10/08/2024 Update

* Fixed a bug while handling charged molecules.

Author: Augus1999

README.md

@@ -3,7 +3,7 @@
 [![PyPI](https://img.shields.io/pypi/v/mol2chemfigPy3?color=ff69b4)](https://pypi.org/project/mol2chemfigPy3/)
 [![Downloads](https://static.pepy.tech/personalized-badge/mol2chemfigpy3?period=total&units=international_system&left_color=black&right_color=green&left_text=Downloads)](https://pepy.tech/project/mol2chemfigpy3)
 ![OS](https://img.shields.io/badge/OS-Win%20|%20Linux%20|%20macOS-blue?color=00B16A)
-![python](https://img.shields.io/badge/Python-3.8%20|%203.9%20|%203.10-blue.svg?color=dd9b65)
+![python](https://img.shields.io/badge/Python->3.8%20-blue.svg?color=dd9b65)
 ![black](https://img.shields.io/badge/code%20style-black-black)
 ![pytest](https://github.com/Augus1999/mol2chemfigPy3/actions/workflows/pytest.yml/badge.svg)
 

mol2chemfigPy3/__init__.py

@@ -5,7 +5,8 @@
 mol2chemfig generates chemfig code from mol files.
 """
 import re
-from typing import Optional, Any
+from pathlib import Path
+from typing import Optional, Union
 from .main import main
 from .processor import process
 from .common import program_version
@@ -18,7 +19,7 @@
 
 
 def mol2chemfig(
-    content: Any,
+    content: Union[int, str, Path],
     *args: str,
     rotate: float = 0.0,
     aromatic: bool = True,

mol2chemfigPy3/chemfig_mappings.py

@@ -118,7 +118,7 @@ def num_round(num: Union[int, float], sig: Union[int, float]) -> Union[int, floa
         # one hydrogen
         one_h=dict(
             east=(r"%(element)sH^{%(charge)s}", 1),
-            h_west=(r"^{%(charge)s}H%(element)s", 3),
+            west=(r"^{%(charge)s}H%(element)s", 3),
             north=(r"\mcfaboveright{%(element)s}{H}{^{%(charge)s}}", 0),
             south=(r"\mcfbelowright{%(element)s}{H}{^{%(charge)s}}", 0),
         ),
@@ -262,7 +262,9 @@ def format_bond(
     return bond_code + modifier + specifiers
 
 
-def fill_atom(keys: Tuple, data: Dict, phantom: str, phantom_pos: int = 0) -> tuple:
+def fill_atom(
+    keys: Tuple[str, str, str], data: Dict, phantom: str, phantom_pos: int = 0
+) -> tuple:
     """
     helper for finalizing atom code. phantom_pos is the
     target position of a bond attaching to a phantom;
@@ -330,7 +332,6 @@ def format_atom(
     """
 
     _mt = macro_templates  # shortcuts
-    _at = atom_templates
 
     # collect elements in a dict that then is used to fill
     # the configured string templates.
@@ -474,7 +475,7 @@ def format_aromatic_ring(
     return ring_bond_code, ring_code, comment
 
 
-def strip_output(output_list: List) -> List:
+def strip_output(output_list: List[str]) -> List[str]:
     """
     remove white space and comments
 
@@ -505,7 +506,7 @@ def strip_output(output_list: List) -> List:
     return chunked
 
 
-def format_output(options: Dict, output_list: List) -> str:
+def format_output(options: Dict, output_list: List[str]) -> str:
     """
     optionally wrap the translated output into a command,
     to ease inclusion in LaTeX documents with \\input

mol2chemfigPy3/common.py

@@ -4,7 +4,7 @@
 """
 from .options import getParser
 
-program_version = "1.5.9"
+program_version = "1.5.10"
 
