SCRIPT is a deterministic, sovereign molecular notation system and RDKit-independent cheminformatics engine. Built on a Paninian linguistic model, SCRIPT provides a "one true string" for every molecule, reaction, material, and quantum state with 100% native round-trip consistency.
SMILES has served chemistry for 35 years, but its limitations are critical for modern AI/ML and materials science applications:
- Non-canonical: Same molecule = multiple valid SMILES strings
- Ambiguous rings: Global ring labels (
C1...C1) create parsing complexity - Stereochemistry fragility: Neighbor ordering affects chirality interpretation
- No validation: Invalid strings parse without error
- No materials support: SMILES cannot express alloys, surfaces, or quantum states
SCRIPT addresses all of these systematically:
| Problem | SMILES | SCRIPT V3 |
|---|---|---|
| Canonicalization | Multiple valid strings | Path-invariant DFS traversal |
| Ring notation | Global labels C1...C1 |
Topological &N: (invariant size) |
| Aromaticity | c1ccccc1 (lowercase hack) |
Anubandha : (Grammar state) |
| Tautomers | Multiple forms | Mobile =: (Unified form) |
| Validation | Post-hoc | Generative state machine (Sandhi) |
| Organometallics | Partial | Dative ->, Coordinate >, Haptic *n |
| Alloys | Not supported | Fractional occupancy <~0.9> |
| Crystallography | Not supported | Macroscopic context [[Rutile]] |
| Surfaces | Not supported | Phase boundary | |
| Quantum states | Not supported | Spin/excitation <s:3>, <*> |
| Polymers | Not supported | Stochastic chains {[CC]}n |
Morgan-invariant ranking with DFS traversal ensures every molecule has exactly one canonical SCRIPT string.
SMILES: CC(=O)Oc1ccccc1C(=O)O (or many others)
SCRIPT: CC(=O)OC:C:C:C:C:C&6:C(=O)O (one and only one)
Ring closure index &6: is an instruction ("connect back 6 atoms along the DFS path"), not a global label.
SMILES: C1CCCCC1 # Global label
SCRIPT: CCCCC&6. # Topological: 6-membered ring, single bond
SCRIPT (benzene): C:C:C:C:C:C&6: # 6-membered ring, aromatic
Chirality is resolved using the DFS sequence order as the native coordinate frame.
C[C@H](O)C(=O)O # L-Lactic Acid
# Order: [parent, H, O, C(=O)O] -> @ = CCW in Vak space
Generative state machine catches invalid structures during parsing (e.g., valence violations).
# C(C)(C)(C)(C)(C) -> Rejected: Carbon valence > 4
Zero dependencies for core operations. RDKit is optional for interop only.
Ti<~0.9>N<~0.1> # Doped Titanium Nitride
Fe<~0.5>Ni<~0.5> # Iron-Nickel alloy
[[Rutile]] Ti(O)2 # TiO2 in Rutile phase
[[Anatase]] Ti(O)2 # Same formula, different structure
[[bcc]] Fe # Ferrite (body-centered cubic)
[[fcc]] Fe # Austenite (face-centered cubic)
[[Pt_111]] | >C=O # CO adsorbed on Platinum 111 surface
[[LiCoO2]] | Li<+> # Li-ion in LiCoO2 battery lattice
{[A.G.S]} # Peptide chain (Ala-Gly-Ser)
{[dA.dG.dC.dT]} # DNA oligonucleotide (Adenine-Guanine-Cytosine-Thymine)
{[m5C.m6A]} # Modified nucleotides (5-methylcytosine, N6-methyladenine)
[#6] # Atomic number query (Carbon)
[!N] # Not Nitrogen
[R] # Any ring atom
[r5] # Atom in 5-membered ring
[v3] # Atom with valence 3
O=O<s:3> # Triplet oxygen (ground state diradical)
O=O<s:1,*> # Singlet oxygen (excited state)
{[CC]}n # Polyethylene
{[CC]}<n:50-100> # Stochastic PE, 50-100 units
To prove that the Topological Back-counting and Anubandha systems scale to real-world complexity, SCRIPT was validated against these high-complexity scaffolds:
-
Taxol (Paclitaxel): 11 stereocenters, fused/bridged system.
TAXOL: O[C@H]C[C@H]([C@@](C)C([C@H](OC(C)=O)C=C([C@@H](C[C@H]([C@H](OC(C:C:C:C:C:C&6:)=O)[C@H]&10.[C@]&14.(OC(=O)C)C&16.)C&6.(C)C)OC([C@H]([C@@H](C:C:C:C:C:C&6:)NC(C:C:C:C:C:C&6:)=O)O)=O)C)=O)O
-
Strychnine: Dense polycyclic structure.
