Merge pull request #38 from timbernat/feature-cleanup

Merge branch "feature cleanup"

README.md

@@ -38,7 +38,7 @@ Once you have a package manager installed, you may proceed with one of the provi
 A fully-featured install in a safe virtual environment (named "polymerist-env", here) can be obtained by running the following terminal commands:
 
 #### Mamba install (basic)
-```sh
+```bash
 mamba create -n polymerist-env python=3.11
 mamba activate polymerist-env
 pip install polymerist
@@ -47,7 +47,7 @@ mamba install -c conda-forge openff-toolkit mbuild openbabel
 
 #### Mamba install (extended)
 An extended install with [Jupyter Notebook](https://jupyter.org/) support, molecular visualization capability, and chemical data querying capability can be obtained very similarly:
-```sh
+```bash
 mamba create -n polymerist-env python=3.11
 mamba activate polymerist-env
 pip install polymerist[interactive,chemdb]
@@ -56,7 +56,7 @@ mamba install -c conda-forge openff-toolkit mbuild openbabel
 
 #### Conda install (not recommended)
 Equivalent commands using `conda` (in case `mamba` has not been installed or the user is too stubborn to use it) are given below. These will perform the same installation, just much more slowly:
-```sh
+```bash
 conda create -n polymerist-env python=3.11
 conda activate polymerist-env
 pip install polymerist[interactive,chemdb]
@@ -67,7 +67,7 @@ In either case, the final [openff-toolkit](https://github.com/openforcefield/ope
 
 #### 1.1) Testing installation
 To see if the installation was successful, one can run the following short set of commands which should yield the outputs shown:
-```sh
+```python
 mamba activate polymerist-env; python
 >>> import polymerist as ps
 >>> print(ps.pascal(5))
@@ -82,7 +82,7 @@ mamba activate polymerist-env; python
 Assigning atomic partial charges using some flavor of [AM1-BCC](https://docs.eyesopen.com/toolkits/python/quacpactk/molchargetheory.html#am1bcc-charges) with `polymerist` also requires installation of some supplementary toolkits.
 
 One can mix-and-match installing any combination of the toolkits below to taste or (if impatient or indifferent) opt for a "shotgun" approach and install all 3 with the following commands:
-```sh
+```bash
 mamba activate polymerist-env
 mamba install -c openeye openeye-toolkits
 mamba install -c conda-forge espaloma_charge openff-nagl
@@ -102,7 +102,7 @@ This is an OpenFF-specific GNN based on similar architecture to Espaloma with a
 Polymerist can also be installed directly from the source code in this repository. To install, execute the following set of terminal commands in whichever directory you'd like the installation to live on your local machine:
 
