Innovator-VL
Collection
A Multimodal Large Language Model for Scientific Discovery
•
10 items
•
Updated
id
stringlengths 1
4
| question
stringclasses 60
values | answer
stringlengths 1
2.6k
| images
images listlengths 1
4
|
|---|---|---|---|
1
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**n1c(N(*)C2CCN(**)CC2)nc2c(*)cc(*)cc12<sep><a>0:R[1]</a><a>1:G</a><a>5:R[5]</a><a>10:Alk</a><a>11:R[7a]</a><a>17:R[2b]</a><a>20:R[3a]</a>
| |
2
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*C(C1C2C(=CC=CC=2)SC=1)=O<sep><a>0:<dum></a>
| |
3
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C(C1=CC=CN=C1N(C)C)*<sep><a>10:<dum></a>
| |
4
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(C)[C@H]1CC[C@H](O*)CC1<sep><a>8:<dum></a>
| |
5
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
N[C@@H]1C[C@@H](C(O)=O)C1.*<sep><a>8:HCl</a>
| |
6
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*C(*)Cn1c(=O)oc2ccc(Br)cc21<sep><a>0:Me</a><a>2:NHBoc</a>
| |
7
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
[N+]([O-])(=O)[C@]1(C)CCC(=O)N(Cc2ccccc2)C1=O<sep>
| |
8
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCOC(=O)C(C)n1ccnc1C(=O)O<sep>
| |
9
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCOC(C(C(OCC)=O)(C([2H])([2H])[2H])C)=O<sep>
| |
10
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C=CCCn1ccnc1C(=O)O<sep>
| |
11
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CC(Nc1ccc2c(c1)OCCO2)C(=O)Nc1cc(C(F)(F)F)ccc1N1CCOCC1<sep>
| |
12
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(c1ccco1)[C@@H]1C(=O)c2ccccc2O[C@@H]1c1ccc(O)c(OCC2CC2)c1<sep>
| |
13
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(C1CCS(=O)(=O)CC1)N1CCN(c2ccccn2)CC1c1cccc(F)c1F<sep>
| |
14
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCC(=O)Nc1nc(C)c(C(=O)N[C@@H](C)c2ccc(O[C@@H]3CCN(c4ccc(OC[C@H]5CC5(F)F)cn4)C3)cc2)s1<sep>
| |
15
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCOC(=O)c1c(NC(=O)c2c[nH]c3c(OC)cc(Cl)c(OC)c3c2=O)sc(C)c1-c1ccc(Cl)cc1<sep>
| |
16
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCNc1nc(Cl)c(-c2ccccc2)n(CC(=O)NCc2ccc(C(=N)N)cc2)c1=O<sep>
| |
17
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CC1(C)C[C@H](Nc2ccc3cc(Br)ccc3c2)C(C)(C)O1<sep>
| |
18
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
Cc1cc(C[C@@]2(C)C[C@H](c3cccc(Cl)c3)[C@@H](c3ccc(Cl)cc3)N([C@H](CS(=O)(=O)C(C)(C)C)C3CC3)C2=O)ncc1C(=O)O<sep>
| |
19
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCCCCCCCCCCCCCCCOCCCOP(=O)(O)COC(COCC)Cn1cnc2c(N)ncnc12<sep>
| |
20
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(N/N=C/c1ccc(-c2cccc(C(F)(F)F)c2)o1)c1cc(I)ccc1Cl<sep>
| |
21
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C[C@@H](NCCCC#N)c1cscc1Br<sep>
| |
22
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(O)CCC(C(=O)O)c1csc(NC(=O)c2cccc(COc3ccccc3)n2)n1<sep>
| |
23
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
COc1ccc(NC(=S)NC(=O)c2ccccc2)cn1<sep>
| |
24
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
COc1cc(C)c(N2CC(C)(CO)C2)c(C)c1<sep>
| |
25
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
Cc1cc(O)c(C(=O)/C=C/c2ccc(Cl)c(Cl)c2)c(=O)o1<sep>
| |
26
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CC(=O)NS(=O)(=O)c1ccc(-n2ccc3c(c2=O)C(=O)OC3(C)C)cc1<sep>
| |
27
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C[C@]12CCC(=O)CC1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@@H](O)[C@H](CCCO)C[C@@H]12<sep>
| |
28
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
