_invalid | REQUEST: Setting up a reaction. I need the number of non hydrogen atoms, which element is at index 13, the formula I should put on the vial, and the total bonds in the structure.
STRUCTURE:
SMILES: CC[N+](C)(C)c1cc2c(c1)CCC2
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen se... | DERIVATION: Read the structure. It does not parse as a molecule: kekulization_failure. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "kekulization_failure"}
``` | invalid_structure | kekulization_failure | n/a | 8 | scaffold_enumerator | CC0-1.0 | train | null | contract_aromatic_ring | |
mp-10000073 | CNNCNCCNOOOCOCOCCCCCOCCCCNCCNONNCCOOCCCCCNOOOOCCCCNOCCCCCCCNCOC | [] | {} | out_of_scope | REQUEST: For my notebook I need the formula and the number of heavy atoms.
STRUCTURE:
SMILES: CNNCNCCNOOOCOCOCCCCCOCCCCNCCNONNCCOOCCCCCNOOOOCCCCNOCCCCCCCNCOC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure ... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000074 | NC(=O)C[C@H](N)C(=O)O | [
"element_counts",
"bond_count",
"heavy_atom_count"
] | {} | compute | REQUEST: Before I weigh this out I want a per element breakdown, the bond count for the skeleton, and the count of non hydrogen atoms.
STRUCTURE:
SMILES: NC(=O)C[C@H](N)C(=O)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically;... | DERIVATION: Walk 0 N H2 1 C H0 2 O H0 3 C H2 4 C H1 5 N H2 6 C H0 7 O H0 8 O H1. Tally C4 H8 N2 O3. Heavy 9. No ring closures. element_counts from the tally. bond_count 8. heavy_atom_count 9.
```json
{"status": "ok", "element_counts": {"C": 4, "H": 8, "N": 2, "O": 3}, "bond_count": 8, "heavy_atom_count": 9}
``` | ok | null | canonical | 5 | wwPDB CCD | ASN | CC0-1.0 | train | null | null |
mp-10000075 | CC[N+](C)(C)c1nn(CCO)c(N2CCO(C)CC2)c1CC1CCC1 | [] | {} | chem_invalid | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label, the heavy atoms total, the count of each element on the label, the bond distance between 12 and 16, the number of bonds in the skeleton, and the atom at index 15 for the record.
STRUCTURE:
SMILES: CC[N+](C)(C)c1nn(CCO)c(N2... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | overbond_heteroatom | |
mp-10000076 | QCNC(=O)c1nnn([N+](C)(C)C)c1C | [] | {} | syntax_invalid | REQUEST: Could you look at this and tell me which element occupies index 11, how many heavy atoms are in it, the formula for it, the number of atoms of each element, the shortest path from atom 0 to atom 11, and how many bonds it has?
STRUCTURE:
SMILES: QCNC(=O)c1nnn([N+](C)(C)C)c1C
CONVENTIONS: Report the molecular ... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000077 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: Working up a sample today. Please report a SMILES string for it.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 N, 3 C, 4 O, 5 C, 6 C, 7 O, 8 C, 9 C, 10 S, 11 S, 12 C, 13 C, 14 C, 15 O, 16 N, 17 C, 18 C, 19 C, 20 O, 21 N, 22 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 double, 3-5 single, 5-6 single, 6-7 single, 6-10 sing... | DERIVATION: Walk 0 C H3 1 C H2 2 N H1 3 C H0 4 O H0 5 C H2 6 C H1 7 O H0 8 C H2 9 C H3 10 S H0 11 S H0 12 C H1 13 C H2 14 C H0 15 O H0 16 N H1 17 C H2 18 C H3 19 C H0 20 O H0 21 N H1 22 C H3. Tally C14 H27 N3 O4 S2. Heavy 23. No ring closures. read the table in index order and close the rings.
```json
{"status": "ok",... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"N"
],
[
3,
"C"
],
[
4,
"O"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"O"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000078 | CC(=O)C1CCC(N2CCOC2)C(C2(CCC2)CN1 | [] | {} | syntax_invalid | REQUEST: Working up a sample today. Please report the total bonds, the path length between atoms 8 and 7, and the heavy atom total.
