hjxdl 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

hdl/jupyfuncs/chem/mol.py

@@ -0,0 +1,548 @@
+# Jupyter funcs
+import os
+import re
+import itertools
+from copy import deepcopy
+# from collections import defaultdict
+
+from rdkit import Chem
+from rdkit.Chem.Draw import IPythonConsole
+from rdkit.Chem.Draw.IPythonConsole import addMolToView
+# from rdkit.Chem import rdDepictor
+from rdkit.Chem.Draw import rdMolDraw2D
+from IPython.display import SVG
+from rdkit.Chem import AllChem
+from ipywidgets import (
+    interact,
+    # interactive,
+    fixed,
+)
+from rdkit.Chem.rdRGroupDecomposition import (
+    RGroupDecomposition,
+    # RGroupDecompositionParameters,
+    # RGroupMatching,
+    # RGroupScore,
+    # RGroupLabels,
+    # RGroupCoreAlignment,
+    RGroupLabelling
+)
+import pandas as pd
+from rdkit.Chem import PandasTools
+from rdkit.Chem import Draw
+from IPython.display import HTML
+# from rdkit import rdBase
+from IPython.display import display
+
+from rdkit import Chem
+from rdkit.Chem import rdmolops
+from rdkit.Chem import Draw
+from rdkit.Chem.Draw import IPythonConsole
+from rdkit.Chem import rdRGroupDecomposition
+from rdkit.Chem import rdqueries
+from rdkit.Chem import rdDepictor
+from rdkit.Chem.Draw import rdMolDraw2D
+from rdkit.Chem.MolStandardize import rdMolStandardize
+from rdkit import Geometry
+rdDepictor.SetPreferCoordGen(True)
+import pandas as pd
+from PIL import Image as pilImage
+from io import BytesIO
+from IPython.display import SVG, Image
+from ipywidgets import interact
+import molvs as mv
+
+
+IPythonConsole.ipython_useSVG = True
+IPythonConsole.molSize = (450, 350)
+params = Chem.SubstructMatchParameters()
+params.aromaticMatchesConjugated = True 
+
+__all__ = [
+    'draw_mol',
+    'draw_confs',
+    'show_decomp',
+    'get_ids_folds',
+    'show_pharmacophore',
+    'mol_without_indices',
+    'norm_colors',
+    'drawmol_with_hi',
+    'draw_mols_surfs',
+]
+
+
+COLORS = {
+    # "Tol" colormap from https://davidmathlogic.com/colorblind
+    'tol': [
+        (51, 34, 136),
+        (17, 119, 51),
+        (68, 170, 153),
+        (136, 204, 238),
+        (221, 204, 119),
+        (204, 102, 119),
+        (170, 68, 153),
+        (136, 34, 85)
+    ],
+    # "IBM" colormap from https://davidmathlogic.com/colorblind
+    'ibm': [
+        (100, 143, 255),
+        (120, 94, 240),
+        (220, 38, 127),
+        (254, 97, 0),
+        (255, 176, 0)
+    ],
+    # Okabe_Ito colormap from https://jfly.uni-koeln.de/color/
+    'okabe': [
+        (230, 159, 0),
+        (86, 180, 233),
+        (0, 158, 115),
+        (240, 228, 66),
+        (0, 114, 178),
+        (213, 94, 0),
+        (204, 121, 167)
+    ]
+}
+
+
+# def get_his_for_onemol(mol_sm, pat_sm):
+#     atom_ids = []
+#     bond_ids = []
+#     m = Chem.MolFromSmiles(mol_sm)
+#     pt = Chem.MolFromSmiles(pat_sm)
+#     hi_id = m.GetSubstructMatches(pt, params=params)
+#     if len(m.GetSubstructMatches(pt, params=params)) == 0:
+#         Chem.Kekulize(m)       
+#         hi_id = m.GetSubstructMatches(pt, params=params) 
+#     if len(hi_id) == 0:
+#         return
+#     atom_ids.append(itertools.chain.from_iterable(hi_id))
+
+
+# def get_match_his(mol_sms, pat_sms):
+#     highlightatoms = defaultdict(list)
+#     highlightbonds = defaultdict(list)
+#     for i in range(len(df)):
+#         try:
+#             mm = df.iloc[i, 0][2:-2]
+#             pm = df.iloc[i, 2]
+#             m = Chem.MolFromSmiles(mm) 
+#             pt = Chem.MolFromSmiles(pm)
+#             hi_id = m.GetSubstructMatches(pt, params=params)
+#             if len(m.GetSubstructMatches(pt, params=params)) == 0:
+#                 Chem.Kekulize(m)       
+#                 hi_id = m.GetSubstructMatches(pt, params=params)
+#             mols.append(m)
+#             hi_ids.append(hi_id)
+#         except:
+#             pass
+#         pass
+
+
+def norm_colors(colors=COLORS):
+    colors = deepcopy(COLORS)