Cc1nc2ccc(Oc3ccc4ncsc4c3)nc2c(=O)n1C[C@H]1CCCN(C(C)C)C1<sep>
| |
29
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CC1=CC=C[CH]N1Cc1cccc(C)c1<sep>
| |
30
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
Cc1cc(F)c([N+](=O)[O-])cc1S(=O)(=O)NCC(=O)NCC(F)(F)F<sep>
| |
31
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCN(CC)C(=O)N1CCN(CCc2ccncc2)CC1<sep>
| |
32
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CSc1ccccc1NCCCCCC(=O)O<sep>
| |
33
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*c1ccc2c(c1)OC/C(=C\c1ccc(O)c(O)c1)C2=O<sep><a>0:OCH3</a>
| |
34
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*O[Si](*)(C)Cc1ccc(Br)cc1<sep>|Sg:n|
| |
35
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*c1cc(Cl)c(Nc2c(*)cnc3cc4cc(OCCN5CCC(O)CC5)c(*)cc4cc23)cc1*<sep><a>0:Me</a><a>9:CN</a><a>28:OMe</a><a>35:OMe</a>
| |
36
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
Cc1cn(CCOc2ccc(Cl)cc2)c(=O)n(Cc2ccccc2)c1=O<sep>
| |
37
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
COc1ccc2c(c1)CCc1c(C(=O)Nc3cc(OC)c(Cl)cc3OC)noc1-2<sep>
| |
38
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*CCc1cc(OCCCCCCCCCCCC)c(C(*)=O)cc1C<sep>|Sg:n|
| |
39
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*C(*)=CCC/C(*)=C/CC/C(*)=C/CSc1ccccc1C(=O)OCCCCCCOc1no[n+]([O-])c1S(*)(=O)=O<sep><a>0:CH3</a><a>2:CH3</a><a>7:CH3</a><a>12:CH3</a><a>39:Ar</a>
| |
40
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*CC(C)(C)C1C(=O)N(c2ccccc2C)C(=O)C1*<sep>|Sg:n|
| |
41
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**1:*c(S(=O)(=O)Nc2cc(*)on2)c(*)c(*)c1[N+](=O)[O-]<sep><a>0:R[11]</a><a>1:Y</a><a>2:W</a><a>11:R[4d]</a><a>15:G[4]</a><a>17:Hyy</a>
| |
42
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CCNc1nc(NCC)n2c(SCC(=O)Nc3ccccc3F)nnc2n1<sep>
| |
43
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
c1ccc2c(c1)ccc1ccc3c4ccc5c(ccc6c7ccccc7c7ccc8ccccc8c7c65)c4c4ccccc4c3c12<sep>
| |
44
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**S(=O)(=O)c1nnc(N(*)C(=*)C2(*)C*(*)C2*)s1<sep><a>0:<dum></a><a>1:R[b]</a><a>10:Q</a><a>12:W</a><a>14:R[3]</a><a>16:R[3]</a><a>17:R[T]</a><a>19:R[14]</a>
| |
45
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*CCCCCCCCCCCC(=O)NCCCCCCCCCCCCCC/C=C/COCC(=O)O*<sep>|Sg:n|
| |
46
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*[Ge](*)(*)CCCCCCCCCCOc1ccc(-c2ccc(-c3ccc(COC*)cc3)cc2)cc1<sep><a>3:CH3</a><a>30:Am</a>|Sg:n|
| |
47
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
b1c2c(cc3c1c1cc4cc5ccc6c(c5cc4cc1c1ccccc31)=CC=6)-c1occc1-2<sep>
| |
48
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*c1cn2cc(-c3cc4ccc(N5CCNCC5)cc4oc3=O)nc2c(*)n1<sep><a>0:Me</a><a>26:Me</a>
| |
49
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*CCOCCOCC(C*)OC(=O)c1ccc(-c2ccc([N+](=O)[O-])cc2)cc1<sep>|Sg:n|
| |
50
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**1c(*)ccc(-c2nc(C(*)c3*(*)c(*)ccc3*)sc2C(*)C(=O)O)c1*<sep><a>0:R[13]</a><a>1:Z</a><a>3:X</a><a>11:R[8]</a><a>13:Y</a><a>14:R[3]</a><a>16:R[2]</a><a>20:R[4]</a><a>24:Q</a><a>29:R[7]</a><r>0:R[15]?r</r>
| |
51
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**1C*=C(*)C(C(*)N(*)C(=O)c2*(*)ccn2C(*)c2c*cc(*)c2*)=C1*<sep><a>0:R[12]</a><a>1:Q</a><a>3:X</a><a>5:W[6]</a><a>8:R[5]</a><a>10:R[13]</a><a>14:R[4]</a><a>15:Hal</a><a>20:R[c]</a><a>23:M</a><a>26:R[5c]</a><a>28:M</a><a>30:R[1]</a>
| |
52
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
COc1ccc(-c2ccc3[nH]c(=O)c4nnn(-c5ccc(N6CCNCC6)c(C)c5)c4c3c2)cn1<sep>
| |
53
