Omar That was an easy fix. Thanks a lot! I really appreciate it.
Jerry From: Omar H94 <omar8...@gmail.com> Date: Saturday, December 19, 2020 at 5:58 AM To: "Parks, Jerry M." <park...@ornl.gov> Cc: "rdkit-discuss@lists.sourceforge.net" <rdkit-discuss@lists.sourceforge.net> Subject: [EXTERNAL] Re: [Rdkit-discuss] Using FindMCS and CalcRMS to calculate RMS between docked poses of a set of similar molecules Dear Jerry, When calculating the RMS, try: rms = AllChem.CalcRMS(probeMol, refMol, map=[list(zip(mv, refMatch))]) Note that you are calculating MCS across all mols, however; you might want to consider pairwise-MCS (i.e. MCS between each docked ligand and the ref ligand individually and then calculate RMS based on it) since you want difference between each docked ligand and reference ligand. I hope this works for you. Best regards, Omar On Sat, Dec 19, 2020 at 2:03 AM Parks, Jerry M. via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hello I’m trying to calculate RMSDs between a reference molecule from an X-ray structure and a series of similar but somewhat different molecules with a common scaffold that I have docked to the protein. I don’t want to align the structures, I just want to measure how different their docked poses are to the reference structure. All of the molecules have the same core structure, but have different functional groups. This functionality is available in the recently developed web server LigRMSD (https://ligrmsd.appsbio.utalca.cl), but I need to make some modifications to the procedure. Following this thread (https://sourceforge.net/p/rdkit/mailman/message/35678724/) and this blog post (http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html), I’ve written the following code: from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions from rdkit.Chem import rdFMCS import glob # Load a set of mol files. mols = [] for m in glob.glob('*.mol'): tmpmol = Chem.MolFromMolFile(m) name_without_suffix = m[:-4] tmpmol.SetProp('_Name', name_without_suffix) mols.append(tmpmol) # Draw the molecules. Chem.Draw.MolsToGridImage(mols, molsPerRow=2, subImgSize=(350, 350), legends=[mol.GetProp('_Name') for mol in mols]) # Find the MCS. mcs = rdFMCS.FindMCS(mols,threshold=1.0, ringMatchesRingOnly=True, completeRingsOnly=True) # Align everything to the reference molecule. patt = Chem.MolFromSmarts(mcs.smartsString) refMol = mols[0] refMatch = refMol.GetSubstructMatch(patt) rmsVs = [] for probeMol in mols[1:]: mv = probeMol.GetSubstructMatch(patt) rms = AllChem.AlignMol(probeMol, refMol, atomMap=list(zip(mv, refMatch)), maxIters=0) print(probeMol.GetProp('_Name'), f'{rms:.2f}') rmsVs.append(rms) However, even though I set maxIters=0 in the call to AlignMol, the molecules have all been translated to a common origin (which is not what I want). I tried replacing that line of code with the following call to CalcRMS (using the same atom mapping): rms = AllChem.CalcRMS(probeMol, refMol, map=list(zip(mv, refMatch))) but then I got the following error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-7-0faef2f852d9> in <module>() 8 mv = probeMol.GetSubstructMatch(patt) 9 #rms = AllChem.AlignMol(probeMol, refMol, atomMap=list(zip(mv, refMatch)), maxIters=0) ---> 10 rms = AllChem.CalcRMS(probeMol, refMol, map=list(zip(mv, refMatch))) 11 print(probeMol.GetProp('_Name'), f'{rms:.2f}') 12 rmsVs.append(rms) ValueError: sequence does not support length query Any suggestions for fixing the code would be appreciated. Thank you, Jerry Parks _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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