+    for k, v in colors.items():
+        for i, color in enumerate(v):
+            colors[k][i] = tuple(y / 255 for y in color)
+    return colors
+
+
+def drawmol_with_hi(
+    mol,
+    legend,
+    atom_hi_dict,
+    bond_hi_dict,
+    atomrads_dict,
+    widthmults_dict,
+    width=350,
+    height=200,
+):
+    d2d = rdMolDraw2D.MolDraw2DCairo(width, height)
+    d2d.ClearDrawing()
+    d2d.DrawMoleculeWithHighlights(
+        mol, legend, 
+        atom_hi_dict,
+        bond_hi_dict, 
+        atomrads_dict,
+        widthmults_dict
+    )
+    d2d.FinishDrawing()
+    png = d2d.GetDrawingText()
+    return png
+
+
+def show_atom_number(mol, label='atomNote'):
+    new_mol = deepcopy(mol)
+    for atom in new_mol.GetAtoms():
+        atom.SetProp(label, str(atom.GetIdx()))
+    return new_mol
+
+
+def moltosvg(mol, molSize=(500, 500), kekulize=True):
+    mc = mol
+    drawer = rdMolDraw2D.MolDraw2DSVG(molSize[0], molSize[1])
+    drawer.DrawMolecule(mc)
+    drawer.FinishDrawing()
+    svg = drawer.GetDrawingText()
+    return svg.replace('svg:', '')
+
+
+def draw_mol(mol):
+    return SVG(moltosvg(show_atom_number(mol)))
+
+
+def drawit(m, p, confId=-1):
+    mb = Chem.MolToMolBlock(m, confId=confId)
+    p.removeAllModels()
+    p.addModel(mb, 'sdf')
+    p.setStyle({'stick': {}})
+    p.setBackgroundColor('0xeeeeee')
+    p.zoomTo()
+    return p.show()
+
+
+def draw_confs(m):
+    import py3Dmol
+    p = py3Dmol.view(width=500, height=500)
+    return interact(drawit,
+                    m=fixed(m),
+                    p=fixed(p),
+                    confId=(0, m.GetNumConformers() - 1))
+
+
+def do_decomp(mols, cores, options):
+    options.rgroupLabelling = RGroupLabelling.AtomMap
+    decomp = RGroupDecomposition(cores, options)
+    for mol in mols:
+        decomp.Add(mol)
+    decomp.Process()
+    return decomp
+
+
+def show_decomp(mols, cores, options, item=False):
+    decomp = do_decomp(mols, cores, options)
+    if item:
+        rows = decomp.GetRGroupsAsRows()
+        items = [
+            '{}:{}'.format(
+                group, Chem.MolToSmiles(row[group])
+            )
+            for row in rows for group in row
+        ]
+        return ' '.join(items)
+    else:
+        cols = decomp.GetRGroupsAsColumns()
+        cols['mol'] = mols
+        cols['input core'] = cores[0]
+        df = pd.DataFrame(cols)
+        PandasTools.ChangeMoleculeRendering(df)
+        return HTML(df.to_html())
+
+
+def get_ids_folds(id_list, num_folds, need_shuffle=False):
+    if need_shuffle:
+        from random import shuffle
+        shuffle(id_list)
+    num_ids = len(id_list)
+    assert num_ids >= num_folds
+    
+    num_each_fold = int(num_ids / num_folds)
+    
+    blocks = []
+    
+    for i in range(num_folds):
+        start = num_each_fold * i
+        end = start + num_each_fold
+        if end > num_ids - 1:
+            end = num_ids - 1
+        
+        blocks.append(id_list[start: end])
+    
+    id_blocks = []
+    for i in range(num_folds):
+        id_blocks.append(
+            (list(itertools.chain.from_iterable([blocks[j] for j in range(num_folds) if j != i])),
+             blocks[i])
+        )
+        
+    return id_blocks
+
+
+keep = ["Donor", "Acceptor", "Aromatic", "Hydrophobe", "LumpedHydrophobe"]
+
+
+def show_pharmacophore(
+    sdf_path,
+    keep=keep,
+    fdf_dir=os.path.join(
+        os.path.dirname(__file__),
+        "..",
+        "datasets",
+        'defined_BaseFeatures.fdef'
+    )
+):
+    template_mol = [m for m in Chem.SDMolSupplier(sdf_path)][0]
+    fdef = AllChem.BuildFeatureFactory(
+        fdf_dir
+    )
+    prob_feats = fdef.GetFeaturesForMol(template_mol)
+    prob_feats = [f for f in prob_feats if f.GetFamily() in keep]
+    # prob_points = [list(x.GetPos()) for x in prob_feats]
+
+    for i, feat in enumerate(prob_feats):
+        atomids = feat.GetAtomIds()
+        print(
+            "pharamcophore index:{0}; feature:{1}; type:{2}; atom id:{3}".format(