STRUCTURE:
SMILES: CC(=O)C1CCC(N2CCOC2)C(C2(CCC2)CN1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphab... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000079 | CNCC | [] | {} | out_of_scope | REQUEST: Before I weigh this out I want the molecular formula in Hill order and the count of non hydrogen atoms.
STRUCTURE:
SMILES: CNCC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, o... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000080 | CC(=O)NC(N)=NC(Q)C(Cl)(Cl)Cl | [] | {} | syntax_invalid | REQUEST: Before I weigh this out I want what element sits at index 9, the bond count for the skeleton, and the steps between atom 9 and atom 2.
STRUCTURE:
SMILES: CC(=O)NC(N)=NC(Q)C(Cl)(Cl)Cl
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 5 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000081 | CCCC(C(C)P(=O)(O)O)[N+](C)(C)C | [
"element_counts",
"path_len",
"bond_count",
"atom_at_index",
"formula"
] | {
"atom_at_index": {
"k": 13
},
"path_len": {
"i": 6,
"j": 10
}
} | near_miss | REQUEST: Before I weigh this out I want a per element breakdown, the steps between atom 6 and atom 10, the bond count for the skeleton, what element sits at index 13, and the molecular formula in Hill order.
STRUCTURE:
SMILES: CCCC(C(C)P(=O)(O)O)[N+](C)(C)C
CONVENTIONS: Report the molecular formula in Hill notation, ... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 C H1 4 C H1 5 C H3 6 P H0 7 O H0 8 O H1 9 O H1 10 N H0 11 C H3 12 C H3 13 C H3. Tally C9 H23 N1 O3 P1. Heavy 14. No ring closures. element_counts from the tally. path 6 to 10 via 6 4 3 10 is 3 bonds. bond_count 13. index 13 is C. formula C9H23NO3P+.
```json
{"status": "ok", "ele... | ok | null | canonical | 5 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000083 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: I am checking a supplier record and I need the SMILES string I should store.
STRUCTURE:
ATOMS: 0 O, 1 C, 2 C, 3 C, 4 N, 5 N, 6 C, 7 C, 8 C, 9 C, 10 C, 11 C, 12 C, 13 C, 14 C, 15 C, 16 C, 17 C, 18 C, 19 C, 20 C, 21 C, 22 C, 23 C, 24 C, 25 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 single, 4-5 single, 5-6... | DERIVATION: Walk 0 O H1 1 C H2 2 C H2 3 c H0 4 n H1 5 n H0 6 c H1 7 c H0 8 c H0 9 c H1 10 c H1 11 c H0 12 c H0 13 c H1 14 c H1 15 c H0 16 c H1 17 c H0 18 C H2 19 C H1 20 C H2 21 C H2 22 c H1 23 c H1 24 c H0 25 c H1. Tally C23 H22 N2 O1. Heavy 26. Closures: digit 1 joins 3 to 7, digit 2 joins 19 to 21, digit 3 joins 15 ... | ok | null | canonical | 7 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"O"
],
[
1,
"C"
],
[
2,
"C"
],
[
3,
"C"
],
[
4,
"N"
],
[
5,
"N"
],
[
6,
"C"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000084 | CNC | [] | {} | out_of_scope | REQUEST: Could you look at this and tell me the formula for it and how many heavy atoms are in it?
STRUCTURE:
SMILES: CNC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, order every elem... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000085 | Brc1c(C2CC2)csc2cncnc12 | [] | {} | chem_invalid | REQUEST: For my notebook I need how many of each element there are, the bond distance from atom 0 to atom 9, the formula, and the number of bonds.
STRUCTURE:
SMILES: Brc1c(C2CC2)csc2cncnc12
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements a... | DERIVATION: Read the structure. It does not parse as a molecule: kekulization_failure. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "kekulization_failure"}
``` | invalid_structure | kekulization_failure | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | carbon_to_chalcogen_aromatic | |
mp-10000088 | C[N+](C1OC([N+](=O)[O-])OC1[N+](C)(C)C)(C)C | [
"atom_at_index",
"bond_count",
"element_counts",
"path_len",
"heavy_atom_count"
] | {
"atom_at_index": {
"k": 13
},
"path_len": {
"i": 8,
"j": 4
}
} | near_miss | REQUEST: I have a compound here and I need which element sits at index 13, the bond count, the element counts including hydrogen, the shortest path between atoms 8 and 4, and the heavy atom count.
