Yes you're correct! Now things work again! Perfect!
Best,
Staffan
2017-07-24 12:37 GMT+02:00 John Mayfield <john.wilkinson...@gmail.com>:
> 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 <john.wilkinson...@gmail.com>
> 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 <staffan.arvids...@gmail.com>
>> 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
>>>
>>> ------------------------------------------------------------
>>> ------------------
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>>>
>>
>
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