From dac47f859c638b92ed4fc460cc7f423ea340ba43 Mon Sep 17 00:00:00 2001
From: Timotej Bernat <tibe3324@colorado.edu>
Date: Wed, 10 Apr 2024 19:39:16 -0600
Subject: [PATCH] Created new module specific to SMIDGE string parsing and
 validation

---
 polymerist/polymers/smidgelib/__init__.py | 77 +++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 polymerist/polymers/smidgelib/__init__.py

diff --git a/polymerist/polymers/smidgelib/__init__.py b/polymerist/polymers/smidgelib/__init__.py
new file mode 100644
index 0000000..168270a
--- /dev/null
+++ b/polymerist/polymers/smidgelib/__init__.py
@@ -0,0 +1,77 @@
+'''Utilities for parsing, validating, and translating SMILES-like Monomer Interconnectivity and Degree Graph Encoding (SMIDGE) string'''
+
+import re
+from rdkit import Chem
+
+from typing import ClassVar, Union, Optional
+from dataclasses import dataclass, field
+from polymerist.rdutils.smileslib.primitives import BONDTYPE_BY_BOND_SMARTS, BOND_SMARTS_BY_BONDTYPE, BOND_PRIMITIVES_FOR_REGEX
+
+
+# PROCESSING BOND TOKENS IN SMIDGE STRINGS
+BOND_TOKEN_RE = re.compile(
+    r'(?P<incoming_flavor>\d*)' \
+    f'(?P<bondtype>{BOND_PRIMITIVES_FOR_REGEX})' \
+    r'(?P<outgoing_flavor>\d*)'
+)
+
+@dataclass
+class MonomerGraphBondInfo:
+    '''Encapsulated information about an intermonomer bond in a monomer graph'''
+    DEFAULT_BONDTYPE : ClassVar[Chem.BondType] = Chem.BondType.UNSPECIFIED
+    DEFAULT_FLAVOR   : ClassVar[int] = 0
+
+    incoming_flavor : int    = field(default=DEFAULT_FLAVOR)
+    bondtype : Chem.BondType = field(default=DEFAULT_BONDTYPE)
+    outgoing_flavor : int    = field(default=DEFAULT_FLAVOR)
+
+    def __post_init__(self) -> None:
+        '''Perform appropriate type conversions and apply defaults'''
+        if self.incoming_flavor is None:
+            self.incoming_flavor = self.DEFAULT_FLAVOR
+
+        if self.bondtype is None:
+            self.bondtype = self.DEFAULT_BONDTYPE
+
+        if self.outgoing_flavor is None:
+            self.outgoing_flavor = self.DEFAULT_FLAVOR
+
+    @property
+    def bond_str(self) -> str:
+        '''SMARTS representation of the current bondtype (defaults to the default symbol if None or invalid bondtype is provided)'''
+        return BOND_SMARTS_BY_BONDTYPE.get(self.bondtype, BOND_SMARTS_BY_BONDTYPE.get(self.DEFAULT_BONDTYPE))
+
+    def __str__(self) -> str:
+        return f'{self.incoming_flavor or ""}{self.bond_str}{self.outgoing_flavor or ""}'
+
+    
+    @staticmethod
+    def parse_str_dict(str_dict : dict[str, str]) -> dict[str, Optional[Union[str, Chem.BondType]]]:
+        '''Parse string-valued dict into dict of correct types and NoneType defaults for empty keys'''
+        # 0) create copy of dict to avoid any in-place modification
+        imb_info = {k : v for k, v in str_dict.items()}
+        
+        # 1) process bond type
+        imb_info['bondtype'] = BONDTYPE_BY_BOND_SMARTS.get(imb_info.get('bondtype')) # set to None either if no bondtype is provided OR the provided type is not a registered primitive
+
+        # 2) process port flavors
+        for flavor_attr in ('incoming_flavor', 'outgoing_flavor'):
+            if not (flavor_str := imb_info.get(flavor_attr)): # raised when the flavor_str is either not present or empty
+                imb_info[flavor_attr] = None
+            elif isinstance(flavor_str, str) and flavor_str.isdigit():
+                imb_info[flavor_attr] = int(flavor_str) # convert parsed strings to ints where possible
+
+        return imb_info
+
+    @classmethod
+    def from_dict(cls, str_dict : dict[str, str]) -> 'MonomerGraphBondInfo':
+        '''Initialize from dictionary of values, after sanitizing'''
+        return cls(**cls.parse_str_dict(str_dict))
+
+    @classmethod
+    def from_match(cls, match : Optional[re.Match]) -> 'MonomerGraphBondInfo':
+        '''Initialize from groupdict of regex Match'''
+        if match is None:
+            # TODO: add logged warning
+            return cls()
+        return cls.from_dict(match.groupdict())
\ No newline at end of file