STRUCTURE:
SMILES: C[N+](C1OC([N+](=O)[O-])OC1[N+](C)(C)C)(C)C
CONVENTIONS: Report the molecular formula in Hill notation... | DERIVATION: Walk 0 C H3 1 N H0 2 C H1 3 O H0 4 C H1 5 N H0 6 O H0 7 O H0 8 O H0 9 C H1 10 N H0 11 C H3 12 C H3 13 C H3 14 C H3 15 C H3. Tally C9 H21 N3 O4. Heavy 16. Closures: digit 1 joins 2 to 9. index 13 is C. bond_count 16. element_counts from the tally. path 8 to 4 via 8 4 is 1 bonds. heavy_atom_count 16.
```json... | ok | null | random | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000089 | OCNC | [] | {} | out_of_scope | REQUEST: I have a compound here and I need the molecular formula and the heavy atom count.
STRUCTURE:
SMILES: OCNC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, order every element alp... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000090 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: Could you look at this and tell me this converted to a SMILES string?
STRUCTURE:
ATOMS: 0 C, 1 C, 2 N, 3 C, 4 C, 5 N, 6 C, 7 C, 8 C, 9 C, 10 P, 11 O, 12 O, 13 O
BONDS: 0-1 single, 1-2 single, 2-3 single, 2-8 single, 3-4 single, 4-5 single, 5-6 single, 5-7 single, 8-9 single, 9-10 single, 10-11 double, 10-12 s... | DERIVATION: Walk 0 C H3 1 C H2 2 N H0 3 C H2 4 C H2 5 N H0 6 C H3 7 C H3 8 C H2 9 C H2 10 P H0 11 O H0 12 O H1 13 O H1. Tally C8 H21 N2 O3 P1. Heavy 14. No ring closures. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CCN(CCN(C)C)CCP(=O)(O)O"}
``` | ok | null | canonical | 6 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"N"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"N"
],
[
6,
"C"
],
[
7,
"C"
],
[
8,
"C"
],
[
9,
... | null | |
mp-10000091 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: For my notebook I need the SMILES string.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 O, 3 C, 4 C, 5 C, 6 C, 7 O, 8 O, 9 C, 10 C, 11 C, 12 C, 13 N, 14 C, 15 C, 16 N, 17 C, 18 C
BONDS: 0-1 single, 1-2 double, 1-3 single, 3-4 single, 4-5 single, 4-13 single, 5-6 single, 5-9 single, 6-7 double, 6-8 single, 9-10 single, 10-11 ... | DERIVATION: Walk 0 C H3 1 C H0 2 O H0 3 C H2 4 C H1 5 C H1 6 C H0 7 O H0 8 O H1 9 C H1 10 C H2 11 C H2 12 C H2 13 N H0 14 C H2 15 C H2 16 N H1 17 C H2 18 C H2. Tally C14 H24 N2 O3. Heavy 19. Closures: digit 1 joins 9 to 12, digit 2 joins 13 to 18. read the table in index order and close the rings.
```json
{"status": "... | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"O"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"C"
],
[
6,
"C"
],
[
7,
"O"
],
[
8,
"O"
],
[
9,
... | null | |
mp-10000092 | CC[Si](C)(C)C(C#CC(CS(C)=O)[B-](F)(F)F)C[N+](=O)[O-] | [
"bond_count",
"atom_at_index",
"formula",
"element_counts",
"heavy_atom_count",
"path_len"
] | {
"atom_at_index": {
"k": 14
},
"path_len": {
"i": 13,
"j": 14
}
} | near_miss | REQUEST: Working up a sample today. Please report the total bonds, which element is at position 14, the empirical composition, the counts of each element, the heavy atom total, and the path length between atoms 13 and 14.