STRYCHNINE: O=CNCCCCN(CCC&10.)CC=C&5.OCC&10.C&6.(C=&13.C=CC=C&18.)CC&5.C=C
- 100% native round-trip (SCRIPT -> CoreMolecule -> SCRIPT)
- 100% RDKit InChI parity on diverse benchmarking dataset
- 22/22 V3 Materials tests passing
python benchmark.py
# Round-trip: 100.0% (97 compounds passing)
pytest tests/test_v3.py
# TOTAL: 22 passed, 0 failed out of 22 (Materials & State)
# Tier 3 verified: Query atoms and Nucleotide modifications expanded.# Core engine (RDKit-free)
pip install lark
# With RDKit bridge for interop
pip install rdkitfrom script.parser import SCRIPTParser
from script.canonical import SCRIPTCanonicalizer
parser = SCRIPTParser()
result = parser.parse("CC(=O)OC1=CC=CC=C1C(=O)O")
mol = result["molecule"]
print(f"Atoms: {len(mol.atoms)}")
print(f"Bonds: {len(mol.bonds)}")
# Canonicalize CoreMolecule to SCRIPT string
canonicalizer = SCRIPTCanonicalizer()
script_str = canonicalizer.canonicalize_core(mol)
print(f"Canonical: {script_str}")parser = SCRIPTParser()
# Alloy - get fractional occupancy
res = parser.parse("Ti<~0.9>N<~0.1>")
mol = res["molecule"]
print(mol.atoms[0].occupancy) # 0.9
# Crystallographic context
res = parser.parse("[[Rutile]] Ti(O)2")
mol = res["molecule"]
print(mol.macroscopic_context) # "Rutile"
# Surface adsorption
res = parser.parse("[[Pt_111]] | >C=O")
print(res["success"]) # True
# Electronic state
res = parser.parse("O=O<s:3>")
mol = res["molecule"]
print(mol.atoms[-1].spin) # 3# Reaction with atom-to-atom mapping
res = parser.parse("[C:1]OCO>>[C:1]O")
# Salt / solvent system
res = parser.parse("[Na+].[Cl-]") # NaClparser.parse("{A.G.S[A]K}") # Ala-Gly-Ser-Lys with disulfide bridge
parser.parse("{[CC]}n") # Polyethylene
parser.parse("{[CC]}<n:50-100>") # Stochastic PE, 50-100 unitsfrom rdkit import Chem
from script.rdkit_bridge import SCRIPTFromMol, MolFromSCRIPT
mol = Chem.MolFromSmiles("CC(=O)Oc1ccccc1C(=O)O")
script_str = SCRIPTFromMol(mol)
print(f"SCRIPT: {script_str}")
mol_back = MolFromSCRIPT(script_str)
inchi = Chem.MolToInchi(mol_back)script-notation/
├── script/ # Core engine (RDKit-free)
│ ├── mol.py # CoreAtom / CoreBond / CoreMolecule (V3 fields)
│ ├── parser.py # Lark-based SCRIPT parser (V3 interpreter)
│ ├── canonical.py # DFS canonicalization engine
│ ├── chiral.py # Stereochemistry perception
│ ├── cip.py # CIP priority calculator
│ ├── state_machine.py # Sandhi validation (Generative)
│ ├── writer.py # Native SCRIPT string writer
│ ├── grammar.lark # SCRIPT V3 LALR grammar
│ ├── ranking.py # Morgan invariant ranking
│ ├── local_rings.py # Topological ring resolution
│ └── rdkit_bridge.py # Optional RDKit interop
├── docs/ # All documentation (domain guides + deep-dives)
│ ├── organic_aromatic_stereo.md
│ ├── metals_organometallics.md
│ ├── materials_polymers_states.md
│ ├── reactions_salts_radicals.md
│ ├── SPEC.md # Complete SCRIPT specification
│ ├── CIP_STEREO_THEORY.md # Stereochemistry reconciliation theory
│ └── STANDALONE_ARCHITECTURE.md
├── tests/
│ ├── test_parser.py
│ └── test_rdkit_integration.py
├── examples/
│ ├── basic_usage.py
│ └── rdkit_demo.py
├── benchmark.py # 100-compound RDKit round-trip validation
├── test_v3.py # V3 materials test suite (22 cases)
└── LICENSE # MIT + Commons Clause
start: macroscopic_structure
macroscopic_structure: [[context]]? (reaction|script) (| (reaction|script))*
reaction: script (>> | =>) script
script: component (. | ~ component)*
component: molecular_chain | peptide_chain | polymer | ring_closure
molecular_chain: bond? atom_expr (bond? (atom_expr | local_ring | branch))*
atom_expr: (ELEMENT | [bracket_atom] | ATOM<state_block>) multiplier?
state_block: < INT | CHARGE | GEOMETRY | h INT | m | ~FLOAT | s:INT | * >
bond: -> | <- | - | = | # | : | =: | / | \ | > | *INT?
ring_closure: &INT (: | .)
polymer: {[ unit ]} (<n:INT> | <n:INT-INT> | n)?
peptide_chain: { AMINO_ACID (. AMINO_ACID)* }
| Feature | SMILES | SELFIES | InChI | SCRIPT V3 |
|---|---|---|---|---|
| Canonical | No* | No | Yes | Yes |
| Human-readable | Yes | No | No | Yes |
| Invalid-proof | No | Yes | N/A | Yes (Sandhi) |
| Stereochemistry | Fragile | Limited | Robust | Robust (Vak+CIP) |
| Organometallics | Partial | No | No | Yes |
| Alloys | No | No | No | Yes |
| Crystallography | No | No | Partial | Yes |
| Surfaces | No | No | No | Yes |
| Quantum states | No | No | No | Yes |
| Polymers | No | No | No | Yes |
| RDKit-free core | No | No | N/A | Yes |
Sharma, S. (2026). SCRIPT: Structural Chemical Representation in Plain Text.
A Deterministic Molecular Notation System with Materials & State Expansion (V3).
https://github.com/script-notation/script
MIT License with Commons Clause
Free for academic research, personal projects, and non-commercial open-source development. Commercial use requires a separate licensing agreement.
See LICENSE for full terms.
Developed by Sangeet Sharma and the SCRIPT team.
- GitHub Issues: script-notation/script/issues
- Documentation: See
docs/directory
"A linear script to unfold molecular complexity — from the singlet to the surface."
PS: Sangeet's the name, a daft undergrad splashing through chemistry and code like a toddler; my titrations are a mess, and I've used my mouth to pipette.