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
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