>
> There should be a blank line after M END?
Just checked and no there should not be a blank line. The current writer
does not generate this, after removing the erroneous blank lines I can
round trip it.
try (SDFWriter sdfw = new SDFWriter(System.out)) {
> sdfw.setAlwaysV3000(true);
> while (sdfr.hasNext()) {
> sdfw.write(sdfr.next());
> }
> }
Result:
>
> CDK 0724171132
>
> 0 0 0 0 0 999 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 10 10 0 0 0
> M V30 BEGIN ATOM
> M V30 1 C .0 .0 0 0
> M V30 2 C .0 .0 0 0
> M V30 3 C .0 .0 0 0
> M V30 4 C .0 .0 0 0
> M V30 5 C .0 .0 0 0
> M V30 6 C .0 .0 0 0
> M V30 7 N .0 .0 0 0
> M V30 8 C .0 .0 0 0
> M V30 9 C .0 .0 0 0
> M V30 10 C .0 .0 0 0
> M V30 END ATOM
> M V30 BEGIN BOND
> M V30 1 2 1 2
> M V30 2 1 2 3
> M V30 3 1 3 4
> M V30 4 1 4 5
> M V30 5 1 5 6
> M V30 6 1 6 7
> M V30 7 2 3 8
> M V30 8 1 8 9
> M V30 9 2 9 10
> M V30 10 1 1 10
> M V30 END BOND
> M V30 END CTAB
> M END
> > <Data>
> id1
>
> $$$$
>
> CDK 0724171132
>
> 0 0 0 0 0 999 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 11 11 0 0 0
> M V30 BEGIN ATOM
> M V30 1 C .0 .0 0 0
> M V30 2 C .0 .0 0 0
> M V30 3 S .0 .0 0 0
> M V30 4 O .0 .0 0 0
> M V30 5 O .0 .0 0 0
> M V30 6 C .0 .0 0 0
> M V30 7 C .0 .0 0 0
> M V30 8 C .0 .0 0 0
> M V30 9 C .0 .0 0 0
> M V30 10 C .0 .0 0 0
> M V30 11 C .0 .0 0 0
> M V30 END ATOM
> M V30 BEGIN BOND
> M V30 1 1 1 2
> M V30 2 1 2 3
> M V30 3 2 3 4
> M V30 4 2 3 5
> M V30 5 1 2 6
> M V30 6 2 6 7
> M V30 7 1 7 8
> M V30 8 2 8 9
> M V30 9 1 9 10
> M V30 10 2 10 11
> M V30 11 1 6 11
> M V30 END BOND
> M V30 END CTAB
> M END
> > <Data>
> id2
>
> $$$$
On 24 July 2017 at 11:15, John Mayfield <[email protected]> wrote:
> Which version did you generate it with? There should be a blank line after
> M END?
>
> John
>
> On 24 July 2017 at 11:03, Staffan Arvidsson <[email protected]>
> wrote:
>
>> I just bumped the CDK version in our code repo (from 1.5.13) and found
>> that some of my tests are now failing. The issue is reading v3000 SDF files
>> were properties are not set on the molecules. I attached the file that I've
>> used in one of tests. Basic code for showing things are not working:
>>
>> IteratingSDFReader iter = new IteratingSDFReader(new
>> FileInputStream(file), SilentChemObjectBuilder.getInstance());
>>
>> while(iter.hasNext()){
>>
>> System.out.println(iter.next().getProperties());
>> }
>>
>> The output is simply an empty map. Or did I miss something here?
>>
>> Also, I've found that the keys in properties are somehow 'cleaned' by
>> switching out space, dots, equal signs to lower case character? Any reason
>> behind this?
>>
>>
>> Best,
>> Staffan
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Cdk-user mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