STRUCTURE:
SMILES: CC[Si](C)(C)C(C#CC(CS(C)=O)[B-](F)(F)F)C[N+](=O)[O-]
CONVENTIONS: Report the ... | DERIVATION: Walk 0 C H3 1 C H2 2 Si H0 3 C H3 4 C H3 5 C H1 6 C H0 7 C H0 8 C H1 9 C H2 10 S H0 11 C H3 12 O H0 13 B H0 14 F H0 15 F H0 16 F H0 17 C H2 18 N H0 19 O H0 20 O H0. Tally C11 H20 B1 F3 N1 O3 S1 Si1. Heavy 21. No ring closures. bond_count 20. index 14 is F. formula C11H20BF3NO3SSi-. element_counts from the t... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000093 | CC(C)C(=O)c1cc(Cl)cc(CC2CC2)c1[B-](F)(F)F | [
"heavy_atom_count",
"formula",
"path_len",
"bond_count",
"element_counts"
] | {
"path_len": {
"i": 8,
"j": 14
}
} | compute | REQUEST: Before I weigh this out I want the count of non hydrogen atoms, the molecular formula in Hill order, the steps between atom 8 and atom 14, the bond count for the skeleton, and a per element breakdown.
STRUCTURE:
SMILES: CC(C)C(=O)c1cc(Cl)cc(CC2CC2)c1[B-](F)(F)F
CONVENTIONS: Report the molecular formula in Hi... | DERIVATION: Walk 0 C H3 1 C H1 2 C H3 3 C H0 4 O H0 5 c H0 6 c H1 7 c H0 8 Cl H0 9 c H1 10 c H0 11 C H2 12 C H1 13 C H2 14 C H2 15 c H0 16 B H0 17 F H0 18 F H0 19 F H0. Tally C14 H16 B1 Cl1 F3 O1. Heavy 20. Closures: digit 1 joins 12 to 14, digit 2 joins 5 to 15. heavy_atom_count 20. formula C14H16BClF3O-. path 8 to 14... | ok | null | canonical | 5 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000094 | CN(C)C(=O)c1ncncn1 | [
"atom_at_index",
"element_counts",
"formula",
"heavy_atom_count",
"path_len"
] | {
"atom_at_index": {
"k": 3
},
"path_len": {
"i": 10,
"j": 7
}
} | compute | REQUEST: I have a compound here and I need which element sits at index 3, the element counts including hydrogen, the molecular formula, the heavy atom count, and the shortest path between atoms 10 and 7.
STRUCTURE:
SMILES: CN(C)C(=O)c1ncncn1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon f... | DERIVATION: Walk 0 C H3 1 N H0 2 C H3 3 C H0 4 O H0 5 c H0 6 n H0 7 c H1 8 n H0 9 c H1 10 n H0. Tally C6 H8 N4 O1. Heavy 11. Closures: digit 1 joins 5 to 10. index 3 is C. element_counts from the tally. formula C6H8N4O. heavy_atom_count 11. path 10 to 7 via 10 9 8 7 is 3 bonds.
```json
{"status": "ok", "atom_at_index"... | ok | null | canonical | 1 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000096 | OCCC1SC(CCCCCC2)C1N1CCOCC1 | [] | {} | syntax_invalid | REQUEST: For my notebook I need the number of heavy atoms, the number of bonds, the atom at index 17, and the formula.
STRUCTURE:
SMILES: OCCC1SC(CCCCCC2)C1N1CCOCC1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the str... | DERIVATION: Read the structure. It does not parse as a molecule: unclosed_ring_bond. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unclosed_ring_bond"}
``` | invalid_structure | unclosed_ring_bond | n/a | 3 | scaffold_enumerator | CC0-1.0 | train | null | drop_ring_digit | |
mp-10000098 | O=Cc1cccc2c1C=CEe2 | [] | {} | syntax_invalid | REQUEST: I have a compound here and I need the element counts including hydrogen, the shortest path between atoms 6 and 3, the heavy atom count, and which element sits at index 1.
STRUCTURE:
SMILES: O=Cc1cccc2c1C=CEe2
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, t... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000099 | OCCOOOCOOCCCNOOCOCCCCNCCOCOCOOCCNONNCOCCCOCOONOCCOOCCCCCCOCCONCOC | [] | {} | out_of_scope | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label and the heavy atoms total.
