Re: [Cdk-user] Reg: Reading Jmol generated SDF file using Iterating SDF reader cdk 1.5.8
IIRC JMol was generating them incorrectly, Bob (JMol dev) patched it and we
also updated our code to be more tolerant. Please try CDK 2.3 and if there
is still an issue report via GitHub Issues.
On Sun, 17 Nov 2019 at 09:50, Vinothkumar Mohanakrishnan
wrote:
> Dear Users,
>
> I would like to read a SDF file using IteratingSDFReader. The SDF file is
> generated by jmol (see below).
>
> U:/research/project_opas/Code/MVC_OPAS/build/check.sdf
> __Jmol-14_11161922023D 1 1.0 0.0 0
> Jmol version 14.9.1 2017-02-18 13:47 EXTRACT: ({0:43})
> 22 22 0 0 0 0 1 V2000
> -10.26842 21.30587 -2.02430 N 0 0 0 0 0 0
> -11.14109 20.23272 -2.39821 C 0 0 0 0 0 0
> -10.84018 18.85777 -1.92734 C 0 0 0 0 0 0
> -11.60011 17.94142 -2.23013 O 0 0 0 0 0 0
> -12.38167 20.49262 -3.21797 C 0 0 0 0 0 0
> -12.66761 21.93940 -3.49472 C 0 0 0 0 0 0
> -13.73838 22.56509 -3.02287 C 0 0 0 0 0 0
> -11.88128 22.81522 -4.30956 N 0 0 0 0 0 0
> -12.65747 24.01784 -4.21934 C 0 0 0 0 0 0
> -13.70560 23.88527 -3.49217 N 0 0 0 0 0 0
> -9.64144 18.61510 -1.15438 N 0 0 0 0 0 0
> -6.47461 15.46647 0.53840 C 0 0 0 0 0 0
> -5.16207 15.52031 -0.21484 C 0 0 0 0 0 0
> -4.06313 15.41673 0.72449 N 0 0 0 0 0 0
> -9.80464 17.44463 -0.29800 C 0 0 0 0 0 0
> -8.64600 16.48725 -0.41087 C 0 0 0 0 0 0
> -8.90795 15.33022 -1.01563 C 0 0 0 0 0 0
> -7.33993 16.68411 0.28862 C 0 0 0 0 0 0
> -7.04245 17.86578 0.93854 O 0 0 0 0 0 0
> -6.07225 18.51085 0.19546 C 0 0 0 0 0 0
> -6.39116 19.21376 -0.74531 O 0 0 0 0 0 0
> -4.69541 18.41611 0.56612 N 0 0 0 0 0 0
> 2 1 1 0 0 0
> 2 3 1 0 0 0
> 3 11 1 0 0 0
> 4 3 2 0 0 0
> 5 2 1 0 0 0
> 6 5 1 0 0 0
> 6 7 2 0 0 0
> 8 9 1 0 0 0
> 8 6 1 0 0 0
> 9 10 2 0 0 0
> 10 7 1 0 0 0
> 13 12 1 0 0 0
> 13 14 1 0 0 0
> 15 16 1 0 0 0
> 16 17 2 0 0 0
> 16 18 1 0 0 0
> 18 19 1 0 0 0
> 19 20 1 0 0 0
> 20 21 2 0 0 0
> 20 22 1 0 0 0
> 11 15 1 0 0 0
> 12 18 1 0 0 0
> M END
>
> U:/research/project_opas/Code/MVC_OPAS/build/check.sdf
> __Jmol-14_11161922023D 1 1.0 0.0 0
> Jmol version 14.9.1 2017-02-18 13:47 EXTRACT: ({0:43})
> 22 22 0 0 0 0 1 V2000
> -10.34994 21.23775 -2.14993 N 0 0 0 0 0 0
> -11.34250 20.30777 -2.59501 C 0 0 0 0 0 0
> -11.13198 18.85018 -2.50356 C 0 0 0 0 0 0
> -12.03183 18.12532 -2.90109 O 0 0 0 0 0 0
> -12.62336 20.72709 -3.26233 C 0 0 0 0 0 0
> -12.81469 22.18660 -3.49445 C 0 0 0 0 0 0
> -13.85760 22.84610 -3.01911 C 0 0 0 0 0 0
> -11.99766 23.01098 -4.32672 N 0 0 0 0 0 0
> -12.72729 24.24473 -4.23861 C 0 0 0 0 0 0
> -13.77078 24.16132 -3.50354 N 0 0 0 0 0 0
> -9.86955 18.26965 -2.15583 N 0 0 0 0 0 0
> -7.30122 16.52601 0.75455 C 0 0 0 0 0 0
> -5.96259 17.25681 0.80966 C 0 0 0 0 0 0
> -4.87734 16.30636 0.66950 N 0 0 0 0 0 0
> -12.83689 15.52634 -0.85527 C 0 0 0 0 0 0
