AlignMol does not find substructure match...

[apahl]

... although HasSubstructMatch says there is one:

from rdkit.Chem import AllChem as Chem
from rdkit.Chem import rdMolAlign
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"

import rdkit
rdkit.__version__
# -> '2023.03.1'

smi_core = "Cn2ccc1ccccc12"
smi_mol = "Cn2cc(CC(N)=O)c1ccccc12"
core = Chem.MolFromSmiles(smi_core)
mol = Chem.MolFromSmiles(smi_mol)
mol.HasSubstructMatch(core)
# -> True

core.Compute2DCoords()
mol.Compute2DCoords()
mh = Chem.AddHs(mol)
mh.HasSubstructMatch(core)
# -> True

rdMolAlign.AlignMol(mh, core)
# ->
# RuntimeError                              Traceback (most recent call last)
# ----> 1 rdMolAlign.AlignMol(mh, core)
# RuntimeError: No sub-structure match found between the probe and query mol

Any ideas?

KR Axel

[thegodone]

rdMolAlign.AlignMol(core , mh) is working ... why ? Le jeu. 21 mars 2024 à 15:14, Axel Pahl ***@***.***> a écrit :

…

... although HasSubstructMatch says there is one: from rdkit.Chem import AllChem as Chemfrom rdkit.Chem import rdMolAlignfrom rdkit.Chem import Drawfrom rdkit.Chem.Draw import IPythonConsole from IPython.core.interactiveshell import InteractiveShellInteractiveShell.ast_node_interactivity = "all" import rdkitrdkit.__version__# -> '2023.03.1' smi_core = "Cn2ccc1ccccc12"smi_mol = "Cn2cc(CC(N)=O)c1ccccc12"core = Chem.MolFromSmiles(smi_core)mol = Chem.MolFromSmiles(smi_mol)mol.HasSubstructMatch(core)# -> True core.Compute2DCoords()mol.Compute2DCoords()mh = Chem.AddHs(mol)mh.HasSubstructMatch(core)# -> True rdMolAlign.AlignMol(mh, core)# -># RuntimeError Traceback (most recent call last)# ----> 1 rdMolAlign.AlignMol(mh, core)# RuntimeError: No sub-structure match found between the probe and query mol Any ideas? KR Axel — Reply to this email directly, view it on GitHub <#7285>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJBWYUFOSABJDVMJ7ZMB7TYZLTMJAVCNFSM6AAAAABFBRKHWSVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZWGQYDIMZSGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[apahl]

Are you saying that I am calling the function with the wrong argument order? But I want mh to be aligned to core and the documentation says the first argument is the one that gets aligned.
I guess I have to define an atom map, then.

Thanks for the hint, Guillaume.

[thegodone]

No Axel, I don't understand why the inverse is working... Le jeu. 21 mars 2024 à 21:49, Axel Pahl ***@***.***> a écrit :

…

Are you saying that I am calling the function with the wrong argument order? But I want mh to be aligned to core and the documentation says the first argument is the one that gets aligned. — Reply to this email directly, view it on GitHub <#7285 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJBWYUZ24FINJYHKYG3Q3DYZNBUNAVCNFSM6AAAAABFBRKHWSVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DQNZQHA2DG> . You are receiving this because you commented.Message ID: ***@***.***>

[apahl]

Ah, ok. Please excuse the misunderstanding.

[apahl]

But indeed, creating an atom map does work. So thank you anyway for pointing me into the right direction.

smi_core = "Cn2ccc1ccccc12"
smi_mol = "Cn2cc(CC(N)=O)c1ccccc12"

core = Chem.MolFromSmiles(smi_core)
mol = Chem.MolFromSmiles(smi_mol)

core_match = core.GetSubstructMatch(core)
mol_match = mol.GetSubstructMatch(core)
assert len(core_match) == len(mol_match), "Number of matching atoms is different."
atom_map = list(zip(mol_match, core_match))

core.Compute2DCoords()
mol.Compute2DCoords()

rdMolAlign.AlignMol(mol, core, atomMap=atom_map)

KR Axel

[thegodone]

Great! Le ven. 22 mars 2024 à 09:17, Axel Pahl ***@***.***> a écrit :

…

But indeed, creating an atom map does work. So thank you anyway for pointing me into the right direction. smi_core = "Cn2ccc1ccccc12"smi_mol = "Cn2cc(CC(N)=O)c1ccccc12" core = Chem.MolFromSmiles(smi_core)mol = Chem.MolFromSmiles(smi_mol) core_match = tuple(x.GetIdx() for x in core.GetAtoms())mol_match = mol.GetSubstructMatch(core)assert len(core_match) == len(mol_match), "Number of matching atoms is different."atom_map = list(zip(mol_match, core_match)) core.Compute2DCoords()mol.Compute2DCoords() rdMolAlign.AlignMol(mol, core, atomMap=atom_map) KR Axel — Reply to this email directly, view it on GitHub <#7285 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJBWYU32VYYG5IPM5D2VHTYZPSJ3AVCNFSM6AAAAABFBRKHWSVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DQNZVGA2DS> . You are receiving this because you commented.Message ID: ***@***.***>