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*Oc1ccc(Oc2ccc(C(=O)c3ccc(C(=O)c4ccc(Oc5ccc(*)cc5)cc4)cc3)cc2)cc1C(C)(C)C<sep>|Sg:n|
| |
54
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*OC(*)CCOC(=O)Nc1cc(Br)cc(Oc2ccc(C(*)=O)cc2)c1<sep><a>3:CH3</a>|Sg:n|
| |
55
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*Oc1ccc(/C=C/Nc2ccc(/C=C/c3ccc(OCCC(*)=O)cc3)cc2)cc1<sep>|Sg:n|
| |
56
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
**(c1*c2c(*(*)c1*)CC(*)N(*)C2)S(=O)(=O)c1*c(*)c(*)c(*)c1<sep><a>0:R[6y]</a><a>1:Q'</a><a>3:R[6]</a><a>6:R[7]</a><a>7:R[17]</a><a>9:R[5]</a><a>12:Yev</a><a>14:R[3b]</a><a>20:Z</a><a>22:R[5]</a><a>24:R[4]</a><a>26:R[11]</a>
| |
57
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*CCn1c(*(*)(*)C(*)(*)c2ccc(NC(=O)N(*)c3c*c4c(c3)OC(*)O4)cc2)nc2*c(*)c(*)*(*)c12<sep><a>0:R[9]</a><a>5:X"</a><a>6:R[8]</a><a>7:R[15]</a><a>9:R[16]</a><a>10:R[36]</a><a>19:R[13]</a><a>22:R[3]</a><a>28:R[34]</a><a>34:R[9]</a><a>36:R[8]</a><a>38:R[14]</a><a>39:R[2]</a><a>40:R[2]</a><r>1:R[44]</r>
| |
58
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=P1(CO*)O[C@H](C2C=C(Cl)C=CC=2)CCO1<sep><a>4:<dum></a>
| |
59
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
CC(OC(N[C@H]([C@@H](CNC[C@H]([C@@H](NC([C@@H](C(C)C)NC(OCC1C=CC(C2C=CC=CC=2)=CC=1)=O)=O)CC1C=CC=CC=1)O)O)CC1C=CC=CC=1)=O)(C)C<sep>
| |
60
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C1C=C2C(C=CC=N2)=CN=1<sep>
| |
61
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C([C@@H](CC1CCC1)O)*<sep><a>9:OBn</a>
| |
62
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=c1oc(=O)c2c1c1ccccc1c1cc3c(cc21)c1ccccc1c1c3c(=O)oc1=O<sep>
| |
63
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C1(C(F)(F)F)C=C(C2N(C)N=CC=2)C(C2C3C(=CC(=CC=3)S(NC3SN=CN=3)(=O)=O)N(C(=O)OC)C=2)=CC=1<sep>
| |
64
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*[C@@H](CCCc1cccc2c1CN(C1CCC(=O)NC1=O)C2=O)C(=O)Nc1ccc(C)c(Cl)c1<sep><a>0:NHAc</a>
| |
65
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
O=C(N1CCC1)NC1N=CC=C(OC2C=C(F)C(NC(C3(CC3)C(NC3C=CC(F)=CC=3)=O)=O)=CC=2)C=1<sep>
| |
66
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C1C=C(NC2SC(C(NC3=C(Cl)C=CC=C3C)=O)=CC=2)N=C(NCCCCCN2CCCC2)C=1<sep>
| |
67
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
*C(CO)=O<sep><a>0:<dum></a>
| |
68
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C(F)(F)(F)C1=NN(C2CCC(O)CC2)C=C1<sep>
| |
69
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C(Cn1c(/C(N)=N/O)cc2c(Br)cccc12)(F)(F)F<sep>
| |
70
|
<image>Please write the Extended SMILES (E-SMILES) of the given molecule image.
Below is the definition of Extended SMILES (E-SMILES) Format Writing Rules:
The Extended SMILES (E-SMILES) format used in the MolParser paper is designed to augment a standard RDKit-compatible SMILES string with additional machine-readable annotations, especially useful for representing Markush structures, abstract rings, repeating groups, and other extensions commonly seen in chemical patents.
The general form of an E-SMILES string is:
SMILES<sep>EXTENSION
# Components:
1. SMILES
This is a valid RDKit-compatible SMILES string.
To ensure consistency, the atom indexing starts from 0. You can generate this using RDKit with rootedAtAtom=0.
2. <sep>
A special delimiter separating the base SMILES string from the extension part.
3. EXTENSION
The extension part contains structured XML-like tokens providing additional information.
These tokens annotate atom positions, ring positions, and other special features.