> -11.62686 16.04439 -1.46833 N 0 0 0 0 0 0
> -11.00919 14.97258 -2.22952 C 0 0 0 0 0 0
> -10.70605 16.47306 -0.42756 C 0 0 0 0 0 0
> -9.83868 17.64207 -0.85262 C 0 0 0 0 0 0
> -8.72671 18.07421 0.02162 C 0 0 0 0 0 0
> -8.09045 19.06942 -0.28779 O 0 0 0 0 0 0
> -8.35385 17.36976 1.15010 O 0 0 0 0 0 0
> 2 1 1 0 0 0
> 2 3 1 0 0 0
> 3 11 1 0 0 0
> 4 3 2 0 0 0
> 5 2 1 0 0 0
> 6 5 1 0 0 0
> 6 7 2 0 0 0
> 8 9 1 0 0 0
> 8 6 1 0 0 0
> 9 10 2 0 0 0
> 10 7 1 0 0 0
> 13 12 1 0 0 0
> 13 14 1 0 0 0
> 15 16 1 0 0 0
> 16 17 1 0 0 0
> 16 18 1 0 0 0
> 18 19 1 0 0 0
> 19 20 1 0 0 0
> 20 21 2 0 0 0
> 20 22 1 0 0 0
> 11 19 1 0 0 0
> 12 22 1 0 0 0
> M END
>
>
> I am using CDK 1.5.8 (I have to stick to this version for compatibility
> issues). I am trying to read the SDF file using the below snippet
>
> public static List readFragments(String fileName) throws
> IOException, CDKException {
>
> List frags = new ArrayList<>();
>
> File sdfFile = new File(fileName);
>
>IteratingSDFReader sdfReader = new IteratingSDFReader(new
> FileInputStream(sdfFile),DefaultChemObjectBuilder.getInstance());
>
> while (sdfReader.hasNext()) {
>
> IAtomContainer molecule =
> (IAtomContainer)sdfReader.next();
>
> frags.add(molecule);
>
> }
> sdfReader.close();
>
> return frags;
> }
>
> The function works perfectly fine for sdf files genrated by CDK and Openbabel
> and returns null for Jmol generated
[Cdk-user] Reg: Reading Jmol generated SDF file using Iterating SDF reader cdk 1.5.8
Dear Users,
I would like to read a SDF file using IteratingSDFReader. The SDF file
is generated by jmol (see below).
U:/research/project_opas/Code/MVC_OPAS/build/check.sdf
__Jmol-14_11161922023D 1 1.0 0.0 0
Jmol version 14.9.1 2017-02-18 13:47 EXTRACT: ({0:43})
22 22 0 0 0 0 1 V2000
-10.26842 21.30587 -2.02430 N 0 0 0 0 0 0
-11.14109 20.23272 -2.39821 C 0 0 0 0 0 0
-10.84018 18.85777 -1.92734 C 0 0 0 0 0 0
-11.60011 17.94142 -2.23013 O 0 0 0 0 0 0
-12.38167 20.49262 -3.21797 C 0 0 0 0 0 0
-12.66761 21.93940 -3.49472 C 0 0 0 0 0 0
-13.73838 22.56509 -3.02287 C 0 0 0 0 0 0
-11.88128 22.81522 -4.30956 N 0 0 0 0 0 0
-12.65747 24.01784 -4.21934 C 0 0 0 0 0 0
-13.70560 23.88527 -3.49217 N 0 0 0 0 0 0
-9.64144 18.61510 -1.15438 N 0 0 0 0 0 0
-6.47461 15.46647 0.53840 C 0 0 0 0 0 0
-5.16207 15.52031 -0.21484 C 0 0 0 0 0 0
-4.06313 15.41673 0.72449 N 0 0 0 0 0 0
-9.80464 17.44463 -0.29800 C 0 0 0 0 0 0
-8.64600 16.48725 -0.41087 C 0 0 0 0 0 0
-8.90795 15.33022 -1.01563 C 0 0 0 0 0 0
-7.33993 16.68411 0.28862 C 0 0 0 0 0 0
-7.04245 17.86578 0.93854 O 0 0 0 0 0 0
-6.07225 18.51085 0.19546 C 0 0 0 0 0 0
-6.39116 19.21376 -0.74531 O 0 0 0 0 0 0
-4.69541 18.41611 0.56612 N 0 0 0 0 0 0
2 1 1 0 0 0
2 3 1 0 0 0
3 11 1 0 0 0
4 3 2 0 0 0
5 2 1 0 0 0
6 5 1 0 0 0
6 7 2 0 0 0
8 9 1 0 0 0