+                i, 
+                feat.GetFamily(), 
+                feat.GetType(),
+                atomids
+            )
+        )
+        display(
+            Draw.MolToImage(
+                template_mol,
+                highlightAtoms=list(atomids),
+                highlightColor=[0, 1, 0],
+                useSVG=True
+            )
+        )
+
+
+def mol_without_indices( 
+    mol_input: Chem.Mol, 
+    remove_indices=[], 
+    keep_properties=[] 
+): 
+     
+    atom_list, bond_list, idx_map = [], [], {}  # idx_map: {old: new} 
+    for atom in mol_input.GetAtoms(): 
+         
+        props = {} 
+        for property_name in keep_properties: 
+            if property_name in atom.GetPropsAsDict(): 
+                props[property_name] = atom.GetPropsAsDict()[property_name] 
+        symbol = atom.GetSymbol() 
+         
+        if symbol.startswith('*'): 
+            atom_symbol = '*' 
+            props['molAtomMapNumber'] = atom.GetAtomMapNum() 
+        elif symbol.startswith('R'): 
+            atom_symbol = '*' 
+            if len(symbol) > 1: 
+                atom_map_num = int(symbol[1:]) 
+            else: 
+                atom_map_num = atom.GetAtomMapNum() 
+            props['dummyLabel'] = 'R' + str(atom_map_num) 
+            props['_MolFileRLabel'] = str(atom_map_num) 
+            props['molAtomMapNumber'] = atom_map_num 
+             
+        else: 
+            atom_symbol = symbol 
+        atom_list.append( 
+            ( 
+                atom_symbol, 
+                atom.GetFormalCharge(), 
+                atom.GetNumExplicitHs(), 
+                props 
+            ) 
+        ) 
+    for bond in mol_input.GetBonds(): 
+        bond_list.append( 
+            ( 
+                bond.GetBeginAtomIdx(), 
+                bond.GetEndAtomIdx(), 
+                bond.GetBondType() 
+            ) 
+        ) 
+    mol = Chem.RWMol(Chem.Mol()) 
+     
+    new_idx = 0 
+    for atom_index, atom_info in enumerate(atom_list): 
+        if atom_index not in remove_indices: 
+            atom = Chem.Atom(atom_info[0]) 
+            atom.SetFormalCharge(atom_info[1]) 
+            atom.SetNumExplicitHs(atom_info[2]) 
+             
+            for property_name in atom_info[3]: 
+                if isinstance(atom_info[3][property_name], str): 
+                    atom.SetProp(property_name, atom_info[3][property_name]) 
+                elif isinstance(atom_info[3][property_name], int): 
+                    atom.SetIntProp(property_name, atom_info[3][property_name]) 
+            mol.AddAtom(atom) 
+            idx_map[atom_index] = new_idx 
+            new_idx += 1 
+    for bond_info in bond_list: 
+        if ( 
+            bond_info[0] not in remove_indices 
+            and bond_info[1] not in remove_indices 
+        ): 
+            mol.AddBond( 
+                idx_map[bond_info[0]], 
+                idx_map[bond_info[1]], 
+                bond_info[2] 
+            ) 
+        else: 
+            one_in = False 
+            if ( 
+                (bond_info[0] in remove_indices) 
+                and (bond_info[1] not in remove_indices) 
+            ): 
+                keep_index = bond_info[1] 
+                # remove_index = bond_info[0] 
+                one_in = True 
+            elif ( 
+                (bond_info[1] in remove_indices) 
+                and (bond_info[0] not in remove_indices) 
+            ): 
+                keep_index = bond_info[0] 
+                # remove_index = bond_info[1] 
+                one_in = True 
+            if one_in:  
+                if atom_list[keep_index][0] == 'N': 
+                    old_num_explicit_Hs = mol.GetAtomWithIdx( 
+                        idx_map[keep_index] 
+                    ).GetNumExplicitHs() 
+
+                    mol.GetAtomWithIdx(idx_map[keep_index]).SetNumExplicitHs( 
+                        old_num_explicit_Hs + 1 
+                    ) 
