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InChI generation error #20

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AimeeD90 opened this Issue Jan 2, 2019 · 1 comment

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@AimeeD90 @schymane
@AimeeD90

AimeeD90 commented Jan 2, 2019

Hello,
I have tried to use a LocalSDF database of the latest version of HMDB, but an InChI generation error occurred. The error logs are pasted as follows. Is there any solution for this problem?
Besides, at the end of the letter, I provided a specific example that causing this error. Hope that could help test.

ERROR LOGS:
$ java -jar MetFrag2.4.3-CL.jar parameter.txt
org.openscience.cdk.exception.CDKException: Failed to generate InChI: Unsupported bond type
at org.openscience.cdk.inchi.InChIGenerator.generateInchiFromCDKAtomContainer(InChIGenerator.java:307)
at org.openscience.cdk.inchi.InChIGenerator.(InChIGenerator.java:172)
at org.openscience.cdk.inchi.InChIGenerator.(InChIGenerator.java:130)
at org.openscience.cdk.inchi.InChIGeneratorFactory.getInChIGenerator(InChIGeneratorFactory.java:147)
at de.ipbhalle.metfraglib.additionals.MoleculeFunctions.getInChIInfoFromAtomContainer(MoleculeFunctions.java:235)
at de.ipbhalle.metfraglib.database.LocalSDFDatabase.readCandidatesFromFile(LocalSDFDatabase.java:148)
at de.ipbhalle.metfraglib.database.LocalSDFDatabase.getCandidateIdentifiers(LocalSDFDatabase.java:31)
at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.retrieveCompounds(CombinedMetFragProcess.java:77)
at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:104)
java.lang.NullPointerException
at de.ipbhalle.metfraglib.additionals.MoleculeFunctions.getInChIInfoFromAtomContainer(MoleculeFunctions.java:239)
at de.ipbhalle.metfraglib.database.LocalSDFDatabase.readCandidatesFromFile(LocalSDFDatabase.java:148)
at de.ipbhalle.metfraglib.database.LocalSDFDatabase.getCandidateIdentifiers(LocalSDFDatabase.java:31)
at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.retrieveCompounds(CombinedMetFragProcess.java:77)
at de.ipbhalle.metfrag.commandline.CommandLineTool.main(CommandLineTool.java:104)
ERROR de.ipbhalle.metfrag.commandline.CommandLineTool - Error when retrieving compounds.

