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#1357 Circular FP - rubricTetrahedral
Null pointer Exception
Tested on KEGG molecules:
For example
a) C00524, C00658, C00676, C01003, etc.
java.lang.NullPointerException
at org.openscience.cdk.fingerprint.CircularFingerprinter.rubricTetrahedral(CircularFingerprinter.java:853)
at org.openscience.cdk.fingerprint.CircularFingerprinter.excavateMolecule(CircularFingerprinter.java:597)
at org.openscience.cdk.fingerprint.CircularFingerprinter.calculate(CircularFingerprinter.java:193)
at org.openscience.cdk.fingerprint.CircularFingerprinter.getBitFingerprint(CircularFingerprinter.java:259)
Hi Asad,
Have you modified the molecule at all? I don't get any problems from the KEGG molfiles.
J
Hi John,
Yes I do modify the molecule by adding Hydrogen etc.
I agree with you that the direct conversion (SMILES to fingerprint) doesn’t show this error!
Something strange might be taking place in my conversion code…
Asad
Related
Bugs:
#1357Your molecule is in an inconsistent state. Some of the atoms have
coordinates some don't (the hydrogens). You either need to layout the
hydrogens with the SDG or remove them.
I will fix the code to avoid the NPE though.
Regards,
John W May
john.wilkinsonmay@gmail.com
On 11 February 2015 at 11:29, Asad asadrahman@users.sf.net wrote:
Related
Bugs:
#1357I managed to reproduce it but not with hydrogens. Other atoms must have null coordinates.
IAtomContainer container = new MDLV2000Reader(new StringReader(" \n" + " \n" + " \n" + " 65 70 0 0 1 0 0 0 0 0999 V2000\n" + " 26.4746 -25.8650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 25.2321 -26.4070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 26.5689 -24.5105 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0\n" + " 27.8058 -26.3773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 23.9534 -25.8965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.8883 -24.1959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 28.6144 -25.3428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.7474 -26.5017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 23.7390 -24.5468 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 28.3756 -22.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 23.6445 -21.6212 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0\n" + " 21.7775 -25.5972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.4080 -24.3266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.8766 -21.7589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 23.8171 -20.2717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.2950 -21.8591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.8673 -23.1261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 28.4886 -20.5280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 26.5329 -21.5502 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.5863 -19.6959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 25.0480 -19.6132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.6541 -20.6702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.5200 -19.5888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 26.3136 -20.2193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.5747 -18.3230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.2870 -20.6702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.5084 -18.2157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 23.7584 -17.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.8441 -20.3026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 30.7582 -21.4129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.7688 -27.8205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.0096 -28.5705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 28.9731 -30.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 30.2137 -30.7626 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 27.7100 -30.7117 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.6923 -27.8455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.4956 -28.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.4406 -29.8206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.2439 -30.4449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 22.5755 -30.5470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.3364 -25.6635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.9222 -25.4060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 25.0654 -23.0671 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.3689 -17.6419 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.3552 -16.2332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.1156 -15.5332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 18.9275 -16.2344 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.1022 -14.1346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 18.8582 -13.4317 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 21.2818 -13.4382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 30.3412 -18.9756 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 31.7328 -18.7439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 32.2236 -17.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 33.6210 -17.2020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 31.3349 -16.3545 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 34.5216 -18.2967 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 34.1110 -15.8951 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 18.9275 -17.6344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.9349 -16.3545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 18.8582 -12.0317 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 35.5110 -15.8951 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 17.7151 -18.3344 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.2349 -15.1421 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 20.1399 -18.3344 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 29.2349 -17.5669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 11 16 1 0 0 0\n" + " 13 17 2 0 0 0\n" + " 14 18 1 0 0 0\n" + " 14 19 2 0 0 0\n" + " 15 20 2 0 0 0\n" + " 15 21 1 0 0 0\n" + " 16 22 2 0 0 0\n" + " 18 23 2 0 0 0\n" + " 19 24 1 0 0 0\n" + " 20 25 1 0 0 0\n" + " 22 26 1 0 0 0\n" + " 23 27 1 0 0 0\n" + " 6 7 1 0 0 0\n" + " 12 13 1 0 0 0\n" + " 16 17 1 0 0 0\n" + " 20 22 1 0 0 0\n" + " 21 24 2 0 0 0\n" + " 23 24 1 0 0 0\n" + " 25 28 1 0 0 0\n" + " 18 29 1 0 0 0\n" + " 29 30 1 0 0 0\n" + " 1 2 2 0 0 0\n" + " 4 31 1 0 0 0\n" + " 1 3 1 0 0 0\n" + " 31 32 1 0 0 0\n" + " 1 4 1 0 0 0\n" + " 32 33 1 0 0 0\n" + " 2 5 1 0 0 0\n" + " 33 34 2 0 0 0\n" + " 3 6 1 0 0 0\n" + " 33 35 1 0 0 0\n" + " 4 7 2 0 0 0\n" + " 8 36 1 0 0 0\n" + " 5 8 1 0 0 0\n" + " 36 37 1 0 0 0\n" + " 5 9 2 0 0 0\n" + " 37 38 1 0 0 0\n" + " 6 10 2 0 0 0\n" + " 38 39 1 0 0 0\n" + " 8 12 2 0 0 0\n" + " 38 40 2 0 0 0\n" + " 9 13 1 0 0 0\n" + " 12 41 1 0 0 0\n" + " 10 14 1 0 0 0\n" + " 7 42 1 0 0 0\n" + " 11 15 1 0 0 0\n" + " 11 43 1 0 0 0\n" + " 3 43 1 0 0 0\n" + " 25 44 1 0 0 0\n" + " 44 45 1 0 0 0\n" + " 46 45 1 6 0 0\n" + " 46 47 1 0 0 0\n" + " 46 48 1 0 0 0\n" + " 48 49 1 0 0 0\n" + " 48 50 2 0 0 0\n" + " 29 51 1 0 0 0\n" + " 51 52 1 0 0 0\n" + " 53 52 1 6 0 0\n" + " 53 54 1 0 0 0\n" + " 53 55 1 0 0 0\n" + " 54 56 2 0 0 0\n" + " 54 57 1 0 0 0\n" + " 47 58 1 0 0 0\n" + " 55 59 1 0 0 0\n" + " 49 60 1 0 0 0\n" + " 57 61 1 0 0 0\n" + " 58 62 1 0 0 0\n" + " 59 63 1 0 0 0\n" + " 58 64 2 0 0 0\n" + " 59 65 2 0 0 0\n" + "M END")).read(new AtomContainer()); AtomContainerManipulator.convertImplicitToExplicitHydrogens(container); new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6).calculate(container);patch https://github.com/cdk/cdk/pull/116