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"babel -i fs ... -s SMILES" - Substructure Search with Index
How to perform a substructure search using the fastsearch index file with the "babel" command?
✍: FYIcenter.com
If you want to perform a substructure search using the fastsearch index
file, you can use the following "babel" command syntax:
babel -i fs index_file output_section -s SMILES
In the above command:
Here is an example of substructure search of benzene ring molecule SMILES in a fastsearch index file.
fyicenter$ babel -i fs molecules-index.fs -o smiles -s 'c1ccccc1' 210 candidates from fingerprint search phase [Fe].O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC.O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC 499518 O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC 499519 S(=O)(=O)(O)c1c2c(c(S(=O)(=O)O)ccc2Nc2cc3c(nc2C)c(OC)cc([N+](=O)[O-])c3OC)cc(S(=O)(=O)O)c1 499522 [nH]1c2c(NCCN(C)C)ncnc2nc1c1cc2c(cc1)cccc2 499528 N(CCN(C)C)c1nc(nc2nc[nH]c12)c1cc2c(cc1)cccc2 499529 [Co+2].ClCC[NH+](CCN)CCCl.[S-]C(=S)N(CC)CC.[S-]C(=S)N(CC)CC.c1(ccccc1)[B-](c1ccccc1)(c1ccccc1)c1ccccc1 499531 [Co+2].ClCCN(c1cc(N)c(N)cc1)CCCl.[S-]C(=S)N(CC)CC.[S-]C(=S)N(CC)CC 499532 O(N=C1C2(C(C3C(CC2)c2c(CC3)cc(OC)cc2)CC1)C)CCN1CCCCC1 499539 [Ni+2].[S-]CCP(c1ccccc1)c1ccccc1.[S-]CCP(c1ccccc1)c1ccccc1 499544 SCCP(c1ccccc1)c1ccccc1 499545 ... O=C(c1cc2CCCCc2cc1)C[n+]1ccncc1 499990 [P+](C1c2c(c3c1cccc3)cccc2)(c1ccccc1)(c1ccccc1)c1ccccc1 499996 Brc1[n+](Cc2c(C[n+]3c(Br)cccc3)cccc2)cccc1 499997 Brc1[n+](Cc2cc(C[n+]3c(Br)cccc3)ccc2)cccc1 499998 Fc1c2c(C(=O)N(C(c3ccccc3)C)C2=O)c(F)c(F)c1F 499999 208 molecules converted 7241 audit log messages
Here is an example of the same substructure search as above with resulting molecules saved in a file.
fyicenter$ babel -i fs molecules-index.fs -o smiles result.smi -s 'c1ccccc1' 210 candidates from fingerprint search phase 208 molecules converted 7241 audit log messages fyicenter$ head result.smi [Fe].O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC.O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC 499518 O(C(=O)c1ccc(NC(=O)[C]2[CH][CH][CH][CH]2)cc1)CC 499519 S(=O)(=O)(O)c1c2c(c(S(=O)(=O)O)ccc2Nc2cc3c(nc2C)c(OC)cc([N+](=O)[O-])c3OC)cc(S(=O)(=O)O)c1 499522 [nH]1c2c(NCCN(C)C)ncnc2nc1c1cc2c(cc1)cccc2 499528 N(CCN(C)C)c1nc(nc2nc[nH]c12)c1cc2c(cc1)cccc2 499529 [Co+2].ClCC[NH+](CCN)CCCl.[S-]C(=S)N(CC)CC.[S-]C(=S)N(CC)CC.c1(ccccc1)[B-](c1ccccc1)(c1ccccc1)c1ccccc1 499531 [Co+2].ClCCN(c1cc(N)c(N)cc1)CCCl.[S-]C(=S)N(CC)CC.[S-]C(=S)N(CC)CC 499532 O(N=C1C2(C(C3C(CC2)c2c(CC3)cc(OC)cc2)CC1)C)CCN1CCCCC1 499539 [Ni+2].[S-]CCP(c1ccccc1)c1ccccc1.[S-]CCP(c1ccccc1)c1ccccc1 499544 SCCP(c1ccccc1)c1ccccc1 499545
Note that the substructure search command with index file is identical with the similarity search with index file, except that the similarity search has an extra option "-at ..." to specify the top similarity selection criteria.
⇒ "babel -i fs ... -s query_file" - Substructure Search
⇐ "Difficulty opening ..." Error Using Fastsearch Index
2020-05-25, 498👍, 0💬
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