 #### Mamba install (source)
-```sh
+```bash
 git clone https://github.com/timbernat/polymerist
 cd polymerist
 mamba env create -n polymerist-env -f devtools/conda-envs/release-build.yml
@@ -111,7 +111,7 @@ pip install .
 ```
 
 #### Conda install (source, not recommended)
-```sh
+```bash
 git clone https://github.com/timbernat/polymerist
 cd polymerist
 conda env create -n polymerist-env -f devtools/conda-envs/release-build.yml
@@ -122,7 +122,7 @@ Once the source install is complete, you no longer need the clone of the polymer
 
 ### Developer installation (for advanced users only)
 Those developing for `polymerist` may like to have an editable local installation, in which they can make changes to the source code and test behavior changes in real-time. In this case, one requires an "editable build" which mirrors the source files that live in the site_packages directory of the created environment. This type of installation proceeds as follows:
-```sh
+```bash
 git clone https://github.com/timbernat/polymerist
 cd polymerist
 mamba env create -n polymerist-dev -f devtools/conda-envs/dev-build.yml

polymerist/genutils/importutils/dependencies.py

@@ -3,7 +3,7 @@
 __author__ = 'Timotej Bernat'
 __email__ = 'timotej.bernat@colorado.edu'
 
-from typing import Callable, Optional, ParamSpec, TypeVar
+from typing import Callable, Optional, ParamSpec, TypeVar, Union
 
 Params = ParamSpec('Params')
 ReturnType = TypeVar('ReturnType')
@@ -58,7 +58,7 @@ def module_installed(module_name : str) -> bool:
 
     try: # NOTE: opted for this implementation, as it never actually imports the package in question (faster and fewer side-effects)
         return find_spec(module_name) is not None
-    except (ValueError, AttributeError, ModuleNotFoundError): # these could all be raised by 
+    except (ValueError, AttributeError, ModuleNotFoundError): # these could all be raised by a missing module
         return False
 
 def modules_installed(*module_names : list[str]) -> bool:
@@ -80,7 +80,7 @@ def modules_installed(*module_names : list[str]) -> bool:
 
 def requires_modules(
         *required_module_names : list[str],
-        missing_module_error : type[Exception]=ImportError,
+        missing_module_error : Union[Exception, type[Exception]]=ImportError,
     ) -> Callable[[TCall[..., ReturnType]], TCall[..., ReturnType]]:
     '''
     Decorator which enforces optional module dependencies prior to function execution
@@ -99,12 +99,27 @@ def requires_modules(
         Raised if any of the specified packages is not found to be installed
         Exception message will indicate the name of the specific package found missing
     '''
+    # meta-check to ensure type of raised Exception is valid
+    if not isinstance(missing_module_error, Exception):
+        if not (isinstance(missing_module_error, type) and issubclass(missing_module_error, Exception)):
+            # DEV: this is potentially brittle, depending on how the specific Exception subtype is implemented?
+            raise TypeError('Must pass either Exception instance or subtype to "missing_module_error') 
+
+    def tailored_exception(module_name : str) -> Exception:
+        '''Accessory function to generate targetted Exceptions based on the provided
+        mssing_module_error value and the name of a module with no found installation'''
+        if isinstance(missing_module_error, Exception):
+            return missing_module_error
+
+        if isinstance(missing_module_error, type):
+           return missing_module_error(f'No installation found for module "{module_name}"')
+
     def decorator(func) -> TCall[..., ReturnType]:
         @wraps(func)
         def req_wrapper(*args : Params.args, **kwargs : Params.kwargs) -> ReturnType:
             for module_name in required_module_names:
                 if not module_installed(module_name):
-                    raise missing_module_error(f'No installation found for module "{module_name}"')
+                    raise tailored_exception(module_name)
             else:
                 return func(*args, **kwargs)
 

polymerist/genutils/textual/prettyprint.py

@@ -4,8 +4,54 @@
 __email__ = 'timotej.bernat@colorado.edu'
 
 from typing import Any
+
 from textwrap import indent
+from enum import StrEnum
+
+
+class Justification(StrEnum):
+    '''For specifying string justification'''
+    LEFT   = '<'
+    CENTER = '^'
+    RIGHT  = '>'
+Just = Justification # alias for the lazy or hurried
 
+def procrustean_string(
+        string : str,
+        length : int,
+        padding : str=' ',
+        just : Justification=Justification.LEFT,
+    ) -> int:
+    '''Takes a string and a target length and returns a new string which begins
+    with the same characters as the original string but is clamped to the target length,
+    truncating or padding if the original string is too long or short, respectively
+    
+    Parameters
+    ----------
+    string : str
+        The string to stretch or cut
+    length : int
+        The target number of characters in the final string
+    padding : str, default=" "
+        A single character which shold be used as padding 
+        when strings are too short, by default just a space
+        MUST BE EXACTLY ONE CHARACTER!
+    just : Justification, default=Justification.LEFT
+        Enum specifier of how to justify a padded string
+        Options are Justification.LEFT, Justification.CENTER, or Justification.RIGHT  
+        
+    Returns
+    -------
+    fmt_str : str
+        A string which begins with the same characters as "string" but has
+        precisely the specified length, with specified padding as specified
+    '''
+    if not (isinstance(length, int) and (length >= 0)):
+        raise ValueError(f'Target string length must be a non-negative integer (not {length})')
+    if not len(padding) == 1:
+        raise IndexError(f'Padding string must contain exactly one character (passed "{padding}")')
