Edited all comments and docstrings which feature rdtypes classes (e.g…

…. RDMol, RDBond, RDAtom, or RWMol) in preparation for mass-rename

polymerist/monomers/conversion.py

@@ -14,7 +14,7 @@
 
 
 # CUSTOM EXCEPTIONS
-class InvalidRDMol(Exception):
+class InvalidRDKitMol(Exception):
     # raised during validation and error checking to catch invalid inputted/generated monomers
     def __init__(self, message, smarts=""):
         self.message = message
@@ -27,10 +27,10 @@ def __str__(self):
         else:
             return f"rdmol with smarts \"{self.smarts}\" found to be invalid: {self.message}"
 
-class InvalidMonomer(InvalidRDMol):
+class InvalidMonomer(InvalidRDKitMol):
     pass
 
-class InvalidCap(InvalidRDMol):
+class InvalidCap(InvalidRDKitMol):
     pass 
 
  # CONVERTERS

polymerist/monomers/repr.py

@@ -110,7 +110,7 @@ def unique(self, cap_group : Union[str, RDMol]=Chem.MolFromSmarts('[H]-[*]')) ->
         #     monomer = Chem.MolFromSmarts(SMARTS)
         #     clear_atom_map_nums(monomer, in_place=True) 
         #     hydrogenate_monomer_ports(monomer, in_place=True) 
-        #     unique_mono.add(Chem.MolToSmiles(monomer)) # TODO : eventually make this SMART-based (or even better RDMol-based); can't for now since hydrogenated fragments don't equate
+        #     unique_mono.add(Chem.MolToSmiles(monomer)) # TODO : eventually make this SMARTS-based (or even better RDKit Mol-based); can't for now since hydrogenated fragments don't equate
 
         # return unique_mono
 

polymerist/monomers/specification.py

@@ -80,7 +80,7 @@ def compliant_atom_query_from_info(atomic_num : int, degree : int, atom_map_num
     return atom_query
 
 def compliant_atom_query_from_rdatom(rdatom : RDAtom, as_atom : bool=False) -> Union[str, QueryAtom]:
-    '''Construct a monomer-spec compliant atom SMARTS string from an RDKit RDAtom'''
+    '''Construct a monomer-spec compliant atom SMARTS string from an RDKit Atom'''
     return compliant_atom_query_from_info(
         atomic_num   = rdatom.GetAtomicNum(),
         degree       = rdatom.GetDegree(), # counts number of active bonds

polymerist/openfftools/solvation/physprops.py

@@ -12,7 +12,7 @@
 
 
 def molecular_weight(rdmol : RDMol, exact_isotopes : bool=False) -> Quantity:
-    '''Compute the molecular weight of an RDMol'''
+    '''Compute the molecular weight of an RDKit Mol'''
     MW = Descriptors.ExactMolWt(rdmol) if exact_isotopes else Descriptors.MolWt(rdmol)
     return MW * (gram / mole) # attach units
 

polymerist/rdutils/bonding/identification.py

@@ -45,7 +45,7 @@ def enumerate_bondable_port_pairs_internal(ports : Iterable[Port]) -> Generator[
 #     return get_bondable_ports(rdmol, rdmol) # currently, this overcounts by exactly double, as a pair (p1, p2) and its copair (p2, p1) are considered distinct
 
 def get_bondable_port_pairs(rdmol : RDMol, atom_id_1 : Optional[int]=None, atom_id_2 : Optional[int]=None, flavor_pair : tuple[Optional[int], Optional[int]]=(None, None)) -> Generator[tuple[Port, Port], None, None]:
-    '''Get every pair of ports within an RDMol which could be bonded and match a specified flavor pair (could be partially or fully None for less specificity)
+    '''Get every pair of ports within an RDKit Mol which could be bonded and match a specified flavor pair (could be partially or fully None for less specificity)
     Can optionally localize search to only have port bridegehead coinciding with atoms at particular indices
     Pairs are returned n descending order of linker atom index to simplify atom removal if modifying later'''
     # possible_port_pairs = enumerate_bondable_port_pairs_internal( # unpack values after iterating; TODO : make this internal to avoid double counting

polymerist/rdutils/bonding/portlib.py

@@ -75,7 +75,7 @@ def matches_flavor(self, target_flavor : Optional[int]) -> bool:
 