 # pubchem url for retrieving sdf for numerical IDs
 pubchem_url = (

mol2chemfigPy3/optionparser.py

@@ -15,7 +15,7 @@ class attributes and more subclassing than
 import getopt
 import re
 import textwrap
-from typing import Union, Optional, List, Tuple, Dict
+from typing import Union, Optional, Tuple, Any, List, Dict
 
 
 class OptionError(Exception):
@@ -85,7 +85,7 @@ def validate(self, value) -> bool:
             return True
         return False
 
-    def validate_form_value(self, value: any) -> bool:
+    def validate_form_value(self, value: Any) -> bool:
         """
         validation of option value received through a
         web form. May need to be different from CLI,
@@ -96,7 +96,7 @@ def validate_form_value(self, value: any) -> bool:
         """
         return self.validate(value)
 
-    def _validate(self, value: any) -> Tuple[bool, any]:
+    def _validate(self, value: Any) -> Tuple[bool, Any]:
         """
         no-op default
 
@@ -145,7 +145,7 @@ def format_help(self, indent: int = 30, linewidth: int = 80) -> list:
 
         return h_wrap
 
-    def format_tag_value(self, value: any) -> str:
+    def format_tag_value(self, value: Any) -> str:
         """
         format the default value for insertion into form tag
 
@@ -156,7 +156,7 @@ def format_tag_value(self, value: any) -> str:
             return ""
         return str(value)
 
-    def format_tag(self, value: any = None) -> Tuple[str, str, str, str]:
+    def format_tag(self, value: Any = None) -> Tuple[str, str, str, str]:
         """
         render a html form tag
 
@@ -184,7 +184,7 @@ def _default(self) -> bool:
         """
         return False
 
-    def validate(self, value: any = None) -> bool:
+    def validate(self, value: Any = None) -> bool:
         """
         value should be empty; we accept and discard it.
         we simply switch the default value.
@@ -195,7 +195,7 @@ def validate(self, value: any = None) -> bool:
         self.value = not self.default
         return True
 
-    def validate_form_value(self, value: any) -> bool:
+    def validate_form_value(self, value: Any) -> bool:
         """
         if a value arrives through a web form, the box has been
         ticked, so we set to True regardless of default. The passed
@@ -258,7 +258,7 @@ def _validate(self, value: str) -> Tuple[bool, str]:
         """
         return True, value.lower()
 
-    def format_tag(self, value: any = None) -> Tuple[str, str, str, str]:
+    def format_tag(self, value: Any = None) -> Tuple[str, str, str, str]:
         """
         :param value: value
         :return: (key, tag, form text, help text)
@@ -294,7 +294,7 @@ class TypeOption(Option):
         r"""<input type="text" name="%(key)s" value="%(value)s" size="8"/>"""
     )
 
-    def _validate(self, value: any) -> Tuple[bool, any]:
+    def _validate(self, value: Any) -> Tuple[bool, Any]:
         """
         :param value: any value
         :return: (bool, value)

mol2chemfigPy3/processor.py

@@ -6,13 +6,13 @@
 import os.path
 import traceback
 from urllib import request
-from typing import Union, List, Tuple
+from typing import Union, Tuple, List, Any
 from indigo import Indigo, IndigoException, IndigoObject
 from . import common, options, molecule
 
 
 class HelpError(common.MCFError):
-    def __init__(self, text: any):
+    def __init__(self, text: Any):
         self.text = str(text)  # convert error messages to string
 
     def __str__(self):
@@ -28,7 +28,7 @@ def __init__(
         self,
         raw_args: Union[List, str, None],
         data: str,
-        form_fields: any,
+        form_fields: Any,
         program_name: str,
         web_form: bool,
         rpc: bool,
@@ -202,8 +202,8 @@ def parseMolecule(self) -> IndigoObject:
 
 def process(
     raw_args: Union[List, str, None] = None,
-    data: any = None,
-    form_fields: any = None,
+    data: Any = None,
+    form_fields: Any = None,
     program_name: str = "mol2chemfigPy3",
     web_form: bool = False,
     rpc: bool = False,