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Get 3D Chemical Structures - Python Automation

I am working in python and i want to get a series of 3D images for the molecules I'm using.

I have .mol files stored in my folder and for each of them I would like to obtain a 3D render of its 'stick' representation. With py3Dmol i can get a 3D structure of the molecule, but i can only view it and it is not stored anywhere in python. Here a source (from the author of the package) explaining why images cannot be saved

Do you have any suggestion on how to do automatize the creation of 3D structure images for a set of molecule?

Solution

  • OK , here my attempt, please have a look at Multiple PyMOL Instances in Python Script and Launching From a Script that explains how this works:

    """
Yes it's possible to have independent instances. The API has actually been 
around for a long time. For some reason it was never widely adopted and thus is 
not very thoroughly tested. Please report any bugs you encounter.

Example:
"""
import pymol2
p = pymol2.PyMOL()
p.start()
p.cmd.fragment('ala')
p.cmd.show_as('sticks')
p.cmd.zoom()
p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
p.stop()

    Code :

    import pymol2

import os

work_dir = "." 

file_folders = os.listdir(work_dir)  


mol_files = [item for item in file_folders if os.path.isfile(item) and   item.rsplit('.')[1] == 'mol']

print(mol_files)


for mol_file in mol_files:
    

    p = pymol2.PyMOL()
    
    p.start()
    
    mol_name = mol_file.rsplit('.')[0]
    
    print(mol_file.rsplit('.')[0])
    
    try :
     
        p.cmd.load(mol_file , mol_name)
    
        p.cmd.hide(representation = 'sticks' , selection = mol_name)
        
        p.cmd.show(representation = 'lines' , selection = mol_name)
        
        p.cmd.do('set ray_opaque_background, 0')
        ## or to get black background instead of transparent
        #p.cmd.bg_color(color="black")
        #p.cmd.do('set ray_opaque_background, 1')
        
        p.cmd.orient(mol_name)
        
        p.cmd.png(mol_name+'.png' , dpi = 400, width = 5000, ray = 1)
        
        p.cmd.remove(mol_name)
        
        p.stop()
        
    except :
        
        print('\nError ----> something is wrong with ', mol_name+'.mol file \n')
    
print('finished ...............................')

    Note that the molecules are oriented on the screen by pymol.cm.orient() that as per the wiki:

    orient aligns the principal components of the atoms in the selection with the XYZ axes. T

    AS an example here the pic for GLC from Chemical Components in the PDB GLC : Summary

    pic