 # PORT ENUMERATION
 def get_port_ids(rdmol : RDMol) -> Generator[tuple[int, int], None, None]:
-    '''Get the linker and bridgehead indices of all ports found in an RDMol'''
+    '''Get the linker and bridgehead indices of all ports found in an RDKit Mol'''
     for (linker_id, bh_id) in rdmol.GetSubstructMatches(PORT_QUERY):
         yield linker_id, bh_id # unpacked purely for self-documentation
 

polymerist/rdutils/bonding/substitution.py

@@ -32,7 +32,7 @@ def splice_atoms(rwmol : RWMol, atom_id_1 : Optional[int]=None, atom_id_2 : Opti
         increase_bond_order(rwmol, atom_id_1, atom_id_2, flavor_pair=flavor_pair, in_place=True) 
 
 def saturate_ports(rdmol : RDMol, cap : RDMol=Chem.MolFromSmarts('[#0]-[#1]'), flavor_to_saturate : int=0) -> None:
-    '''Takes an RDMol and another "cap" molecule (by default just hydrogen) and caps all valid ports (with the specified flavor) on the target Mol with the cap group'''
+    '''Takes an RDKit Mol and another "cap" molecule (by default just hydrogen) and caps all valid ports (with the specified flavor) on the target Mol with the cap group'''
     flavor_pair : tuple[int, int] = (flavor_to_saturate, get_single_port(cap).flavor) # will raise exception if cap has anything other than 1 port
 
     rwmol = combined_rdmol(rdmol, cap, editable=True) # create initial combination to test if bonding is possible

polymerist/rdutils/labeling/bondwise.py

@@ -16,7 +16,7 @@
 
 # BOND ID QUERYING
 def are_bonded_atoms(rdmol : RDMol, atom_id_1 : int, atom_id_2 : int) -> bool:
-    '''Check if pair of atoms in an RDMol have a bond between them'''
+    '''Check if pair of atoms in an RDKit Mol have a bond between them'''
     return (rdmol.GetBondBetweenAtoms(atom_id_1, atom_id_2) is not None)
 
 def get_bonded_pairs(rdmol : RDMol, *atom_ids : Iterable[int]) -> dict[int, tuple[int, int]]:

polymerist/rdutils/labeling/molwise.py

@@ -8,19 +8,19 @@
 
 # READING FUNCTIONS
 def get_isotopes(rdmol : RDMol, unique : bool=True) -> Union[set[int], list[int]]:
-    '''Return all isotope IDs present in an RDMol. Can optionally return only the unique IDs'''
+    '''Return all isotope IDs present in an RDKit Mol. Can optionally return only the unique IDs'''
     isotope_ids = [atom.GetIsotope() for atom in rdmol.GetAtoms()]
 
     if unique:
         return set(isotope_ids)
     return isotope_ids
 
 def ordered_map_nums(rdmol : RDMol) -> list[int]:
-    '''Get assigned atom map numbers, in the same order as the internal RDMol atom IDs'''
+    '''Get assigned atom map numbers, in the same order as the internal RDKit Mol atom IDs'''
     return [atom.GetAtomMapNum() for atom in rdmol.GetAtoms()]
 
 def map_nums_by_atom_ids(rdmol : RDMol, *query_atom_ids : list[int]) -> Generator[Optional[int], None, None]: # TODO : generalize this to handle case where multiple atoms have the same map num
-    '''Get assigned atom map numbers for a collection of atom ids, in the same order as the internal RDMol atom IDs'''
+    '''Get assigned atom map numbers for a collection of atom ids, in the same order as the internal RDKit Mol atom IDs'''
     for atom_id in query_atom_ids:
         yield(rdmol.GetAtomWithIdx(atom_id).GetAtomMapNum())
 
