Hi, I'm trying to use the rdkit shape-based alignment method to align some chemicals and compare it to another alignment method. The most relevant part of my script is given below:
refShape = builder.GenerateSubshapeShape(ref) probeShape = builder.GenerateSubshapeShape(probe) aligner = SubshapeAligner.SubshapeAligner() algs = aligner.GetSubshapeAlignments(ref, refShape, probe, probeShape, builder) alg = algs[0] scores[i]=1.0-alg.shapeDist My understanding is that algs = aligner.GetSubshapeAlignments(ref, refShape, probe, probeShape, builder) creates a list of alignment objects which have various properties (such as the shapeDist which quantifies how good the alignment was). However, for some chemicals, the list appears to be empty. Does this mean that no alignments were generated (if so why? I naively assumed that the function would always generate alignments but in some instances they may be very poor)? The SubshapeAligner module does not appear to be very well documented so I'm having a hard time identifying work arounds to this/understanding what the root of the problem is. Additionally, here are some of the chemicals where it failed to generate alignments: 1.) Reference Chemical: 1(C(N2C(S1)C(C2=O)NC(=O)COC3=CC=CC=C3)C(=O)O)C Second Chemical: CC1(C(N2C(S1)C(C2=O)NC(=O)COC3=C(CCl)C=CC=C3)C(=O)O)C 2.) Reference Chemical: CC1(C(N2C(S1)C(C2=O)NC(=O)COC3=CC=CC=C3)C(=O)O)C Second Chemical: CC1(C(N2C(S1)C(C2=O)NC(=O)COC3=C(C(CC)(CC)(CC))C=CC=C3)C(=O)O)C 3.) Reference Chemical: c1ccccc1 Second Chemical: Oc1ccccc1 The chemicals are different from one another, and it doesn't seem that a particular class of chemicals is triggering the issue. Any advice on this would be greatly appreciated! Thanks in advance for your time, Serena Debesai Stanford Class of 2023 B.S. Physics | Minor Candidate: Mathematics, African and African American Studies
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