[Rdkit-discuss] Polymers, S-Groups, and molblock-parsing (oh my!)
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[Rdkit-discuss] Polymers, S-Groups, and molblock-parsing (oh my!)
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From: James D. <J.D...@ve...> - 2011-10-19 12:20:20
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Dear All, I just wanted to raise an observation about the behaviour of the molblock parser. I was running some SMARTS-based substructure queries in KNIME, and happened to be looking for aromatic N-oxides - the query was just "nO" - which should maybe be the answer as well! : ) Anyway, I was actually searching DrugBank (via the SDF - http://www.drugbank.ca/system/downloads/current/structures/small_molecul e.sdf.zip) and found Heparin was a hit for my query - which I thought was a bit funny as there are no aromatic nitrogens. It seems, however, that the match is due to the * atoms in the molblock (see below) that are representing the polymer repeat points (leading to *-O, which is matching n-O). As I understand it, the rest of the info about the polymer is stored as S-Group data - and I am presuming that RDKit is not currently interpreting this(?) So I guess the simple question is - should polymers, etc be handled by the parser (maybe if not fully, just partially - eg by deleting the * atoms if the S-Group data are found)? Kind regards James Mrv0541 09201117322D 111114 0 0 1 0 999 V2000 12.8725 -11.1521 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 13.5903 -11.5667 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 12.8725 -10.3272 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.8517 -11.7493 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 14.2992 -11.1521 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 13.5903 -12.3914 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 13.5903 -9.9172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1547 -9.9172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8307 -12.3335 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 14.2992 -10.3272 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 14.9729 -11.9185 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 11.4415 -10.3272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.8307 -13.1582 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.1175 -11.9232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 15.3200 -9.7433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 16.1934 -11.9139 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 10.1175 -13.5728 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.7684 -14.1445 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3996 -12.3335 0.0000 C 0 0 2 0 0 0 0 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26 31 2 0 0 0 0 27 32 1 0 0 0 0 27 33 1 1 0 0 0 28 34 1 0 0 0 0 28 35 1 1 0 0 0 29 36 1 0 0 0 0 32 37 1 0 0 0 0 33 38 1 0 0 0 0 33 39 2 0 0 0 0 34 40 1 6 0 0 0 37 41 1 1 0 0 0 42 41 1 6 0 0 0 42 43 1 0 0 0 0 42 44 1 0 0 0 0 43 45 1 0 0 0 0 43 46 1 1 0 0 0 44 47 1 0 0 0 0 44 48 1 1 0 0 0 45 49 1 0 0 0 0 46 50 1 0 0 0 0 47 51 1 6 0 0 0 49 52 1 0 0 0 0 50 53 1 0 0 0 0 51 54 1 0 0 0 0 53 55 1 0 0 0 0 53 56 2 0 0 0 0 53 57 2 0 0 0 0 54 58 1 0 0 0 0 54 59 2 0 0 0 0 7 10 1 0 0 0 0 19 24 1 0 0 0 0 34 37 1 0 0 0 0 47 49 1 0 0 0 0 18 60 1 0 0 0 0 60 61 2 0 