8 6 1 0 0 0
9 10 2 0 0 0
10 7 1 0 0 0
13 12 1 0 0 0
13 14 1 0 0 0
15 16 1 0 0 0
16 17 2 0 0 0
16 18 1 0 0 0
18 19 1 0 0 0
19 20 1 0 0 0
20 21 2 0 0 0
20 22 1 0 0 0
11 15 1 0 0 0
12 18 1 0 0 0
M END
U:/research/project_opas/Code/MVC_OPAS/build/check.sdf
__Jmol-14_11161922023D 1 1.0 0.0 0
Jmol version 14.9.1 2017-02-18 13:47 EXTRACT: ({0:43})
22 22 0 0 0 0 1 V2000
-10.34994 21.23775 -2.14993 N 0 0 0 0 0 0
-11.34250 20.30777 -2.59501 C 0 0 0 0 0 0
-11.13198 18.85018 -2.50356 C 0 0 0 0 0 0
-12.03183 18.12532 -2.90109 O 0 0 0 0 0 0
-12.62336 20.72709 -3.26233 C 0 0 0 0 0 0
-12.81469 22.18660 -3.49445 C 0 0 0 0 0 0
-13.85760 22.84610 -3.01911 C 0 0 0 0 0 0
-11.99766 23.01098 -4.32672 N 0 0 0 0 0 0
-12.72729 24.24473 -4.23861 C 0 0 0 0 0 0
-13.77078 24.16132 -3.50354 N 0 0 0 0 0 0
-9.86955 18.26965 -2.15583 N 0 0 0 0 0 0
-7.30122 16.52601 0.75455 C 0 0 0 0 0 0
-5.96259 17.25681 0.80966 C 0 0 0 0 0 0
-4.87734 16.30636 0.66950 N 0 0 0 0 0 0
-12.83689 15.52634 -0.85527 C 0 0 0 0 0 0
-11.62686 16.04439 -1.46833 N 0 0 0 0 0 0
-11.00919 14.97258 -2.22952 C 0 0 0 0 0 0
-10.70605 16.47306 -0.42756 C 0 0 0 0 0 0
-9.83868 17.64207 -0.85262 C 0 0 0 0 0 0
-8.72671 18.07421 0.02162 C 0 0 0 0 0 0
-8.09045 19.06942 -0.28779 O 0 0 0 0 0 0
-8.35385 17.36976 1.15010 O 0 0 0 0 0 0
2 1 1 0 0 0
2 3 1 0 0 0
3 11 1 0 0 0
4 3 2 0 0 0
5 2 1 0 0 0
6 5 1 0 0 0
6 7 2 0 0 0
8 9 1 0 0 0
8 6 1 0 0 0
9 10 2 0 0 0
10 7 1 0 0 0
13 12 1 0 0 0
13 14 1 0 0 0
15 16 1 0 0 0
16 17 1 0 0 0
16 18 1 0 0 0
18 19 1 0 0 0
19 20 1 0 0 0
20 21 2 0 0 0
20 22 1 0 0 0
11 19 1 0 0 0
12 22 1 0 0 0
M END
I am using CDK 1.5.8 (I have to stick to this version for
compatibility issues). I am trying to read the SDF file using the
below snippet
public static List readFragments(String fileName)
throws IOException, CDKException {
List frags = new ArrayList<>();
File sdfFile = new File(fileName);
IteratingSDFReader sdfReader = new IteratingSDFReader(new
FileInputStream(sdfFile),DefaultChemObjectBuilder.getInstance());
while (sdfReader.hasNext()) {
IAtomContainer molecule = (IAtomContainer)sdfReader.next();
frags.add(molecule);
}
sdfReader.close();
return frags;
}
The function works perfectly fine for sdf files genrated by CDK and
Openbabel and returns null for Jmol generated sdf file. I am pretty
sure it is the problem with the sdf file generated by Jmol. But I am
able to open the sdf file in the molecule viewer (Jmol, Discovery
Studio) without any errors. I tried all variations by manually
editing the file like the headers and the end of the file, but to no
avail. I tried to read it using MDLV2000 reader but no improvements.
Is there any other reader I can use or which part of the sdf file (is
problematic) I have to edit, so that I can read it using
IteratingSDFReader? Any insights in
