Hello, 1 OpenBabel12081111222D
31 30 0 0 0 0 0 0 0 0999 V2000 2.8660 0.7500 0.0000 O 0 0 0 0 0 2.8660 -2.2500 0.0000 O 0 0 0 0 0 2.0000 -0.7500 0.0000 O 0 0 0 0 0 3.7320 2.2500 0.0000 O 0 0 0 0 0 5.4641 0.2500 0.0000 N 0 0 0 0 0 4.5981 0.7500 0.0000 C 0 0 0 0 0 3.7320 0.2500 0.0000 C 0 0 0 0 0 6.3301 -0.2500 0.0000 C 0 0 0 0 0 5.9641 1.1160 0.0000 C 0 0 0 0 0 4.9641 -0.6160 0.0000 C 0 0 0 0 0 3.7320 -0.7500 0.0000 C 0 0 0 0 0 2.8660 -1.2500 0.0000 C 0 0 0 0 0 2.8660 1.7500 0.0000 C 0 0 0 0 0 2.0000 2.2500 0.0000 C 0 0 0 0 0 4.9966 1.2250 0.0000 H 0 0 0 0 0 4.1996 1.2250 0.0000 H 0 0 0 0 0 3.7320 0.8700 0.0000 H 0 0 0 0 0 6.0201 -0.7869 0.0000 H 0 0 0 0 0 6.8671 -0.5600 0.0000 H 0 0 0 0 0 6.6401 0.2869 0.0000 H 0 0 0 0 0 6.5010 0.8060 0.0000 H 0 0 0 0 0 6.2741 1.6530 0.0000 H 0 0 0 0 0 5.4272 1.4260 0.0000 H 0 0 0 0 0 4.4272 -0.3060 0.0000 H 0 0 0 0 0 4.6541 -1.1530 0.0000 H 0 0 0 0 0 5.5010 -0.9260 0.0000 H 0 0 0 0 0 3.9441 -1.3326 0.0000 H 0 0 0 0 0 4.3426 -0.6423 0.0000 H 0 0 0 0 0 2.3100 2.7869 0.0000 H 0 0 0 0 0 1.4631 2.5600 0.0000 H 0 0 0 0 0 1.6900 1.7131 0.0000 H 0 0 0 0 0 1 7 1 0 0 0 1 13 1 0 0 0 2 12 1 0 0 0 3 12 2 0 0 0 4 13 2 0 0 0 5 6 1 0 0 0 5 8 1 0 0 0 5 9 1 0 0 0 5 10 1 0 0 0 6 7 1 0 0 0 6 15 1 0 0 0 6 16 1 0 0 0 7 11 1 0 0 0 7 17 1 0 0 0 8 18 1 0 0 0 8 19 1 0 0 0 8 20 1 0 0 0 9 21 1 0 0 0 9 22 1 0 0 0 9 23 1 0 0 0 10 24 1 0 0 0 10 25 1 0 0 0 10 26 1 0 0 0 11 12 1 0 0 0 11 27 1 0 0 0 11 28 1 0 0 0 13 14 1 0 0 0 14 29 1 0 0 0 14 30 1 0 0 0 14 31 1 0 0 0 M CHG 2 2 -1 5 1 M END > <PUBCHEM_COMPOUND_CID> 1 > <PUBCHEM_COMPOUND_CANONICALIZED> 1 > <PUBCHEM_CACTVS_COMPLEXITY> 214 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 4 > <PUBCHEM_CACTVS_HBOND_DONOR> 0 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 5 > <PUBCHEM_CACTVS_SUBSKEYS> AAADceByOAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHgAAAAAACBThgAYCCAMABAAIAACQCAAAAAAAAAAAAAEIAAACABQAgAAHAAAFIAAQAAAkAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA== > <PUBCHEM_IUPAC_OPENEYE_NAME> 3-acetoxy-4-(trimethylammonio)butanoate > <PUBCHEM_IUPAC_CAS_NAME> 3-acetyloxy-4-(trimethylammonio)butanoate > <PUBCHEM_IUPAC_NAME> 3-acetyloxy-4-(trimethylazaniumyl)butanoate > <PUBCHEM_IUPAC_SYSTEMATIC_NAME> 3-acetyloxy-4-(trimethylazaniumyl)butanoate > <PUBCHEM_IUPAC_TRADITIONAL_NAME> 3-acetoxy-4-(trimethylammonio)butyrate > <PUBCHEM_IUPAC_INCHI> InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3 > <PUBCHEM_IUPAC_INCHIKEY> RDHQFKQIGNGIED-UHFFFAOYSA-N > <PUBCHEM_XLOGP3_AA> 0.4 > <PUBCHEM_EXACT_MASS> 203.115758 > <PUBCHEM_MOLECULAR_FORMULA> C9H17NO4 > <PUBCHEM_MOLECULAR_WEIGHT> 203.23558 > <PUBCHEM_OPENEYE_CAN_SMILES> CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C > <PUBCHEM_OPENEYE_ISO_SMILES> CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C > <PUBCHEM_CACTVS_TPSA> 66.4 > <PUBCHEM_MONOISOTOPIC_WEIGHT> 203.115758 > <PUBCHEM_TOTAL_CHARGE> 0 > <PUBCHEM_HEAVY_ATOM_COUNT> 14 > <PUBCHEM_ATOM_DEF_STEREO_COUNT> 0 > <PUBCHEM_ATOM_UDEF_STEREO_COUNT> 1 > <PUBCHEM_BOND_DEF_STEREO_COUNT> 0 > <PUBCHEM_BOND_UDEF_STEREO_COUNT> 0 > <PUBCHEM_ISOTOPIC_ATOM_COUNT> 0 > <PUBCHEM_COMPONENT_COUNT> 1 > <PUBCHEM_CACTVS_TAUTO_COUNT> 1 > <PUBCHEM_COORDINATE_TYPE> 1 5 255 > <PUBCHEM_BONDANNOTATIONS> 7 6 3 $$$$ 2 OpenBabel12081111222D 32 31 0 0 0 0 0 0 0 0999 V2000 4.2690 -0.7500 0.0000 O 0 0 0 0 0 2.5369 2.2500 0.0000 O 0 0 0 0 0 4.2690 2.2500 0.0000 O 0 0 0 0 0 2.5369 -0.7500 0.0000 O 0 0 0 0 0 6.0010 0.2500 0.0000 N 0 0 0 0 0 5.1350 0.7500 0.0000 C 0 0 0 0 0 4.2690 0.2500 0.0000 C 0 0 0 0 0 6.8671 -0.2500 0.0000 C 0 0 0 0 0 6.5010 1.1160 0.0000 C 0 0 0 0 0 5.5010 -0.6160 0.0000 C 0 0 0 0 0 3.4030 0.7500 0.0000 C 0 0 0 0 0 3.4030 1.7500 0.0000 C 0 0 0 0 0 3.4030 -1.2500 0.0000 C 0 0 0 0 0 3.4030 -2.2500 0.0000 C 0 0 0 0 0 5.5335 1.2250 0.0000 H 0 0 0 0 0 4.7365 1.2250 0.0000 H 0 0 0 0 0 4.8059 -0.0600 0.0000 H 0 0 0 0 0 6.5571 -0.7869 0.0000 H 0 0 0 0 0 7.4040 -0.5600 0.0000 H 0 0 0 0 0 7.1771 0.2869 0.0000 H 0 0 0 0 0 7.0380 0.8060 0.0000 H 0 0 0 0 0 6.8110 1.6530 0.0000 H 0 0 0 0 0 5.9641 1.4260 0.0000 H 0 0 0 0 0 4.9641 -0.3060 0.0000 H 0 0 0 0 0 5.1910 -1.1530 0.0000 H 0 0 0 0 0 6.0380 -0.9260 0.0000 H 0 0 0 0 0 2.7924 0.8577 0.0000 H 0 0 0 0 0 3.1909 0.1674 0.0000 H 0 0 0 0 0 2.7830 -2.2500 0.0000 H 0 0 0 0 0 3.4030 -2.8700 0.0000 H 0 0 0 0 0 4.0230 -2.2500 0.0000 H 0 0 0 0 0 2.0000 1.9400 0.0000 H 0 0 0 0 0 1 7 1 0 0 0 1 13 1 0 0 0 2 12 1 0 0 0 2 32 1 0 0 0 3 12 2 0 0 0 4 13 2 0 0 0 5 6 1 0 0 0 5 8 1 0 0 0 5 9 1 0 0 0 5 10 1 0 0 0 6 7 1 0 0 0 6 15 1 0 0 0 6 16 1 0 0 0 7 11 1 0 0 0 7 17 1 0 0 0 8 18 1 0 0 0 8 19 1 0 0 0 8 20 1 0 0 0 9 21 1 0 0 0 9 22 1 0 0 0 9 23 1 0 0 0 10 24 1 0 0 0 10 25 1 0 0 0 10 26 1 0 0 0 11 12 1 0 0 0 11 27 1 0 0 0 11 28 1 0 0 0 13 14 1 0 0 0 14 29 1 0 0 0 14 30 1 0 0 0 14 31 1 0 0 0 M CHG 1 5 1 M END > <PUBCHEM_COMPOUND_CID> 2 > <PUBCHEM_COMPOUND_CANONICALIZED> 1 > <PUBCHEM_CACTVS_COMPLEXITY> 219 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 4 > <PUBCHEM_CACTVS_HBOND_DONOR> 1 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 