0 0 0 60 62 2 0 0 0 0 60 63 1 0 0 0 0 6 64 1 0 0 0 0 64 65 2 0 0 0 0 64 66 2 0 0 0 0 64 67 1 0 0 0 0 40 68 1 0 0 0 0 68 69 2 0 0 0 0 68 70 2 0 0 0 0 68 71 1 0 0 0 0 1 72 1 1 0 0 0 2 73 1 6 0 0 0 3 74 1 6 0 0 0 5 75 1 1 0 0 0 8 76 1 0 0 0 0 8 77 1 0 0 0 0 9 78 1 6 0 0 0 10 79 1 1 0 0 0 11 80 1 0 0 0 0 12 81 1 0 0 0 0 13 82 1 1 0 0 0 17 83 1 6 0 0 0 19 84 1 1 0 0 0 20 85 1 1 0 0 0 21 86 1 0 0 0 0 24 87 1 1 0 0 0 25 88 1 0 0 0 0 27 89 1 6 0 0 0 28 90 1 6 0 0 0 30 91 1 0 0 0 0 34 92 1 1 0 0 0 35 93 1 0 0 0 0 37 94 1 6 0 0 0 38 95 1 0 0 0 0 42 96 1 1 0 0 0 43 97 1 6 0 0 0 44 98 1 6 0 0 0 46 99 1 0 0 0 0 46100 1 0 0 0 0 47101 1 1 0 0 0 48102 1 0 0 0 0 49103 1 0 0 0 0 51104 1 0 0 0 0 55105 1 0 0 0 0 58106 1 0 0 0 0 58107 1 0 0 0 0 58108 1 0 0 0 0 63109 1 0 0 0 0 67110 1 0 0 0 0 71111 1 0 0 0 0 M STY 1 1 SRU M SCN 1 1 HT M SAL 1 15 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 M SAL 1 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 M SAL 1 15 31 32 33 34 35 37 38 39 40 41 42 43 44 45 46 M SAL 1 15 47 48 49 50 51 53 54 55 56 57 58 59 60 61 62 M SAL 1 15 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 M SAL 1 15 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 M SAL 1 15 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 M SAL 1 4 108 109 110 111 M SDI 1 4 6.8467 -4.6587 6.8467 -16.3159 M SDI 1 4 24.3752 -16.3159 24.3752 -4.6587 M SBL 1 2 35 51 M SMT 1 n M END > <DRUGBANK_ID> DB01109 > <DRUG_GROUPS> approved; investigational > <GENERIC_NAME> Heparin > <SYNONYMS> Alpha-Heparin; Heparin sodium; Heparin sodium preservative Free; Heparin sodium salt; Heparin sulfate; Heparinate; Heparinic acid; Sodium heparin; heparin > <BRANDS> Ariven; Arteven; Calcilean; Calciparine; Certoparin; Depo-Heparin; Eparina [DCIT]; Hed-Heparin; Hepalean; Heparin Cy 216; Heparin Leo; Heparin Lock Flush; Hepathrom; Leparan; Lipo-Hepin; Liquaemin; Liquaemin Sodium; Liquemin; Multiparin; Novoheparin; Pabyrin; Parvoparin; Pularin; Thromboliquine; Vetren > <CHEMICAL_FORMULA> C26H42N2O37S5 > <MOLECULAR_WEIGHT> 1134.928 > <EXACT_MASS> 1134.006993818 > <IUPAC_NAME> 3-[(5-{[6-carboxy-4,5-dihydroxy-3-(sulfooxy)oxan-2-yl]oxy}-6-(hydroxymet hyl)-3-(sulfoamino)-4-(sulfooxy)oxan-2-yl)oxy]-6-({5-acetamido-4,6-dihyd roxy-2-[(sulfooxy)methyl]oxan-3-yl}oxy)-4-hydroxy-5-(sulfooxy)oxane-2-ca rboxylic acid > <INCHI_IDENTIFIER> InChI=1S/C26H42N2O37S5/c1-4(30)27-7-9(31)13(6(56-23(7)39)3-55-67(43,44)4 5)58-26-19(65-70(52,53)54)12(34)16(20(62-26)22(37)38)60-24-8(28-66(40,41 )42)15(63-68(46,47)48)14(5(2-29)57-24)59-25-18(64-69(49,50)51)11(33)10(3 2)17(61-25)21(35)36/h5-20,23-26,28-29,31-34,39H,2-3H2,1H3,(H,27,30)(H,35 ,36)(H,37,38)(H,40,41,42)(H,43,44,45)(H,46,47,48)(H,49,50,51)(H,52,53,54 ) > <INCHI_KEY> InChIKey=HTTJABKRGRZYRN-UHFFFAOYSA-N > <SMILES> CC(=O)NC1C(O)OC(COS(O)(=O)=O)C(OC2OC(C(OC3OC(CO)C(OC4OC(C(O)C(O)C4OS(O)( =O)=O)C(O)=O)C(OS(O)(=O)=O)C3NS(O)(=O)=O)C(O)C2OS(O)(=O)=O)C(O)=O)C1O > <JCHEM_ACCEPTOR_COUNT> 33.0 > <JCHEM_DONOR_COUNT> 15.0 > <JCHEM_ACIDIC_PKA> -2.37 > <ALOGPS_LOGP> -1.68 > <JCHEM_LOGP> -8.35 > <ALOGPS_LOGS> -2.02 > <JCHEM_POLARIZABILITY> 93.37 > <JCHEM_POLAR_SURFACE_AREA> 610.49 > <JCHEM_REFRACTIVITY> 195.91 > <JCHEM_ROTATABLE_BOND_COUNT> 20 > <ALOGPS_SOLUBILITY> 1.08e+01 g/l $$$$ ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. 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