Dear all I have observed some unexpected behaviour with the chiral version of the Morgan Fingerprints in RDKit
When reading the Rogers paper (http://doi.org/10.1021/ci100050t ) I find: "If the atom is a possible stereoatom but is not yet disambiguated, and all attachment atoms have different identifiers, then the atom is marked as disambiguated, and a stereochemical flag is appended to the array, depending on the marked stereochemistry. (Step 4 is only performed if stereochemical fingerprints are requested.)" In this aspect I believe that the rdkit implementation does not follow exactly the ECFP paper. As a test I calculated the pairwise similarity between the enatiomers of butan-2-ol, hexan-3-ol, octan-4-ol, decan-5-ol, ... Eventually the both alkyl chains should grow too long to become disambiguated within the fingerprint radius, there for the chirality on the chiral center should not be recognised any more, and the fingerprint of the enantiomers should become equal to 1, once the chains outgrow the fingerprint radius. Strangely that doesn't happen, as can be seen in the attached notebook, all fingerprints with radius > 0 will always give similarities < 1.0 for the enantiomer pairs. This contrasts with the Pipeline Pilot implementation, where with the similarity of the enantiomers indeed becomes 1.0 once the chains outgrow the fingerprint radius. For your reference I added also fingerprints and similarity values obtained at different ECFP diameters Is this difference in behaviour intentional? I always assumed so far that rdkit Morgan and Pipeline Pilot ECFP would give identical similarity results. With best regards Ansgar Schuffenhauer Senior Investigator I T +41 79 608 9063 ansgar.schuffenha...@novartis.com<mailto:ansgar.schuffenha...@novartis.com> Novartis Pharma AG NIBR Novartis Campus Virchow 16-4.249.09 4056 Basel Switzerland ________________________________ _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you.
ChiralMorganTest.ipynb
Description: ChiralMorganTest.ipynb
n smiles_a smiles_b ECFP_0#S_B[1] ECFP_0#S_B[2] ECFP_0#S_B[3] ECFP_0#S_B[4] ECFP_0#S_A[1] ECFP_0#S_A[2] ECFP_0#S_A[3] ECFP_0#S_A[4] 0 ECFP_2#S_B[1] ECFP_2#S_B[2] ECFP_2#S_B[3] ECFP_2#S_B[4] ECFP_2#S_B[5] ECFP_2#S_B[6] ECFP_2#S_B[7] ECFP_2#S_B[8] ECFP_2#S_B[9] ECFP_2#S_B[10] ECFP_2#S_A[1] ECFP_2#S_A[2] ECFP_2#S_A[3] ECFP_2#S_A[4] ECFP_2#S_A[5] ECFP_2#S_A[6] ECFP_2#S_A[7] ECFP_2#S_A[8] ECFP_2#S_A[9] ECFP_2#S_A[10] 1 ECFP_4#S_B[1] ECFP_4#S_B[2] ECFP_4#S_B[3] ECFP_4#S_B[4] ECFP_4#S_B[5] ECFP_4#S_B[6] ECFP_4#S_B[7] ECFP_4#S_B[8] ECFP_4#S_B[9] ECFP_4#S_B[10] ECFP_4#S_B[11] ECFP_4#S_B[12] ECFP_4#S_B[13] ECFP_4#S_B[14] ECFP_4#S_B[15] ECFP_4#S_B[16] ECFP_4#S_A[1] ECFP_4#S_A[2] ECFP_4#S_A[3] ECFP_4#S_A[4] ECFP_4#S_A[5] ECFP_4#S_A[6] ECFP_4#S_A[7] ECFP_4#S_A[8] ECFP_4#S_A[9] ECFP_4#S_A[10] ECFP_4#S_A[11] ECFP_4#S_A[12] ECFP_4#S_A[13] ECFP_4#S_A[14] ECFP_4#S_A[15] ECFP_4#S_A[16] 2 ECFP_6#S_B[1] ECFP_6#S_B[2] ECFP_6#S_B[3] ECFP_6#S_B[4] ECFP_6#S_B[5] ECFP_6#S_B[6] ECFP_6#S_B[7] ECFP_6#S_B[8] ECFP_6#S_B[9] ECFP_6#S_B[10] ECFP_6#S_B[11] ECFP_6#S_B[12] ECFP_6#S_B[13] ECFP_6#S_B[14] ECFP_6#S_B[15] ECFP_6#S_B[16] ECFP_6#S_B[17] ECFP_6#S_B[18] ECFP_6#S_B[19] ECFP_6#S_B[20] ECFP_6#S_B[21] ECFP_6#S_B[22] ECFP_6#S_B[23] ECFP_6#S_A[1] ECFP_6#S_A[2] ECFP_6#S_A[3] ECFP_6#S_A[4] ECFP_6#S_A[5] ECFP_6#S_A[6] ECFP_6#S_A[7] ECFP_6#S_A[8] ECFP_6#S_A[9] ECFP_6#S_A[10] ECFP_6#S_A[11] ECFP_6#S_A[12] ECFP_6#S_A[13] ECFP_6#S_A[14] ECFP_6#S_A[15] ECFP_6#S_A[16] ECFP_6#S_A[17] ECFP_6#S_A[18] ECFP_6#S_A[19] ECFP_6#S_A[20] ECFP_6#S_A[21] ECFP_6#S_A[22] ECFP_6#S_A[23] 