py2opsin

https://jacksonburns.github.io/py2opsin/

Admin

py2opsin is a Python library that provides a simple passthrough to the OPSIN name-to-structure...

Tokens:811

Snippets:7

Trust Score:9.7

Update:4 months ago

Show doc for...

Tokens:

Raw

### py2opsin.py2opsin.pkg_fopen

Source: https://jacksonburns.github.io/py2opsin/py2opsin.html

Opens a specified file name. This function appears to be a utility for file operations within the package.

```APIDOC
## pkg_fopen() API

### Description
Opens a specified file name. This function is a utility for file operations.

### Parameters
* **_fname_**: The name of the file to open.
```

--------------------------------

### py2opsin.py2opsin.py2opsin

Source: https://jacksonburns.github.io/py2opsin/py2opsin.html

A simple passthrough to OPSIN, converting chemical names to specified output formats. It supports various formats like SMILES, InChI, and more, with options to control interpretation of acids, radicals, and stereochemistry.

```APIDOC
## py2opsin() API

### Description
Simple passthrough to OPSIN, returning results as Python strings. Converts chemical names to various formats.

### Parameters
* **chemical_name** (str | list) - Required - IUPAC name of chemical as string, or list of strings.
* **output_format** (str, optional) - One of "SMILES", "ExtendedSMILES", "CML", "InChI", "StdInChI", or "StdInChIKey". Defaults to "SMILES".
* **allow_acid** (bool, optional) - Allow interpretation of acids. Defaults to False.
* **allow_radicals** (bool, optional) - Enable radical interpretation. Defaults to False.
* **allow_bad_stereo** (bool, optional) - Allow OPSIN to ignore uninterpreatable stereochem. Defaults to False.
* **wildcard_radicals** (bool, optional) - Output radicals as wildcards. Defaults to False.
* **jar_fpath** (str, optional) - Filepath to OPSIN jar file. Defaults to "default", which causes py2opsin to use its included jar.
* **tmp_fpath** (str, optional) - Name for temporary file used for calling OPSIN. Defaults to "py2opsin_temp_input.txt". When multiprocessing, set this to a unique name for each process.

### Returns
Species in requested format, or False if not found or an error occurred. List of strings if input is list.

### Return Type
str
```

Tokens:

Raw