Noel, Thanks for your reply. I seem to have found the issue. The following molecule (in SDF format) appears to be the problem:
*CID 10832764 45 45 0 0 0 0 0 0 0 0999 V2000 -4.5473 -1.4088 -2.6901 C 0 0 0 0 0 -5.4165 -2.0450 -2.8690 H 0 0 0 0 0 -4.6254 0.0247 -3.0188 C 0 0 0 0 0 -5.5532 0.4285 -3.4297 H 0 0 0 0 0 -3.9299 0.7720 -1.9589 C 0 0 0 0 0 -4.3347 1.7254 -1.6153 H 0 0 0 0 0 -3.4341 -0.1985 -0.9724 C 0 0 0 0 0 -3.4572 0.0472 0.0898 H 0 0 0 0 0 -3.8044 -1.5461 -1.4275 C 0 0 0 0 0 -4.1150 -2.2930 -0.6952 H 0 0 0 0 0 10.1118 -0.1072 -1.0531 C 0 0 0 0 0 11.0116 -0.6217 -0.7437 H 0 0 0 0 0 10.0099 1.3551 -1.0301 C 0 0 0 0 0 10.8334 1.9806 -0.7129 H 0 0 0 0 0 8.6134 1.7095 -0.7671 C 0 0 0 0 0 8.3349 2.6288 -0.2730 H 0 0 0 0 0 7.8586 0.4655 -0.6399 C 0 0 0 0 0 8.7768 -0.6591 -0.8155 C 0 0 0 0 0 8.6212 -1.6267 -0.3600 H 0 0 0 0 0 6.4109 0.3622 -0.3525 C 0 0 0 0 0 6.2081 -0.3220 0.8999 N 0 0 0 0 0 5.0616 -0.9415 1.2841 C 0 0 0 0 0 4.9460 -1.4962 2.3676 O 0 0 0 0 0 4.0816 -0.8758 0.3425 O 0 0 0 0 0 2.9168 -1.6591 0.6263 C 0 0 0 0 0 1.9117 -0.9082 1.4997 C 0 0 0 0 0 1.5241 0.4760 0.9757 C 0 0 0 0 0 0.8664 0.4639 -0.3691 C 0 0 0 0 0 -0.0280 -0.3898 -0.9697 C 0 0 0 0 0 -0.3686 0.0491 -2.2444 N 0 0 0 0 0 0.3555 1.1482 -2.4053 C 0 0 0 0 0 1.1066 1.4426 -1.2968 N 0 0 0 0 0 -1.9075 -0.6661 -3.2877 Fe 0 0 0 0 0 5.9025 -0.1765 -1.1593 H 0 0 0 0 0 5.9468 1.3505 -0.2651 H 0 0 0 0 0 6.9424 -0.3114 1.5971 H 0 0 0 0 0 3.1893 -2.6172 1.0856 H 0 0 0 0 0 2.4654 -1.9092 -0.3396 H 0 0 0 0 0 2.3423 -0.7703 2.4989 H 0 0 0 0 0 1.0173 -1.5298 1.6277 H 0 0 0 0 0 2.4109 1.1211 0.9522 H 0 0 0 0 0 0.8270 0.9356 1.6883 H 0 0 0 0 0 -0.4327 -1.2943 -0.5237 H 0 0 0 0 0 0.4027 1.7914 -3.2787 H 0 0 0 0 0 1.7344 2.2340 -1.1840 H 0 0 0 0 0 1 9 1 0 0 0 1 3 1 0 0 0 1 2 1 0 0 0 3 5 1 0 0 0 3 4 1 0 0 0 5 7 1 0 0 0 5 6 1 0 0 0 7 9 1 0 0 0 7 8 1 0 0 0 9 10 1 0 0 0 11 18 1 0 0 0 11 13 1 0 0 0 11 12 1 0 0 0 13 15 1 0 0 0 13 14 1 0 0 0 15 17 1 0 0 0 15 16 1 0 0 0 17 18 1 0 0 0 17 20 1 0 0 0 18 19 1 0 0 0 20 21 1 0 0 0 20 34 1 0 0 0 20 35 1 0 0 0 21 22 1 0 0 0 21 36 1 0 0 0 22 24 1 0 0 0 22 23 2 0 0 0 24 25 1 0 0 0 25 26 1 0 0 0 25 37 1 0 0 0 25 38 1 0 0 0 26 27 1 0 0 0 26 39 1 0 0 0 26 40 1 0 0 0 27 28 1 0 0 0 27 41 1 0 0 0 27 42 1 0 0 0 28 29 2 0 0 0 28 32 1 0 0 0 29 30 1 0 0 0 29 43 1 0 0 0 30 31 2 0 0 0 31 32 1 0 0 0 31 44 1 0 0 0 32 45 1 0 0 0M RAD 10 1 2 3 2 5 2 7 2 9 2 11 2 13 2 15 2 17 2 18 2M CHG 1 33 2M END* When I try to make a fastsearch index with this molecule, I get the following error: *babel file.sdf -ofs* *==============================* **** Open Babel Error in ReadMolecule* * Error in line:* *M RAD 10 1 2 3 2 5 2 7 2 9 2 11 2 13 2 15 2 17 2 18 2* *0 molecules converted* *1 errors 2 audit log messages * Seems to be a problem with the molecule being a radical. Wallace On Wed, Oct 28, 2015 at 3:16 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > Convert to smi and figure out which molecules are missing. > > - Noel > > On 28 October 2015 at 18:36, Wallace Chan <walla...@umich.edu> wrote: > > Dear All, > > > > I am having trouble with creating a fast search index. My command and > output > > are as follows: > > > > Command > > babel glass.sdf -ofs > > > > Output > > This will prepare an index of glass.sdf and may take some time... > > It took 55 seconds > > 41258 molecules converted > > 15 audit log messages > > > > The problem lies in the fact that glass.sdf has 186,342 molecules, while > > only > > 41,258 molecules succeeded in being converted. This is puzzling because > this > > has always worked for me in the past. I speculated that I may have > messed up > > the dollar sign formatting in molecule separation, but upon inspection, > the > > format seems fine. > > > > This has been driving me crazy and any help given will be much > appreciated. > > Thanks! > > > > -- > > Wallace Chan > > PhD Candidate > > Zhang Lab > > Department of Biological Chemistry > > University of Michigan > > walla...@umich.edu > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- Wallace Chan PhD Candidate Zhang Lab Department of Biological Chemistry University of Michigan walla...@umich.edu
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