Substructure search failure

Hi,


JChem substructure search appears to be failing in my situation. To keep things testable, below is the code I'm using, as well as the input coordinate files for both the query and the target. The target contains the structure of the query and should be detected as a hit, but it doesn't happen.


When the query is a simple aromatic ring, the search succeeds, but as soon as the query gets more complex, it starts failing.


Any suggestions would be very much appreciated





Thanks





Sasha





####### code #####





String query = ... (read from the query SDF file, below)


String target = ... (read from the target mol2 file, below)





#get the query


MolImporter mi = new MolImporter(new ByteArrayInputStream(record.getBytes()));


Molecule mol = mi.read();


mi.close();





mol.aromatize();





MolSearch search = new MolSearch();


search.setQuery(mol);





#get the target


mi = new MolImporter(new ByteArrayInputStream(struct.getBytes()));


Molecule molecule = mi.read();


mi.close();





molecule.aromatize();


search.setTarget(molecule);





int[][] hits = null;


hits = search.findAll();





########## end of code ###########





Query








18 20 0 0 0 0 0 0 0 V2000


11.0644 -7.8213 7.1522 C 0 0 0 0 0 0 0 0 0 0 0


9.8914 -8.4451 6.7512 C 0 0 0 0 0 0 0 0 0 0 0


8.9223 -7.7472 6.0883 C 0 0 0 0 0 0 0 0 0 0 0


9.1092 -6.3895 5.8084 C 0 0 0 0 0 0 0 0 0 0 0


10.2979 -5.7575 6.2148 C 0 0 0 0 0 0 0 0 0 0 0


11.2709 -6.4839 6.8874 C 0 0 0 0 0 0 0 0 0 0 0


10.1971 -4.4439 5.8005 N 0 0 0 0 0 0 0 0 0 0 0


8.9853 -4.3074 5.1790 C 0 0 0 0 0 0 0 0 0 0 0


8.3523 -5.4547 5.1841 N 0 0 0 0 0 0 0 0 0 0 0


8.4702 -3.0543 4.5851 C 0 0 0 0 0 0 0 0 0 0 0


9.2350 -1.8879 4.6389 C 0 0 0 0 0 0 0 0 0 0 0


8.7520 -0.7199 4.0850 C 0 0 0 0 0 0 0 0 0 0 0


7.5142 -0.7015 3.4697 C 0 0 0 0 0 0 0 0 0 0 0


6.7428 -1.8561 3.4160 C 0 0 0 0 0 0 0 0 0 0 0


7.2192 -3.0345 3.9702 C 0 0 0 0 0 0 0 0 0 0 0


5.4882 -1.8309 2.7980 N 0 0 0 0 0 0 0 0 0 0 0


4.4827 -2.5858 3.2833 C 0 0 0 0 0 0 0 0 0 0 0


4.6876 -3.3515 4.2053 O 0 0 0 0 0 0 0 0 0 0 0


1 6 4 0 0 0 0


1 2 4 0 0 0 0


2 3 4 0 0 0 0


3 4 4 0 0 0 0


4 5 4 0 0 0 0


4 9 1 0 0 0 0


5 6 4 0 0 0 0


5 7 1 0 0 0 0


7 8 1 0 0 0 0


8 9 2 0 0 0 0


8 10 1 0 0 0 0


10 11 4 0 0 0 0


10 15 4 0 0 0 0


11 12 4 0 0 0 0


12 13 4 0 0 0 0


13 14 4 0 0 0 0


14 15 4 0 0 0 0


14 16 1 0 0 0 0


16 17 1 0 0 0 0


17 18 2 0 0 0 0


M END


$$$$











@<TRIPOS>MOLECULE


TARGET


42 46 0 0 0


SMALL


USER_CHARGES





@<TRIPOS>ATOM


1 C1 9.5294 -8.8201 6.6505 C.ar 1 <0> -0.0966


2 C2 10.6479 -8.1869 7.1739 C.ar 1 <0> -0.1288


3 C3 10.8495 -6.8508 6.9744 C.ar 1 <0> -0.0593


4 C4 9.9218 -6.1085 6.2362 C.ar 1 <0> 0.0448


5 C5 8.7882 -6.7501 5.7064 C.ar 1 <0> 0.0569


6 C6 8.6011 -8.1089 5.9199 C.ar 1 <0> -0.1143


7 N1 8.0708 -5.7767 5.0390 N.pl3 1 <0> -0.5946


8 H1 7.2085 -5.9059 4.5494 H 1 <0> 0.4298


9 C7 8.7608 -4.6021 5.1729 C.2 1 <0> 0.3138


10 N2 9.8502 -4.8049 5.8725 N.2 1 <0> -0.4503


11 C8 8.3430 -3.3010 4.6075 C.ar 1 <0> -0.0005


12 C9 7.1039 -3.1765 3.9795 C.ar 1 <0> -0.0952


13 C10 6.7192 -1.9542 3.4516 C.ar 1 <0> 0.1524


14 C11 7.5692 -0.8580 3.5439 C.ar 1 <0> -0.1153


15 C12 8.7947 -0.9789 4.1705 C.ar 1 <0> -0.0891


16 C13 9.1879 -2.1930 4.7002 C.ar 1 <0> -0.0128


17 Cl1 10.7318 -2.3411 5.4800 Cl 1 <0> -0.0200


18 N3 5.4772 -1.8248 2.8204 N.am 1 <0> -0.6668


19 C14 4.9589 -2.8623 2.1337 C.2 1 <0> 0.5690


20 O1 5.6103 -3.8780 1.9835 O.2 1 <0> -0.5119


21 C15 3.6009 -2.7655 1.5641 C.ar 1 <0> -0.1342


22 C16 2.8508 -1.5994 1.7360 C.ar 1 <0> -0.0692


23 C17 1.5830 -1.5112 1.2042 C.ar 1 <0> -0.1075


24 C18 1.0463 -2.5782 0.4960 C.ar 1 <0> 0.0685


25 C19 1.7904 -3.7457 0.3208 C.ar 1 <0> 0.0257


26 C20 3.0619 -3.8401 0.8519 C.ar 1 <0> -0.0374


27 O2 1.0452 -4.6324 -0.4022 O.3 1 <0> -0.3027


28 C21 0.0047 -3.8487 -1.0155 C.3 1 <0> 0.2117


29 O3 -0.1616 -2.7365 -0.1166 O.3 1 <0> -0.3024


30 H2 9.3848 -9.8774 6.8169 H 1 <0> 0.1313


31 H3 11.3666 -8.7565 7.7444 H 1 <0> 0.1306


32 H4 11.7235 -6.3682 7.3863 H 1 <0> 0.1302


33 H5 7.7325 -8.6069 5.5151 H 1 <0> 0.1237


34 H6 6.4461 -4.0298 3.9052 H 1 <0> 0.1423


35 H7 7.2690 0.0923 3.1278 H 1 <0> 0.1428


36 H8 9.4493 -0.1229 4.2426 H 1 <0> 0.1482


37 H9 4.9891 -0.9884 2.8769 H 1 <0> 0.4154


38 H10 3.2649 -0.7671 2.2857 H 1 <0> 0.1435


39 H11 1.0048 -0.6089 1.3382 H 1 <0> 0.1474


40 H12 3.6388 -4.7430 0.7166 H 1 <0> 0.1514


41 H13 -0.9177 -4.4252 -1.0862 H 1 <0> 0.1384


42 H14 0.3169 -3.5015 -2.0004 H 1 <0> 0.0911


@<TRIPOS>BOND


1 1 6 ar


2 1 2 ar


3 1 30 1


4 2 3 ar


5 2 31 1


6 3 4 ar


7 3 32 1


8 4 10 1


9 4 5 ar


10 5 6 ar


11 5 7 1


12 6 33 1


13 7 8 1


14 7 9 1


15 9 10 2


16 9 11 1


17 11 16 ar


18 11 12 ar


19 12 13 ar


20 12 34 1


21 13 14 ar


22 13 18 1


23 14 15 ar


24 14 35 1


25 15 16 ar


26 15 36 1


27 16 17 1


28 18 19 am


29 18 37 1


30 19 20 2


31 19 21 1


32 21 26 ar


33 21 22 ar


34 22 23 ar


35 22 38 1


36 23 24 ar


37 23 39 1


38 24 29 1


39 24 25 ar


40 25 26 ar


41 25 27 1


42 26 40 1


43 27 28 1


44 28 29 1


45 28 41 1


46 28 42 1

Hi Sasha,





Your mol2 file contains charges. On atom #7 (nitrogen) the charge is -0.5946 that is converted to -1 (since it's less than -0.5) and the ring that contains this atom cannot be aromatised. The same problem occurs at atoms #18, #19 and #20.


You can check charges and valence errors by importing the molecule into Marvin.





Best regards,


Tamás

Thank you, Tamas.


That explains it. I edited the code to set all charges to zero, and it worked.





Thanks again





Sasha