Parser Module¶

MolPy includes a flexible parser layer for converting string representations of molecules and polymers into internal data structures (Atomistic, Monomer, Polymer, …).

The parser module focuses on:

• SMILES and BigSMILES‑like notations
• Turning parsed structures into Atomistic and wrapper objects
• Feeding results into builders, reacters and typifiers

From SMILES/BigSMILES to Atomistic¶

While the parser API is still evolving, the core idea is:

1. Take a string (e.g. SMILES or BigSMILES).
2. Parse it into an intermediate representation (IR).
3. Convert the IR into an Atomistic structure (atoms + bonds).

In [1]:

from molpy.parser import SmartsParser, SmilesParser

# Parse SMILES string
smiles_parser = SmilesParser()
smiles_ir = smiles_parser.parse_smiles("CCO")
print(f"Parsed SMILES: {smiles_ir}")

# Parse SMARTS pattern
smarts_parser = SmartsParser()
smarts_ir = smarts_parser.parse_smarts("[C;H2,H3]")  # Carbon with 2 or 3 hydrogens
print(f"Parsed SMARTS: {smarts_ir}")

from molpy.parser import SmartsParser, SmilesParser # Parse SMILES string smiles_parser = SmilesParser() smiles_ir = smiles_parser.parse_smiles("CCO") print(f"Parsed SMILES: {smiles_ir}") # Parse SMARTS pattern smarts_parser = SmartsParser() smarts_ir = smarts_parser.parse_smarts("[C;H2,H3]") # Carbon with 2 or 3 hydrogens print(f"Parsed SMARTS: {smarts_ir}")

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[1], line 4
      1 from molpy.parser import SmartsParser, SmilesParser
      3 # Parse SMILES string
----> 4 smiles_parser = SmilesParser()
      5 smiles_ir = smiles_parser.parse_smiles("CCO")
      6 print(f"Parsed SMILES: {smiles_ir}")

File ~/.asdf/installs/python/3.13.3/lib/python3.13/site-packages/molpy/parser/smiles.py:649, in SmilesParser.__init__(self)
    640 def __init__(self):
    641     config = GrammarConfig(
    642         grammar_path=Path(__file__).parent / "grammar" / "smiles.lark",
    643         start="smiles",
   (...)    647         auto_reload=True,
    648     )
--> 649     super().__init__(config)

File ~/.asdf/installs/python/3.13.3/lib/python3.13/site-packages/molpy/parser/base.py:44, in GrammarParserBase.__init__(self, config)
     42 self._lark: Lark | None = None
     43 self._mtime: float | None = None
---> 44 self._compile_grammar(force=True)

File ~/.asdf/installs/python/3.13.3/lib/python3.13/site-packages/molpy/parser/base.py:77, in GrammarParserBase._compile_grammar(self, force)
     75 path = self.config.grammar_path
     76 if not path.exists():
---> 77     raise FileNotFoundError(f"Grammar file not found: {path}")
     79 grammar_text = path.read_text(encoding="utf-8")
     81 self._lark = Lark(
     82     grammar_text,
     83     start=self.config.start,
   (...)     88     keep_all_tokens=True,
     89 )

FileNotFoundError: Grammar file not found: /opt/buildhome/.asdf/installs/python/3.13.3/lib/python3.13/site-packages/molpy/parser/grammar/smiles.lark

Integration with Molecular Building¶

Parsed Atomistic structures are commonly used as inputs to:

• Monomer / Polymer wrappers
• Reaction workflows via reacter
• Typifiers (molpy.typifier) for assigning atom types

The typical pipeline looks like:

SMILES / BigSMILES string
      ↓
    parser
      ↓
  Atomistic
      ↓
  Monomer / Polymer / Builder / Reacter / Typifier