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 0
> M RAD 10 1 2 3 2 5 2 7 2 9 2 11 2 13 2 15 2 17
> 2 18 2
> M CHG 1 33 2
> M 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
> <mailto: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
> <mailto: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 <mailto:walla...@umich.edu>
> >
> > ------------------------------------------------------------------------------
> >
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> >
>
>
>
> --
> Wallace Chan
> PhD Candidate
> Zhang Lab
> Department of Biological Chemistry
> University of Michigan
> walla...@umich.edu <mailto:walla...@umich.edu>
> ------------------------------------------------------------------------------
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