STRUCTURE:
SMILES: OCCOOOCOOCCCNOOCOCCCCNCCOCOCOOCCNONNCOCCCOCOONOCCOOCCCCCCOCCONCOC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the re... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000100 | COc1ccc(Nc2ncc3nc(Nc4ccccc4F)n(C4CCCC4)c3n2)cc1 | [
"element_counts",
"atom_at_index",
"bond_count",
"heavy_atom_count",
"formula"
] | {
"atom_at_index": {
"k": 0
}
} | compute | REQUEST: Could you look at this and tell me the number of atoms of each element, which element occupies index 0, how many bonds it has, how many heavy atoms are in it, and the formula for it?
STRUCTURE:
SMILES: COc1ccc(Nc2ncc3nc(Nc4ccccc4F)n(C4CCCC4)c3n2)cc1
CONVENTIONS: Report the molecular formula in Hill notation,... | DERIVATION: Walk 0 C H3 1 O H0 2 c H0 3 c H1 4 c H1 5 c H0 6 N H1 7 c H0 8 n H0 9 c H1 10 c H0 11 n H0 12 c H0 13 N H1 14 c H0 15 c H1 16 c H1 17 c H1 18 c H1 19 c H0 20 F H0 21 n H0 22 C H1 23 C H2 24 C H2 25 C H2 26 C H2 27 c H0 28 n H0 29 c H1 30 c H1. Tally C23 H23 F1 N6 O1. Heavy 31. Closures: digit 1 joins 14 to ... | ok | null | canonical | 6 | wwPDB CCD | JBI | CC0-1.0 | train | null | null |
mp-10000101 | CCCCc1nn([C]([Pt])=O)nc1C(=O)OC | [] | {} | out_of_scope | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label and the heavy atoms total.
STRUCTURE:
SMILES: CCCCc1nn([C]([Pt])=O)nc1C(=O)OC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; i... | DERIVATION: Read the structure before counting anything. This request is out of scope because it contains an element outside the supported set stated in the conventions, so the reason code is element_not_supported. The correct response is to decline rather than to report values that would look authoritative and be unsu... | out_of_scope | element_not_supported | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000103 | CCC(=O)C(=O)CC[B-](F)(Ee)F | [] | {} | syntax_invalid | REQUEST: I am checking a supplier record and I need the molecular formula as written on a label, the number of bonds in the skeleton, the atom at index 3 for the record, the bond distance between 9 and 2, and the heavy atoms total.
STRUCTURE:
SMILES: CCC(=O)C(=O)CC[B-](F)(Ee)F
CONVENTIONS: Report the molecular formul... | DERIVATION: Read the structure. It does not parse as a molecule: unknown_element. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unknown_element"}
``` | invalid_structure | unknown_element | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | unknown_element_symbol | |
mp-10000104 | Cc1ccc(/C=N/NC(=S)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)cc1 | [
"path_len",
"bond_count",
"element_counts"
] | {
"path_len": {
"i": 3,
"j": 18
}
} | compute | REQUEST: Before I weigh this out I want the steps between atom 3 and atom 18, the bond count for the skeleton, and a per element breakdown.
STRUCTURE:
SMILES: Cc1ccc(/C=N/NC(=S)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)cc1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen sec... | DERIVATION: Walk 0 C H3 1 c H0 2 c H1 3 c H1 4 c H0 5 C H1 6 N H0 7 N H1 8 C H0 9 S H0 10 N H1 11 C H1 12 O H0 13 C H1 14 C H2 15 O H1 16 C H1 17 O H1 18 C H1 19 O H1 20 C H1 21 O H1 22 c H1 23 c H1. Tally C15 H21 N3 O5 S1. Heavy 24. Closures: digit 1 joins 11 to 20, digit 2 joins 1 to 23. path 3 to 18 via 3 4 5 6 7 8 ... | ok | null | canonical | 5 | wwPDB CCD | 18S | CC0-1.0 | train | null | null |
mp-10000106 | COCCN(C)C(=OCC(Cl)(Cl)Cl | [] | {} | syntax_invalid | REQUEST: I have a compound here and I need the molecular formula, the element counts including hydrogen, the bond count, the heavy atom count, and the shortest path between atoms 10 and 1.