6 > <PUBCHEM_CACTVS_SUBSKEYS> AAADceByOAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHgAACAAACBThgAYCCAMABgAIAACQCAAAAAAAAAAAAAEIAAACABQAgAAHQAAFIAAQAAAkAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA== > <PUBCHEM_IUPAC_OPENEYE_NAME> (2-acetoxy-3-carboxy-propyl)-trimethyl-ammonium > <PUBCHEM_IUPAC_CAS_NAME> (2-acetyloxy-3-carboxypropyl)-trimethylammonium > <PUBCHEM_IUPAC_NAME> (2-acetyloxy-3-carboxypropyl)-trimethylazanium > <PUBCHEM_IUPAC_SYSTEMATIC_NAME> (2-acetyloxy-4-oxidanyl-4-oxidanylidene-butyl)-trimethyl-azanium > <PUBCHEM_IUPAC_TRADITIONAL_NAME> (2-acetoxy-3-carboxy-propyl)-trimethyl-ammonium > <PUBCHEM_IUPAC_INCHI> InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/p+1 > <PUBCHEM_IUPAC_INCHIKEY> RDHQFKQIGNGIED-UHFFFAOYSA-O > <PUBCHEM_XLOGP3_AA> -0.3 > <PUBCHEM_EXACT_MASS> 204.123583 > <PUBCHEM_MOLECULAR_FORMULA> C9H18NO4+ > <PUBCHEM_MOLECULAR_WEIGHT> 204.24352 > <PUBCHEM_OPENEYE_CAN_SMILES> CC(=O)OC(CC(=O)O)C[N+](C)(C)C > <PUBCHEM_OPENEYE_ISO_SMILES> CC(=O)OC(CC(=O)O)C[N+](C)(C)C > <PUBCHEM_CACTVS_TPSA> 63.6 > <PUBCHEM_MONOISOTOPIC_WEIGHT> 204.123583 > <PUBCHEM_TOTAL_CHARGE> 1 > <PUBCHEM_HEAVY_ATOM_COUNT> 14 > <PUBCHEM_ATOM_DEF_STEREO_COUNT> 0 > <PUBCHEM_ATOM_UDEF_STEREO_COUNT> 1 > <PUBCHEM_BOND_DEF_STEREO_COUNT> 0 > <PUBCHEM_BOND_UDEF_STEREO_COUNT> 0 > <PUBCHEM_ISOTOPIC_ATOM_COUNT> 0 > <PUBCHEM_COMPONENT_COUNT> 1 > <PUBCHEM_CACTVS_TAUTO_COUNT> 1 > <PUBCHEM_COORDINATE_TYPE> 1 5 255 > <PUBCHEM_BONDANNOTATIONS> 7 11 3 $$$$ 4 OpenBabel12081111222D 14 13 0 0 0 0 0 0 0 0999 V2000 2.5369 0.7500 0.0000 O 0 0 0 0 0 5.1350 0.2500 0.0000 N 0 0 0 0 0 3.4030 0.2500 0.0000 C 0 0 0 0 0 4.2690 0.7500 0.0000 C 0 0 0 0 0 3.4030 -0.7500 0.0000 C 0 0 0 0 0 3.4030 1.1000 0.0000 H 0 0 0 0 0 4.6675 1.2250 0.0000 H 0 0 0 0 0 3.8705 1.2250 0.0000 H 0 0 0 0 0 2.7830 -0.7500 0.0000 H 0 0 0 0 0 3.4030 -1.3700 0.0000 H 0 0 0 0 0 4.0230 -0.7500 0.0000 H 0 0 0 0 0 5.6720 0.5600 0.0000 H 0 0 0 0 0 5.1350 -0.3700 0.0000 H 0 0 0 0 0 2.0000 0.4400 0.0000 H 0 0 0 0 0 1 3 1 0 0 0 1 14 1 0 0 0 2 4 1 0 0 0 2 12 1 0 0 0 2 13 1 0 0 0 3 4 1 0 0 0 3 5 1 0 0 0 3 6 1 0 0 0 4 7 1 0 0 0 4 8 1 0 0 0 5 9 1 0 0 0 5 10 1 0 0 0 5 11 1 0 0 0 M END > <PUBCHEM_COMPOUND_CID> 4 > <PUBCHEM_COMPOUND_CANONICALIZED> 1 > <PUBCHEM_CACTVS_COMPLEXITY> 22.9 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 2 > <PUBCHEM_CACTVS_HBOND_DONOR> 2 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 1 > <PUBCHEM_CACTVS_SUBSKEYS> AAADccBCIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHgAQCAAACBThgAYCAABAAgAAAAAAAAAAAAAAAAAAAIAAAAACEAAAAAAAAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA== > <PUBCHEM_IUPAC_OPENEYE_NAME> 1-aminopropan-2-ol > <PUBCHEM_IUPAC_CAS_NAME> 1-amino-2-propanol > <PUBCHEM_IUPAC_NAME> 1-aminopropan-2-ol > <PUBCHEM_IUPAC_SYSTEMATIC_NAME> 1-azanylpropan-2-ol > <PUBCHEM_IUPAC_TRADITIONAL_NAME> 1-aminopropan-2-ol > <PUBCHEM_IUPAC_INCHI> InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3 > <PUBCHEM_IUPAC_INCHIKEY> HXKKHQJGJAFBHI-UHFFFAOYSA-N > <PUBCHEM_XLOGP3> -1 > <PUBCHEM_EXACT_MASS> 75.068414 > <PUBCHEM_MOLECULAR_FORMULA> C3H9NO > <PUBCHEM_MOLECULAR_WEIGHT> 75.10966 > <PUBCHEM_OPENEYE_CAN_SMILES> CC(CN)O > <PUBCHEM_OPENEYE_ISO_SMILES> CC(CN)O > <PUBCHEM_CACTVS_TPSA> 46.2 > <PUBCHEM_MONOISOTOPIC_WEIGHT> 75.068414 > <PUBCHEM_TOTAL_CHARGE> 0 > <PUBCHEM_HEAVY_ATOM_COUNT> 5 > <PUBCHEM_ATOM_DEF_STEREO_COUNT> 0 > <PUBCHEM_ATOM_UDEF_STEREO_COUNT> 1 > <PUBCHEM_BOND_DEF_STEREO_COUNT> 0 > <PUBCHEM_BOND_UDEF_STEREO_COUNT> 0 > <PUBCHEM_ISOTOPIC_ATOM_COUNT> 0 > <PUBCHEM_COMPONENT_COUNT> 1 > <PUBCHEM_CACTVS_TAUTO_COUNT> 1 > <PUBCHEM_COORDINATE_TYPE> 1 5 255 > <PUBCHEM_BONDANNOTATIONS> 3 6 3 $$$$ 5 OpenBabel12081111222D 18 17 0 0 0 0 0 0 0 0999 V2000 3.4030 -0.3170 0.0000 P 0 0 0 0 0 4.2690 0.1830 0.0000 O 0 0 0 0 0 2.5369 -0.8170 0.0000 O 0 0 0 0 0 2.9030 0.5490 0.0000 O 0 0 0 0 0 6.0010 1.1830 0.0000 O 0 0 0 0 0 3.9030 -1.1830 0.0000 O 0 0 0 0 0 7.7331 0.1830 0.0000 N 0 0 0 0 0 5.1350 -0.3170 0.0000 C 0 0 0 0 0 6.0010 0.1830 0.0000 C 0 0 0 0 0 6.8671 -0.3170 0.0000 C 0 0 0 0 0 4.7365 -0.7919 0.0000 H 0 0 0 0 0 5.5335 -0.7919 0.0000 H 0 0 0 0 0 6.4685 -0.7919 0.0000 H 0 0 0 0 0 7.2656 -0.7919 0.0000 H 0 0 0 0 0 8.2700 -0.1270 0.0000 H 0 0 0 0 0 7.7331 0.8030 0.0000 H 0 0 0 0 0 2.0000 -0.5070 0.0000 H 0 0 0 0 0 3.2130 1.0860 0.0000 H 0 0 0 0 0 1 2 1 0 0 0 1 3 1 0 0 0 1 4 1 0 0 0 1 6 2 0 0 0 These are the first 500 Lines. Greetz Am 12.12.2011 um 16:31 schrieb Geoffrey Hutchison: >> I create the joined.sdf as follows: cat *.sdf > joined.txt and then mv >> joined.txt joined.sdf > > It's hard to know, but I suspect your *.sdf don't necessarily have the > correct $$$ and newline to separate one SDF from another. > > If you don't try to filter, how many molecules does babel find? > > % obabel joined.sdf -O joined.smi > > How many molecules are reported? > > Best regards, > -Geoff ------------------------------------------------------------------------------ Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss