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
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M STY 1 1 SRU
M SCN 1 1 HT
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15
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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
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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
$$$$
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