STRUCTURE:
SMILES: COCCN(C)C(=OCC(Cl)(Cl)Cl
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hyd... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 1 | scaffold_enumerator | CC0-1.0 | train | null | drop_close_paren | |
mp-10000107 | CC(=O)Oc1cn([N+](C)(C)Ccc1Br | [] | {} | syntax_invalid | REQUEST: Could you look at this and tell me the formula for it, which element occupies index 13, how many heavy atoms are in it, the shortest path from atom 0 to atom 5, the number of atoms of each element, and how many bonds it has?
STRUCTURE:
SMILES: CC(=O)Oc1cn([N+](C)(C)Ccc1Br
CONVENTIONS: Report the molecular fo... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 6 | scaffold_enumerator | CC0-1.0 | train | null | drop_close_paren | |
mp-10000108 | CCCNC(COC(C)C)SSC(C)C(F)(F)F | [
"heavy_atom_count",
"element_counts",
"bond_count",
"path_len",
"formula",
"atom_at_index"
] | {
"atom_at_index": {
"k": 1
},
"path_len": {
"i": 8,
"j": 7
}
} | compute | REQUEST: For my notebook I need the number of heavy atoms, how many of each element there are, the number of bonds, the bond distance from atom 8 to atom 7, the formula, and the atom at index 1.
STRUCTURE:
SMILES: CCCNC(COC(C)C)SSC(C)C(F)(F)F
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon ... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 N H1 4 C H1 5 C H2 6 O H0 7 C H1 8 C H3 9 C H3 10 S H0 11 S H0 12 C H1 13 C H3 14 C H0 15 F H0 16 F H0 17 F H0. Tally C11 H22 F3 N1 O1 S2. Heavy 18. No ring closures. heavy_atom_count 18. element_counts from the tally. bond_count 17. path 8 to 7 via 8 7 is 1 bonds. formula C11H22... | ok | null | canonical | 3 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000109 | CN(C)N(1CC(CO)CC1C=O | [] | {} | syntax_invalid | REQUEST: Setting up a reaction. I need which element is at index 10, the total bonds in the structure, the number of non hydrogen atoms, the element count including hydrogen, the formula I should put on the vial, and how far apart 10 and 1 sit.
STRUCTURE:
SMILES: CN(C)N(1CC(CO)CC1C=O
CONVENTIONS: Report the molecular... | DERIVATION: Read the structure. It does not parse as a molecule: unbalanced_parenthesis. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "unbalanced_parenthesis"}
``` | invalid_structure | unbalanced_parenthesis | n/a | 8 | scaffold_enumerator | CC0-1.0 | train | null | add_open_paren | |
mp-10000110 | CCC(=O)N(CC[N+](=O)[O-])P(=O)(O)O | [
"heavy_atom_count",
"path_len",
"formula",
"element_counts",
"bond_count"
] | {
"path_len": {
"i": 4,
"j": 8
}
} | near_miss | REQUEST: Working up a sample today. Please report the heavy atom total, the path length between atoms 4 and 8, the empirical composition, the counts of each element, and the total bonds.
STRUCTURE:
SMILES: CCC(=O)N(CC[N+](=O)[O-])P(=O)(O)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon fir... | DERIVATION: Walk 0 C H3 1 C H2 2 C H0 3 O H0 4 N H0 5 C H2 6 C H2 7 N H0 8 O H0 9 O H0 10 P H0 11 O H0 12 O H1 13 O H1. Tally C5 H11 N2 O6 P1. Heavy 14. No ring closures. heavy_atom_count 14. path 4 to 8 via 4 5 6 7 8 is 4 bonds. formula C5H11N2O6P. element_counts from the tally. bond_count 13.
```json
{"status": "ok"... | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000111 | ONC | [] | {} | out_of_scope | REQUEST: Working up a sample today. Please report the empirical composition and the heavy atom total.
STRUCTURE:
SMILES: ONC
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the remaining elements alphabetically; if the structure contains no carbon, order every e... | DERIVATION: Read the structure before counting anything. This request is out of scope because its heavy atom count falls outside the supported size range stated in the conventions, so the reason code is size_out_of_range. The correct response is to decline rather than to report values that would look authoritative and ... | out_of_scope | size_out_of_range | n/a | 4 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000112 | c1ccc2c(N3CCOCC3)c3cccc3cc2c1 | [] | {} | chem_invalid | REQUEST: Quick question about this structure. Can you give me how many heavy atoms it has, what element is at index 8, and how far apart atoms 10 and 11 are?