EXAMPLE:
Mrv0541 04191211592D

95106 0 0 1 0 999 V2000
-0.6472 -1.5655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7591 -0.7620 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.9518 -1.3667 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-2.6231 -1.8463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3741 -1.5048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4538 -0.6837 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7591 0.9361 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.6472 1.7396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3596 2.1164 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.4780 2.9329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8302 3.4437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9487 4.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7149 4.5657 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.9518 1.5366 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.5935 2.0551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7217 1.2401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3634 1.7586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1333 1.4621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7940 1.7396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9183 0.9361 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.7425 0.7870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1566 0.0870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7425 -0.6171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9183 -0.7620 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7940 -1.5655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5313 -1.9465 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
1.6536 -2.7624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4214 -3.0643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5437 -3.8802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3114 -4.1822 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.1235 -1.3667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7616 -1.8896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8954 -1.0755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1235 1.5366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
2.7961 2.0143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5462 1.6707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2188 2.1484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1413 2.9697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.5313 2.1164 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
2.2821 2.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6106 2.9376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3614 3.2795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4408 4.1007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0900 2.1495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0900 2.9745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0900 -1.9797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0900 -2.8047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5708 -0.6171 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.3677 -0.4036 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5708 0.8118 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.3677 0.5983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0741 -3.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7885 -3.5965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5030 -3.1840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.7885 -4.4215 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.5030 -4.8340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5030 -5.6590 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.3280 -5.6590 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0741 -2.3590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3596 -1.9465 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.3596 -2.7715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3008 4.7709 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.0329 2.8002 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.9688 1.8048 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.8983 -4.3941 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.2353 2.5736 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.0453 -1.9845 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.5001 -5.6865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6751 -7.1154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6751 -5.6865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3694 -5.4090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2626 -6.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1231 -5.0734 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4556 -6.2294 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9126 -6.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7376 -6.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5001 -7.1154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9126 -7.8299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1575 -6.7815 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.0712 -7.6020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.8249 -7.9375 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.9964 -8.7445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7811 -8.9994 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.9645 -6.6099 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-1.3000 -5.8563 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3770 -7.3244 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.1974 -7.4107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8457 -7.2080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.6780 -5.6590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.5030 -6.4840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1984 -6.5819 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
-1.4419 -6.6140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0601 0.1366 0.0000 Co 0 0 0 0 0 0 0 0 0 0 0 0
-0.4324 2.9513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0593 3.8036 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
46 1 2 0 0 0 0
1 2 1 0 0 0 0
60 1 1 0 0 0 0
48 2 1 0 0 0 0
2 93 1 0 0 0 0
48 3 1 0 0 0 0
48 50 1 0 0 0 0
3 4 1 1 0 0 0
3 60 1 0 0 0 0
4 5 1 0 0 0 0
5 67 1 0 0 0 0
5 6 2 0 0 0 0
50 7 1 0 0 0 0
50 14 1 0 0 0 0
7 8 2 0 0 0 0
9 8 1 0 0 0 0
8 44 1 0 0 0 0
9 10 1 6 0 0 0
14 9 1 0 0 0 0
10 11 1 0 0 0 0
11 12 1 0 0 0 0
12 62 1 0 0 0 0
12 13 2 0 0 0 0
14 15 1 6 0 0 0
14 16 1 0 0 0 0
16 17 1 0 0 0 0
17 66 1 0 0 0 0
17 18 2 0 0 0 0
44 19 2 0 0 0 0
19 20 1 0 0 0 0
19 39 1 0 0 0 0
20 21 2 0 0 0 0
21 22 1 0 0 0 0
21 34 1 0 0 0 0
22 23 2 0 0 0 0
23 24 1 0 0 0 0
23 31 1 0 0 0 0
24 25 2 0 0 0 0
25 26 1 0 0 0 0
26 27 1 6 0 0 0
26 31 1 0 0 0 0
27 28 1 0 0 0 0
28 29 1 0 0 0 0
29 65 1 0 0 0 0
29 30 2 0 0 0 0
31 32 1 0 0 0 0
31 33 1 0 0 0 0
34 35 1 6 0 0 0
34 39 1 0 0 0 0
35 36 1 0 0 0 0
36 37 1 0 0 0 0
37 64 1 0 0 0 0
37 38 2 0 0 0 0
39 40 1 6 0 0 0
39 41 1 1 0 0 0
41 42 1 0 0 0 0
42 63 1 0 0 0 0
42 43 2 0 0 0 0
20 93 8 0 0 0 0
7 93 8 0 0 0 0
24 93 8 0 0 0 0
44 45 1 0 0 0 0
46 47 1 0 0 0 0
48 49 1 1 0 0 0
50 51 1 6 0 0 0
59 52 1 0 0 0 0
52 53 1 0 0 0 0
53 55 1 0 0 0 0
53 54 2 0 0 0 0
56 55 1 0 0 0 0
57 56 1 0 0 0 0
57 89 1 1 0 0 0
57 58 1 1 0 0 0
57 90 1 0 0 0 0
60 59 1 6 0 0 0
60 61 1 1 0 0 0
46 25 1 0 0 0 0
68 70 2 0 0 0 0
68 75 1 0 0 0 0
72 69 2 0 0 0 0
69 77 1 0 0 0 0
70 73 1 0 0 0 0
70 72 1 0 0 0 0
71 74 1 0 0 0 0
71 73 2 0 0 0 0
74 72 1 0 0 0 0
79 74 1 1 0 0 0
77 75 2 0 0 0 0
75 76 1 0 0 0 0
77 78 1 0 0 0 0
79 84 1 0 0 0 0
79 80 1 0 0 0 0
81 80 1 0 0 0 0
86 81 1 0 0 0 0
81 82 1 6 0 0 0
82 83 1 0 0 0 0
84 86 1 0 0 0 0
84 85 1 1 0 0 0
86 87 1 1 0 0 0
91 87 1 0 0 0 0
91 88 1 0 0 0 0
91 89 1 0 0 0 0
91 92 2 0 0 0 0
93 94 1 0 0 0 0
94 95 3 0 0 0 0
73 93 8 0 0 0 0
M STY 4 1 DAT 2 DAT 3 DAT 4 DAT
M SAL 1 2 20 93
M SDT 1 MRV_COORDINATE_BOND_TYPE
M SDD 1 0.0000 0.0000 DR ALL 0 0
M SED 1 59
M SAL 2 2 7 93
M SDT 2 MRV_COORDINATE_BOND_TYPE
M SDD 2 0.0000 0.0000 DR ALL 0 0
M SED 2 60
M SAL 3 2 24 93
M SDT 3 MRV_COORDINATE_BOND_TYPE
M SDD 3 0.0000 0.0000 DR ALL 0 0
M SED 3 61
M SAL 4 2 73 93
M SDT 4 MRV_COORDINATE_BOND_TYPE
M SDD 4 0.0000 0.0000 DR ALL 0 0
M SED 4 106
M END

