That seems to have done the trick. Many thanks, my friend!
Wallace On Tue, Nov 3, 2015 at 8:07 AM, Fredrik Wallner <fred...@wallner.nu> wrote: > Hi, > > I tried to convert your molecule to SMILES to see what was happening and > it seems like the problem is not so much that it is a radical as it is a > problem with that specific line. According to the error message when trying > to make a smiles string, you can only have 8 entries in an M RAD line, so > splitting the line into two separate lines seems to fix 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 0 > M RAD 8 1 2 3 2 5 2 7 2 9 2 11 2 13 2 15 2 > M RAD 2 17 2 18 2 > M CHG 1 33 2 > M END > > Kind regards, > Fredrik > > 2 nov. 2015 kl. 16:03 skrev Wallace Chan <walla...@umich.edu>: > > 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 > > ------------------------------------------------------------------------------ > _______________________________________________ > 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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