oasa3 0.1.1

OASA Chemoinformatics library ported to python 3

OASA3

What is OASA3

OASA3 is a Python 3 port of the OASA python library, it can be a good alternative to other depiction libraries such as pybel (which ironically is based on OASA itself) and the notoriously hard to install RDKIT.

Do not expect everything to work, unit testing ran 77 tests with only 1 failed run and i have no idea how to fix it because there is no documentation, all depiction functions and coordinate generation tools should work flawlessly though, which is all i needed from this library anyways.

Installation

you can obtain OASA3 from pip :

pip install oasa3

Depiction usage

The following code shows how to generate a 2D depiction from a 3D SDF / MOL file, other formats work too, just adapt your code accordingly.

The process is simple : follow these 4 steps :

• 1 : Import the required stuff.

from oasa3.cairo_out import cairo_out
from oasa3.molfile import file_to_mol   # For MOL / SDF files only, import other modules for other file formats
from oasa3.coords_generator import coords_generator

• 2 : Open the file you want to depict

mFile = open("GDP_model.sdf")      #? opens a molecule file
molecule = file_to_mol(mFile)        #? parse this file into the method to create a molecule object


#? The file_to_mol method can only read .mol or .sdf files, other types can be SMILES or InChI depending on what you imported.

• 3 : Generate coordinates ( Converting 3D to 2D ), and remove unimportant hydrogens if you wish

coordGenerator = coords_generator(18)       #? init coords_generator class with bond length of 18 units
coordGenerator.calculate_coords(mol=molecule,bond_length=20,force=1)     #?Generate coordinates for depiction with bond length 18 units, 2nd argument is to force recalculating coords.
molecule.remove_unimportant_hydrogens() #? this generates a 6th dimentional matrix that handles spacetime conformation of deuterium atoms to gen.... It removes non essential hydrogen atoms in the depiction.

• 4 : Initialize the depiction class and write the image into a file.

#? Initialize cairo_out class with these parameters, feel free to try other ones if you do not like the depiction.
#? Further arguments can be found in the original OASA repo or in the end of file here  :  https://github.com/mimminou/PDBASER/blob/main/GUI/Build/MolHandler.py

c = cairo_out(scaling=4, margin=15, font_size=10, bond_width=2.0,
                                      background_color=(0, 0, 0, 0), bond_second_line_shortening=0.08,
                                      color_bonds=False, space_around_atom=2.0,
                                      line_width=1.2,
                                      show_hydrogens_on_hetero= True,
                                      wedge_width= 5)

#? Write the generated image to a file with .png format, supports also vectors in .svg, and .pdf
c.mol_to_cairo(mol=molecule,filename="GDP.png",format="png")

Bonus step

#? Get molecular weight of this molecule : 
mw = molecule.weight
formated_molecule_weight = "{:.2f}".format(mw)


#! If you liked this fork, please check out the project that inspired me to work on porting this library : 
# https://github.com/mimminou/PDBASER

OASA

Introduction

OASA is a free python library for manipulating and analyzing chemical structures. Even though OASA is already some (current year - 2009) years old project, its API may be unstable. This is mainly because it was never before released outside of BKChem and Reinis Danne followed all significant API changes there. Therefore please do not expect a highly polished, well documented library. OASA is probably rather the opposite. You have been warned.

Features

• reading and writing of SMILES, InChI, Molfile
• atom coordinate generation
• molecule rendering into PNG, PDF and SVG using cairo

Missing features

• documentation
• full streochemistry support (only cis/trans double bond stereochemistry is supported)
• many more I cannot remember now

Sample export

This is an example of PNG export:

Requirements

• OASA3 needs python 3.6 or higher to run properly.

STATUS

bellow are summarized the limitations of the library. it does by no means mean that there are no other limitations, however, for these it has no sense to write bugreports :)

OVERALL:

• no documentation beyond the source code is available
• stereochemistry support is limited to cis/trans stereochemistry on double bonds and only in some formats
• not much effort was invested into optimalization of the code, it may be pretty slow sometimes
• the API might be unstable

SMILES:

• cis/trans stereochemistry is supported, some attempt were made to make tetrahedral stereochemistry work, but it is not very much tested

InChI:

• reading is done natively by OASA
• for writing the original InChI program is needed (cInChI, cInChI.exe)

MOLFILE

• not all data in the properties block (after the bond block) are supported (this means that molfiles containing a properties block might not be read properly)

COORDS GENERATOR:

• coords for molecules like calix[4]arene and similar do not give a very nice picture
• tetrahedral stereochemistry is not taken into account

CAIRO_OUT:

• pycairo may be required to make use of cairo_out functionality (although depiction worked on Ubuntu 21.10 without it installed in python.)
• PNG, PDF and SVG export is supported