<DATABASE_ID>
HMDB0000607

<DATABASE_NAME>
hmdb

OC[C@H]1OC@@HN1C=NC2=CC(C)=C(C)C=C12

<INCHI_IDENTIFIER>
InChI=1S/C62H90N13O14P.CN.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+1/p-1/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1

<INCHI_KEY>
SEKGMJVHSBBHRD-WZHZPDAFSA-M

C63H89CoN14O14P

<MOLECULAR_WEIGHT>
1356.3731

<EXACT_MASS>
1355.575230332

<JCHEM_BIOAVAILABILITY>
0

<JCHEM_FORMAL_CHARGE>
0

<JCHEM_GHOSE_FILTER>
0

<JCHEM_IUPAC>
[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14-tris(2-carbamoylethyl)-3,8,19-tris(carbamoylmethyl)-18-(2-{[(2R)-2-[({[(2R,3S,4R,5S)-5-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl)oxy]propyl]carbamoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltcarbonitrile

<ALOGPS_LOGP>
1.87

<ALOGPS_LOGS>
-4.55

<JCHEM_MDDR_LIKE_RULE>
1

<JCHEM_NUMBER_OF_RINGS>
8

<JCHEM_PHYSIOLOGICAL_CHARGE>
2

<JCHEM_PKA_STRONGEST_ACIDIC>
1.8410431729042473

<JCHEM_PKA_STRONGEST_BASIC>
8.771751821130694

<JCHEM_RULE_OF_FIVE>
0

<ALOGPS_SOLUBILITY>
3.84e-02 g/l

<JCHEM_TRADITIONAL_IUPAC>
[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14-tris(2-carbamoylethyl)-3,8,19-tris(carbamoylmethyl)-18-(2-{[(2R)-2-({[(2R,3S,4R,5S)-5-(5,6-dimethyl-1,3-benzodiazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy(hydroxy)phosphoryl}oxy)propyl]carbamoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltcarbonitrile

<JCHEM_VEBER_RULE>
0

<HMDB_ID>
HMDB0000607

<GENERIC_NAME>
Cyanocobalamin

$$$$
@schymane

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schymane commented Jan 7, 2019

Thanks for the report - are you able to provide the parameters you are using (parameter.txt)?
I can create an InChI without problems from the SMILES of that HMDB record using Open Babel, and CDK Depict also deals with the SMILES fine. You may be able to change a setting to avoid this error, but I need to see your settings first. Does the problem also occur if you use the web interface with the same SDF file (see first screenshot)?

Note also that HMDB is already integrated as a database (second screenshot), so you should be able to access this already using different settings (please try the web interface and download the parameter files to find the correct settings).

https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=OC%5BC%40H%5D1O%5BC%40%40H%5D(%5BC%40H%5D(O)%5BC%40%40H%5D1OP(O)(%3DO)O%5BC%40%5D(%5BH%5D)(C)CNC(%3DO)CC%5BC%40%5D1(C)%5BC%40%40H%5D(CC(%3DO)N)%5BC%40%40%5D2(%5BH%5D)N(%5BCo%5DC%23N)%5CC1%3DC(C)%2FC1%3DN%2FC(%3DC%5CC3%3DN%5CC(%3DC(C)%2FC4%3DN%5BC%40%5D2(C)%5BC%40%40%5D(C)(CC(%3DO)N)%5BC%40%40H%5D4CCC(%3DO)N)%5C%5BC%40%40%5D(C)(CC(%3DO)N)%5BC%40%40H%5D3CCC(%3DO)N)%2FC(C)(C)%5BC%40%40H%5D1CCC(%3DO)N)N1C%3DNC2%3DCC(C)%3DC(C)C%3DC12&abbr=on&hdisp=bridgehead&showtitle=false&zoom=1.6&annotate=none

image

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