<commit_before>mol22lt.py
===========

*mol22lt.py* is a program for converting MOL2 files
into moltemplate (LT) file format.

## *WARNING: ALPHA SOFTWARE. THIS SOFTWARE IS EXPERIMENTAL AS OF 2022-8-16*

## Usage:

```
   mol22lt.py \
      --in FILE.MOL2 \
      --out FILE.LT \
      [--name MOLECULE_NAME] \
      [--charges charges.txt] \
      [--ff FORCE_FIELD_NAME] \
      [--ff-file FORCE_FIELD_FILE_NAME]
```

## Example:

Convert polyphenylene sulfide (PPS) polymer<commit_msg>added a warning to the mol22lt.py documentation<commit_after>mol22lt.py
===========

*mol22lt.py* is a program for converting MOL2 files
into moltemplate (LT) file format.

## *WARNING: ALPHA SOFTWARE. THIS SOFTWARE IS EXPERIMENTAL AS OF 2022-8-16*

## *WARNING: THIS SOFTWARE DOES NOT WORK WITH MOL2 MULTIPLE CHAINS*
This software does not work with MOL2 files
containing multiple "chains".
*("Chains" are optional features located in the
[SUBSTRUCTURE section of some MOL2 files](http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf).)*
As a workaround, if your MOL2 file contains multiple chains,
split it into multiple MOL2 files (one per chain).
Then convert each file separately.  (-Andrew 2022-8-16)


## Usage:

```
   mol22lt.py \
      --in FILE.MOL2 \
      --out FILE.LT \
      [--name MOLECULE_NAME] \
      [--charges charges.txt] \
      [--ff FORCE_FIELD_NAME] \
      [--ff-file FORCE_FIELD_FILE_NAME]
```

## Example:

Convert polyphenylene sulfide (PPS) polymer
{'fraction_non_alphanumeric': 0.1292517006802721, 'fraction_numerical': 0.030612244897959183, 'mean_word_length': 3.239193083573487, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4966426', 'n_tokens_mistral': 555, 'n_tokens_neox': 504, 'n_words': 153}