@@ -36,15 +36,15 @@ def atom_ids_by_map_nums(rdmol : RDMol, *query_map_nums : list[int]) -> Generato
 
 # CHECKING FUNCTIONS
 def has_fully_mapped_atoms(rdmol : RDMol) -> bool:
-    '''Check whether an RDMol has a map number explicitly assigned to each member RDAtom'''
+    '''Check whether an RDKit Mol has a map number explicitly assigned to each member Atom'''
     for atom in rdmol.GetAtoms():
         if atom.GetAtomMapNum() == 0:
             return False
     else:
         return True
 
 def has_uniquely_mapped_atoms(rdmol : RDMol) -> bool:
-    '''Check whether an RDMol has distinct atom map numbers for each member RDAtom'''
+    '''Check whether an RDKit Mol has distinct atom map numbers for each member Atom'''
     map_nums = ordered_map_nums(rdmol)
     return (len(map_nums) == len(set(map_nums))) # NOTE : not using rdmol.GetNumAtoms() as reference to avoid ambiguity with SMILES without explicit Hs
 
@@ -93,12 +93,12 @@ def assign_contiguous_atom_map_nums(*rdmols : Iterable[RDMol], start_from : int=
 # CLEARING FUNCTIONS
 @optional_in_place
 def clear_atom_map_nums(rdmol : RDMol) -> None:
-    '''Removes atom map numbers from all atoms in an RDMol'''
+    '''Removes atom map numbers from all atoms in an RDKit Mol'''
     for atom in rdmol.GetAtoms():
         atom.SetAtomMapNum(0)
 
 @optional_in_place
 def clear_atom_isotopes(rdmol : RDMol) -> None:
-    '''Removes isotope numbers from all atoms in an RDMol'''
+    '''Removes isotope numbers from all atoms in an RDKit Mol'''
     for atom in rdmol.GetAtoms():
         atom.SetIsotope(0)

polymerist/rdutils/rdconvert.py

@@ -1,4 +1,4 @@
-'''For conversion of RDMols back and forth between different format encodings - often imbues a desired side effect (such as 2D-projection)'''
+'''For conversion of RDKit Mols back and forth between different format encodings - often imbues a desired side effect (such as 2D-projection)'''
 
 from abc import ABC, abstractmethod, abstractproperty
 from rdkit import Chem

polymerist/rdutils/rdkdraw.py

@@ -26,13 +26,13 @@ def disable_substruct_highlights() -> None:
     IPythonConsole.highlightSubstructs = False
 
 def set_rdkdraw_size(dim : int=300, aspect : float=3/2):
-    '''Change image size and shape of RDMol images'''
+    '''Change image size and shape of RDKit Mol images'''
     IPythonConsole.molSize = (int(aspect*dim), dim) # Change IPython image display size
 
 
 # SINGLE-MOLECULE DISPLAY OPTIONS
 def clear_highlights(rdmol : RDMol) -> None:
-    '''Removes the highlighted atoms flags from an RDMol if present'''
+    '''Removes the highlighted atoms flags from an RDKit Mol if present'''
     if hasattr(rdmol, '__sssAtoms'):
         del rdmol.__sssAtoms
 

polymerist/rdutils/reactions/reactors.py

@@ -1,4 +1,4 @@
-'''Classes for implementing reactions with respect to some set of reactant RDMols'''
+'''Classes for implementing reactions with respect to some set of reactant RDKit Mols'''
 
 from typing import ClassVar, Generator, Iterable, Optional, Type
 from dataclasses import dataclass, field
@@ -21,7 +21,7 @@
 # REACTOR BASE CLASS 
 @dataclass
 class Reactor:
-    '''Class for executing a reaction template on collections of RDMol "reactants"'''
+    '''Class for executing a reaction template on collections of RDKit Mol "reactants"'''
     rxn_schema : AnnotatedReaction
     _ridx_prop_name : ClassVar[str] = field(init=False, default='reactant_idx') # name of the property to assign reactant indices to; set for entire class