STRUCTURE:
SMILES: c1ccc2c(N3CCOCC3)c3cccc3cc2c1
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the rem... | DERIVATION: Read the structure. It does not parse as a molecule: kekulization_failure. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "kekulization_failure"}
``` | invalid_structure | kekulization_failure | n/a | 2 | scaffold_enumerator | CC0-1.0 | train | null | contract_aromatic_ring | |
mp-10000113 | c12c(ccnc2c(cc([B-](F)(F)F)c1)NC1CCC1)O | [
"heavy_atom_count",
"bond_count",
"element_counts",
"atom_at_index"
] | {
"atom_at_index": {
"k": 1
}
} | compute | REQUEST: Quick question about this structure. Can you give me how many heavy atoms it has, how many bonds there are, the element counts with hydrogen included, and what element is at index 1?
STRUCTURE:
SMILES: c12c(ccnc2c(cc([B-](F)(F)F)c1)NC1CCC1)O
CONVENTIONS: Report the molecular formula in Hill notation, meaning... | DERIVATION: Walk 0 c H0 1 c H0 2 c H1 3 c H1 4 n H0 5 c H0 6 c H0 7 c H1 8 c H0 9 B H0 10 F H0 11 F H0 12 F H0 13 c H1 14 N H1 15 C H1 16 C H2 17 C H2 18 C H2 19 O H1. Tally C13 H13 B1 F3 N2 O1. Heavy 20. Closures: digit 1 joins 0 to 5, digit 2 joins 0 to 13, digit 3 joins 15 to 18. heavy_atom_count 20. bond_count 22. ... | ok | null | random | 2 | scaffold_enumerator | CC0-1.0 | train | null | null | |
mp-10000114 | CCCO(C1OCCOC1N1CCCC1)C | [] | {} | chem_invalid | REQUEST: I am checking a supplier record and I need the count of each element on the label, the atom at index 8 for the record, and the bond distance between 0 and 8.
STRUCTURE:
SMILES: CCCO(C1OCCOC1N1CCCC1)C
CONVENTIONS: Report the molecular formula in Hill notation, meaning carbon first, hydrogen second, then the r... | DERIVATION: Read the structure. It does not parse as a molecule: valence_error. No atom walk is possible, so no counts are reported and no value is invented for a structure that cannot exist.
```json
{"status": "invalid_structure", "reason": "valence_error"}
``` | invalid_structure | valence_error | n/a | 7 | scaffold_enumerator | CC0-1.0 | train | null | overbond_heteroatom | |
mp-10000116 | null | [
"smiles_from_graph"
] | {} | graph2smiles | REQUEST: Working up a sample today. Please report a SMILES string for it.
STRUCTURE:
ATOMS: 0 C, 1 C, 2 C, 3 C, 4 C, 5 S, 6 C, 7 C, 8 F, 9 C
BONDS: 0-1 single, 1-2 single, 2-3 single, 3-4 double, 4-5 single, 5-6 single, 6-7 single, 6-9 double, 7-8 single, 9-3 single
CONVENTIONS: Report the molecular formula in Hill n... | DERIVATION: Walk 0 C H3 1 C H2 2 C H2 3 c H0 4 c H1 5 s H0 6 c H0 7 C H2 8 F H0 9 c H1. Tally C8 H11 F1 S1. Heavy 10. Closures: digit 1 joins 3 to 9. read the table in index order and close the rings.
```json
{"status": "ok", "smiles_from_graph": "CCCc1csc(CF)c1"}
``` | ok | null | canonical | 4 | scaffold_enumerator | CC0-1.0 | train | {
"atoms": [
[
0,
"C"
],
[
1,
"C"
],
[
2,
"C"
],
[
3,
"C"
],
[
4,
"C"
],
[
5,
"S"
],
[
6,
"C"
],
[
7,
"C"
],
[
8,
"F"
],
[
9,
... | null |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.