Automated naming of compounds

name.py

import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import exmol
import skunk
import math
import matplotlib.pyplot as plt
import textwrap
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
import urllib.request

urllib.request.urlretrieve('https://github.com/google/fonts/raw/main/ofl/ibmplexmono/IBMPlexMono-Regular.ttf', 'IBMPlexMono-Regular.ttf')
fe = font_manager.FontEntry(
    fname='IBMPlexMono-Regular.ttf',
    name='plexmono')
font_manager.fontManager.ttflist.append(fe)
plt.rcParams.update({'axes.facecolor':'#f5f4e9', 
            'grid.color' : '#AAAAAA', 
            'axes.edgecolor':'#333333', 
            'figure.facecolor':'#FFFFFF', 
            'axes.grid': False,
            'axes.prop_cycle':   plt.cycler('color', plt.cm.Dark2.colors),
            'font.family': fe.name,
            'figure.figsize': (3.5,3.5 / 1.2),
            'ytick.left': True,
            'xtick.bottom': True   
           })
def ax_grid(count):
    '''make square grid with matplotlib subplots'''
    n = int(math.ceil(math.sqrt(count)))
    fig, ax = plt.subplots(n, n, figsize=(n * 2, n * 2) )
    ax = ax.flatten()
    print(n**2, count)
    for a in ax[count:n**2]:
        a.axis('off')
    return fig, ax
def draw_morgan_bit(mol, bitInfo, key):
    svg = Chem.Draw.DrawMorganBit(
        mol,
        key,
        bitInfo,
        molSize=(300, 200),
        centerColor=None,
        aromaticColor=None,
        ringColor=None,
        extraColor=(0.8, 0.8, 0.8),
        useSVG=True,
    )    
    try:
        svgdata = svg.data
    except AttributeError:
        svgdata = svg
    return svgdata
def draw_mol(m):
    size = (300, 200)
    dos = rdkit.Chem.Draw.MolDrawOptions()
    dos.drawMolsSameScale = False
    #dos.useBWAtomPalette()
    dos.minFontSize = 16
    d = rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(*size)
    d.SetDrawOptions(dos)
    d.DrawMolecule(m)
    d.FinishDrawing()
    return d.GetDrawingText()
def plot(smi):      
    mol = Chem.MolFromSmiles(smi)
    bitInfo = {}
    svg_dict = {}
    AllChem.GetMorganFingerprint(mol, 3, bitInfo=bitInfo)
    names = []
    used_names = set()
    for r in range(4):        
        for b in bitInfo:
            _, ri = bitInfo[b][0]
            if ri != r:
                continue
            name = exmol.exmol._name_morgan_bit(mol, bitInfo, b)
            if name is None or len(name) < 2 or name in used_names:
                continue
            names.append(name)
            s = draw_morgan_bit(mol, bitInfo, b)
            svg_dict[str(b)] = s        
        # ok now ban all names we've seen so far
        used_names |= set(names)
    print(names)
    # set-up plot
    fig, axs = ax_grid(len(svg_dict) + 1)    
    
    mol_svg = draw_mol(mol)
    axs[0].axis('off')
    svg_dict['mol'] = mol_svg
    skunk.connect(axs[0], 'mol')
    
    for ax, k, n in zip(axs[1:], svg_dict.keys(), names):
        ax.axis('off')
        ax.set_title(textwrap.fill(n, 20))
        skunk.connect(ax, str(k))
    fig.tight_layout(pad=1.0)
    svg = skunk.insert(svg_dict)
    plt.close()
    skunk.display(svg)
    
plot('O=C(NCC1CCCCC1N)C2=CC=CC=C2C3=CC=C(F)C=C3C(=O)NC4CCCCC4')