3 ECFP_8#S_B[1] ECFP_8#S_B[2] ECFP_8#S_B[3] ECFP_8#S_B[4] ECFP_8#S_B[5] ECFP_8#S_B[6] ECFP_8#S_B[7] ECFP_8#S_B[8] ECFP_8#S_B[9] ECFP_8#S_B[10] ECFP_8#S_B[11] ECFP_8#S_B[12] ECFP_8#S_B[13] ECFP_8#S_B[14] ECFP_8#S_B[15] ECFP_8#S_B[16] ECFP_8#S_B[17] ECFP_8#S_B[18] ECFP_8#S_B[19] ECFP_8#S_B[20] ECFP_8#S_B[21] ECFP_8#S_B[22] ECFP_8#S_B[23] ECFP_8#S_B[24] ECFP_8#S_B[25] ECFP_8#S_B[26] ECFP_8#S_B[27] ECFP_8#S_B[28] ECFP_8#S_B[29] ECFP_8#S_B[30] ECFP_8#S_B[31] ECFP_8#S_A[1] ECFP_8#S_A[2] ECFP_8#S_A[3] ECFP_8#S_A[4] ECFP_8#S_A[5] ECFP_8#S_A[6] ECFP_8#S_A[7] ECFP_8#S_A[8] ECFP_8#S_A[9] ECFP_8#S_A[10] ECFP_8#S_A[11] ECFP_8#S_A[12] ECFP_8#S_A[13] ECFP_8#S_A[14] ECFP_8#S_A[15] ECFP_8#S_A[16] ECFP_8#S_A[17] ECFP_8#S_A[18] ECFP_8#S_A[19] ECFP_8#S_A[20] ECFP_8#S_A[21] ECFP_8#S_A[22] ECFP_8#S_A[23] ECFP_8#S_A[24] ECFP_8#S_A[25] ECFP_8#S_A[26] ECFP_8#S_A[27] ECFP_8#S_A[28] ECFP_8#S_A[29] ECFP_8#S_A[30] ECFP_8#S_A[31] 4 0 C[C@@H](O)CC C[C@H](O)CC 734603939 -1910270391 -1884411803 1559650422 734603939 -1910270391 -1884411803 1559650422 1 734603939 -1910270391 -1884411803 1559650422 864518973 1885523827 2023785560 -949992060 863188371 734603939 -1910270391 -1884411803 1559650422 864518973 -421476962 2023785560 -949992060 863188371 0.8 734603939 -1910270391 -1884411803 1559650422 864518973 1885523827 2023785560 -949992060 863188371 1997990444 734603939 -1910270391 -1884411803 1559650422 864518973 -421476962 2023785560 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-1910270391 -1884411803 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 441911862 -2144275484 -1166612082 -889426564 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 441911862 -922721817 -1166612082 -889426564 0.904761904761905 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 441911862 -2144275484 -1166612082 -889426564 563730331 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1790802833 196083830 2023785560 -1792133435 -83879862 767803027 -1598563128 764414169 825417534 -86640970 441911862 -922721817 -1166612082 -889426564 563681697 0.826086956521739 3 CCCC[C@@H](O)CCCCC CCCC[C@H](O)CCCCC 734603939 1559650422 -1910270391 -1884411803 734603939 1559650422 -1910270391 -1884411803 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 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-2116439685 1837523319 484902630 -65356119 359527728 799764439 1110695697 173105456 1 6 CCCCCCC[C@@H](O)CCCCCCCC CCCCCCC[C@H](O)CCCCCCCC 734603939 1559650422 -1910270391 -1884411803 734603939 1559650422 -1910270391 -1884411803 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 -86640970 822656426 -2122681104 -2119919996 764414169 -1598563128 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 -86640970 822656426 -2122681104 -2119919996 764414169 -1598563128 1 734603939 1559650422 -1910270391 -1884411803 863188371 -1793471910 -1792133435 -1790802833 196083830 2023785560 -86640970 822656426 -2122681104 -2119919996 764414169 -1598563128 34879675 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