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<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.
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C=CCCn1ccnc1C(=O)O<sep>
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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.
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CC(Nc1ccc2c(c1)OCCO2)C(=O)Nc1cc(C(F)(F)F)ccc1N1CCOCC1<sep>
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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.
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O=C(c1ccco1)[C@@H]1C(=O)c2ccccc2O[C@@H]1c1ccc(O)c(OCC2CC2)c1<sep>
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13
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<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.
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O=C(C1CCS(=O)(=O)CC1)N1CCN(c2ccccn2)CC1c1cccc(F)c1F<sep>
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14
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<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.
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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>
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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.
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CCOC(=O)c1c(NC(=O)c2c[nH]c3c(OC)cc(Cl)c(OC)c3c2=O)sc(C)c1-c1ccc(Cl)cc1<sep>
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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.
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CCNc1nc(Cl)c(-c2ccccc2)n(CC(=O)NCc2ccc(C(=N)N)cc2)c1=O<sep>
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17
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<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.
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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>
|
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