+
+    return f'{string[:length]:{padding}{just.value}{length}}'
 
 def dict_to_indented_str(dict_to_stringify : dict[Any, Any], level_delimiter : str='\t', line_sep : str='\n') -> str:
     '''Generate a pretty-printable string from a (possibly nested) dictionary,

polymerist/polymers/monomers/repr.py

@@ -50,10 +50,10 @@ def _add_monomer(self, resname : str, smarts : Smarts) -> None:
         if resname in self.monomers:
             existing_resgroup = self.monomers[resname]
             if isinstance(existing_resgroup, list) and (smarts not in existing_resgroup):
-                LOGGER.info(f'Extending existing residue category "{resname}" with SMARTS {smarts}')
+                LOGGER.debug(f'Extending existing residue category "{resname}" with SMARTS {smarts}')
                 self.monomers[resname].append(smarts)
         else:
-            LOGGER.info(f'Creating new residue category "{resname}", containing singular SMARTS ["{smarts}"])')
+            LOGGER.debug(f'Creating new residue category "{resname}", containing singular SMARTS ["{smarts}"])')
             self.monomers[resname] = [smarts]
 
     def _add_monomers(self, resname : str, smarts_container : Iterable[Smarts]) -> None:

polymerist/polymers/monomers/specification.py

@@ -19,19 +19,28 @@
 # CHEMICAL INFO SPECIFICATION
 SANITIZE_AS_KEKULE = (Chem.SANITIZE_ALL & ~Chem.SANITIZE_SETAROMATICITY) # sanitize everything EXCEPT reassignment of aromaticity
 
-def expanded_SMILES(smiles : str, assign_map_nums : bool=True, start_from : int=1) -> str:
-    '''Takes a SMILES string and clarifies chemical information, namely explicit hydrogens, kekulized aromatic bonds, and atom map numbers'''
+def expanded_SMILES(
+        smiles : str,
+        assign_map_nums : bool=True,
+        start_from : int=1,
+        kekulize : bool=True,
+    ) -> str:
+    '''
+    Expands and clarifies the chemical information contained within a passed SMILES string
+    namely explicit hydrogens and bond orders, and (optionally) kekulized aromatic bonds and atom map numbers
+    '''
     assert(is_valid_SMILES(smiles))
 
-    rdmol = Chem.MolFromSmiles(smiles, sanitize=True) # TOSELF : determine values of pros/cons of sanitizations (freedom of specificity vs random RDKit errors)
+    rdmol = Chem.MolFromSmiles(smiles, sanitize=True)
     rdmol = Chem.AddHs(rdmol, addCoords=True)
     if assign_map_nums:
         rdmol = molwise.assign_ordered_atom_map_nums(rdmol, start_from=start_from)
-
-    Chem.Kekulize(rdmol, clearAromaticFlags=True)
+
+    if kekulize:
+        Chem.Kekulize(rdmol, clearAromaticFlags=True)
     Chem.SanitizeMol(rdmol)
 
-    return Chem.MolToSmiles(rdmol, kekuleSmiles=True, allBondsExplicit=True, allHsExplicit=True)
+    return Chem.MolToSmiles(rdmol, kekuleSmiles=kekulize, allBondsExplicit=True, allHsExplicit=True)
 
 
 # REGEX TEMPLATES FOR COMPLIANT SMARTS
@@ -66,7 +75,14 @@ def chem_info_from_match(match : re.Match) -> dict[str, Union[int, str, None]]:
 
 
 # SMARTS ATOM QUERY GENERATION
-def compliant_atom_query_from_info(atomic_num : int, degree : int, atom_map_num : int, formal_charge : int=0, isotope : int=0, as_atom : bool=False) -> Union[str, QueryAtom]:
+def compliant_atom_query_from_info(
+        atomic_num : int,
+        degree : int,
+        atom_map_num : int,
+        formal_charge : int=0,
+        isotope : int=0,
+        as_atom : bool=False
+    ) -> Union[str, QueryAtom]:
     '''Construct a monomer-spec compliant atom SMARTS string directly from chemical information'''
     if not isotope: # handles when isotope is literal 0 or NoneType
         isotope = "" # non-specific isotope is not explicitly written in string (left empty)
@@ -126,7 +142,7 @@ def compliant_mol_SMARTS(smarts : str) -> str:
         count=rdmol.GetNumAtoms() # can't possibly replace more queries than there are atoms
     )
     if num_repl > 0:
-        LOGGER.warn(f'Cleaned {num_repl} SMARTS atom query aberrations introduced by RDKit')
+        LOGGER.debug(f'Cleaned {num_repl} SMARTS atom query aberrations introduced by RDKit')
     sanitized_smarts = sanitized_smarts.replace('#0', '*') # replace explicit atom number 0 calls with star (easier to do post-processing, as #0 is easier to implement)
 
     return sanitized_smarts

polymerist/rdutils/__init__.py

@@ -2,3 +2,11 @@
 
 __author__ = 'Timotej Bernat'
 __email__ = 'timotej.bernat@colorado.edu'
+
+from .rdkdraw import (
+    set_rdkdraw_size,
+    enable_substruct_highlights,
+    disable_substruct_highlights,
+    enable_kekulized_drawing,
+    disable_kekulized_drawing,
+)

polymerist/rdutils/rdkdraw.py

@@ -20,6 +20,10 @@
 
 
 # GLOBAL PREFERENCES
+def set_rdkdraw_size(dim : int=300, aspect : float=3/2):
+    '''Change image size and shape of RDKit Mol images'''
+    IPythonConsole.molSize = (int(aspect*dim), dim) # Change IPython image display size
+
 def enable_substruct_highlights() -> None:
     '''Turns on highlighting of found substructures when performing substructure matches'''
     IPythonConsole.highlightSubstructs = True
@@ -28,9 +32,13 @@ def disable_substruct_highlights() -> None:
     '''Turns off highlighting of found substructures when performing substructure matches'''
     IPythonConsole.highlightSubstructs = False
 
-def set_rdkdraw_size(dim : int=300, aspect : float=3/2):
-    '''Change image size and shape of RDKit Mol images'''
-    IPythonConsole.molSize = (int(aspect*dim), dim) # Change IPython image display size
+def enable_kekulized_drawing() -> None:
+    '''Turns on automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks'''
+    IPythonConsole.kekulizeStructures = True
+
+def disable_kekulized_drawing() -> None:
+    '''Turns off automatic kekulization of aromatic bonds before drawing molecules in Jupyter Notebooks'''
+    IPythonConsole.kekulizeStructures = False
 
 
 # SINGLE-MOLECULE DISPLAY OPTIONS