+    mol = Chem.Mol(mol) 
+    return mol
+
+
+def draw_mols_surfs(
+    mols,
+    width=400,
+    height=400,
+    surface=True,
+    surface_opacity=0.5
+):
+    import py3Dmol
+
+    view = py3Dmol.view(width=width, height=height)
+    view.setBackgroundColor('0xeeeeee')
+    view.removeAllModels()
+    for mol in mols:
+        addMolToView(mol, view)
+    if surface:
+        view.addSurface(
+            py3Dmol.SAS,
+            {'opacity': surface_opacity}
+        )
+    view.zoomTo()
+    return view.show()
+
+
+def draw_rxn(
+    rxn_smiles,
+    use_smiles: bool = True,
+):
+    rxn = AllChem.ReactionFromSmarts(rxn_smiles, useSmiles=use_smiles)
+    d2d = Draw.MolDraw2DCairo(2000, 500)
+    d2d.DrawReaction(rxn, highlightByReactant=True)
+    png = d2d.GetDrawingText()
+    display(Image(png))
+
+
+def react(rxn_smarts, reagents):
+    try:
+        rxn = AllChem.ReactionFromSmarts(rxn_smarts)
+        # n_reactants = rxn.GetNumReactantTemplates()
+        products = rxn.RunReactants([
+            Chem.MolFromSmiles(smi) for smi in reagents
+        ])
+        return products
+    except Exception as e:
+        print(e)
+        return []
+
+
+def match_pattern(mol, patt):
+    if mol:
+        return mol.HasSubstructMatch(patt)
+    else:
+        return False
+
+
+def split_rxn_smiles(smi):
+    try:
+        reagents1, reagents2, products = smi.split('>')
+        if len(reagents2) > 0:
+            reagents = '.'.join([reagents1, reagents2])
+        else:
+            reagents = reagents1
+        return reagents, products
+    except Exception as e:
+        print(e)
+        return '', ''
+
+
+def find_mprod(rxn_smi):
+    # ref: https://github.com/LiamWilbraham/uspto-analysis/blob/master/reaction-stats-uspto.ipynb
+    rxn_smarts = '[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]'
+    patt_acid = Chem.MolFromSmarts('[CX3](=O)[OX2H1]')
+    patt_amine = Chem.MolFromSmarts('[N;H3,H2,H1]')  # ammonia or primary/secondary amine
+    
+    products = split_rxn_smiles(rxn_smi)[1].split('.')
+        
+    reactants = [r for r in split_rxn_smiles(rxn_smi)[0].split('.')]
+    cooh = [
+        r
+        for r in reactants
+        if match_pattern(Chem.MolFromSmiles(r), patt_acid)
+    ]
+    
+    cooh = [re.sub('@', '', i) for i in cooh]
+    
+    amine = [
+        r for r in reactants
+        if match_pattern(Chem.MolFromSmiles(r), patt_amine)
+    ]
+    amine = [re.sub('@', '', i) for i in amine]
+
+    for perm in itertools.product(cooh, amine):
+        
+        cooh_i = perm[0]
+        amine_i = perm[1]
+        
+        smarts_products = react(rxn_smarts, perm)
+
+        for p_1 in smarts_products:
+            for p_2 in products:
+                p_2 = re.sub('@', '', p_2)
+                patt = Chem.MolFromSmiles(p_2)  
+                if Chem.MolToInchiKey(p_1[0]) == Chem.MolToInchiKey(patt):  
+                    return cooh_i, amine_i, p_2
+    return None
+
+
+def get_largest_mol(smiles, to_smiles=False):
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        return
+    mol_frags = rdmolops.GetMolFrags(mol, asMols=True)
+    largest_mol = max(mol_frags, default=mol, key=lambda m: m.GetNumAtoms())
+    if to_smiles:
+        return mv.standardize_smiles(Chem.MolToSmiles(largest_mol))
+    return largest_mol
+
+
+def standardize_tautomer(mol, max_tautomers=1000):
+    params = rdMolStandardize.CleanupParameters()
+    params.maxTautomers = max_tautomers
+    enumerator = rdMolStandardize.TautomerEnumerator(params)
+    cm = enumerator.Canonicalize(mol)
+    return cm
+
+
+def reorder_tautomers(m):
+    enumerator = rdMolStandardize.TautomerEnumerator()
+    canon = enumerator.Canonicalize(m)
+    csmi = Chem.MolToSmiles(canon)
+    res = [canon]
+    tauts = enumerator.Enumerate(m)
+    smis = [Chem.MolToSmiles(x) for x in tauts]
+    stpl = sorted(
+        (x, y) for x, y in zip(smis, tauts) if x!=csmi
+    )
+    res += [y for _, y in stpl]
+    return res