There are three types of tags:
<a>ATOM_INDEX:[GROUP_NAME]</a> — attaches a group to a specific atom.
<r>RING_INDEX:[GROUP_NAME]</r> — attaches a group to any position on a ring.
<c>CIRCLE_INDEX:[CIRCLE_NAME]</c> — defines abstract repeating rings.
A special token <dum> can be used to represent a connection point.
# Definitions:
ATOM_INDEX: Index of the atom in the SMILES string (starting from 0).
RING_INDEX: Index of the ring in the molecule (starting from 0).
CIRCLE_INDEX: Index of the abstract repeating ring (starting from 0).
GROUP_NAME: The name of the substituent or group, which may be:
A standard group: R, X, Y, Z, Ph, Me, OMe, CF3, etc.
An arbitrary or custom-defined group with superscripts or subscripts, e.g., R[1], X[2], R1, R₃.
# Examples:
(1)*c1ccccc1<sep><a>0:R[1]</a>
→ Adds substituent R[1] to atom 0.
(2)clccecc1<sep><r>0:R[1]</r><r>0:R[2]</r>
→ Adds two substituents R[1], R[2] to ring 0.
(3)*C1*C(*)C(C(*)C2=CC=N=C2)N=1<sep><a>0:R[4]</a><a>1:X</a><r>1:R[5]</r>
→ Complex structure with atom-level and ring-level substitutions.
(4)*c(NC(*)C(*)C(*)C(*)C(=O)N(*)<sep><a>0:R[1]</a><a>2:R[3]</a><a>5:R[2]</a><a>7:R[5]</a><a>8:R[4]</a><c>0:B</c><a>13:R[7]</a><a>14:R[6]</a>
→ Shows the usage of abstract ring <c>, with multiple atom-level substitutions.
|
C12=C(*)C(*)=C(*)C(*)=C1C=C(C(O)=O)S2<sep><a>2:R1</a><a>4:R2</a><a>6:R3</a><a>8:R4</a>
|
End of preview. Expand
in Data Studio
MolParse Bench
MolParse
| HuggingFace | Code |
🔥 Latest News
- [2026/01] MolParse v1.0 is officially released.
Overview
MolParse is a large-scale multimodal dataset for optical chemical structure parsing, designed to evaluate and train models that convert molecular structure images into structured chemical representations.
The dataset focuses on realistic chemical diagrams commonly found in scientific literature and patents, emphasizing robustness to visual noise, diverse drawing styles, and complex molecular layouts. MolParse supports tasks that require precise visual perception and structured chemical understanding, rather than simple text recognition.
Benchmark Scope
MolParse evaluates models across the following core capability dimensions:
1. Molecular Structure Perception
Assess the ability to accurately recognize:
- Atoms and bonds
- Ring systems and fused structures
- Substituents and functional groups
- Variable attachment points and abstract structures
2. Structured Chemical Representation
Evaluate the capacity to translate molecular images into:
- Linearized chemical strings
- Structured symbolic representations
- Machine-readable formats suitable for downstream reasoning
3. Robustness in Real-World Documents
Test model stability under:
- Noisy or low-quality scans
- Diverse drawing conventions
- Crowded layouts and overlapping annotations
- Variations in resolution and aspect ratio
Dataset Characteristics
- Task Format: Image-to-Structure Parsing
- Modalities: Image + Text
- Domain: Chemistry
- Languages: English
- Annotation: Expert-verified
- Data Scale: Large-scale (millions of image–structure pairs)
Task Types
Each MolParse sample supports one or more of the following task types:
Molecular Image Captioning
Convert molecular diagrams into structured chemical strings.Symbol and Topology Recognition
Identify atoms, bonds, rings, and connection patterns.Complex Structure Parsing
Handle abstract rings, variable groups, and non-canonical layouts.Noise-Robust Recognition
Maintain parsing accuracy under visual distortion or interference.
Data Usage
MolParse is suitable for:
- Training end-to-end optical chemical structure recognition models
- Evaluating vision-language and vision-only chemical parsers
- Scientific document understanding pipelines
- Downstream chemical reasoning and information extraction
Download MolParse Dataset
You can load the MolParse dataset using the HuggingFace datasets library:
from datasets import load_dataset
dataset = load_dataset("InnovatorLab/MolParse")
Evaluations
We use lmms-eval for evaluations.
Please refer to the files under ./evaluation for detailed evaluation configurations and scripts.
License
MolParse is released under the MIT License.
See LICENSE for more details.
- Downloads last month
- -
Size of downloaded dataset files:
34.5 MB
Size of the auto-converted Parquet files:
34.5 MB
Number of rows:
2,000