I believe so, if you gave it methane as '[H]C([H])([H])[H]' it would only
show C (or maybe CH4).
J
Regards,
John W May
john.wilkinson...@gmail.com
On 26 January 2016 at 20:50, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> OK, so making more sense to me now.
> But what does this option do:
>
> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/renderer/generators/BasicAtomGenerator.ShowExplicitHydrogens.html
>
> Is it just a way to turn off display off explicit H with the default being
> to display them?
>
> Tim
>
>
>
>
> On 26/01/2016 18:58, John M wrote:
>
> Sorry bit confused here.. hydrogens are always shown especially with
> explicit.
>
> J
>
>
> http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=%5BN%5D1C%3DCC%3DC1.%5BNH%5D1C%3DCC%3DC1.%5BH%5DN1C%3DCC%3DC1&zoom=1.3&annotate=none
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 26 January 2016 at 17:29, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
>> Any chance to change this?
>> Displaying explicit H is pretty important when dealing with query
>> structures.
>> Not sure if there are other "critical" "advanced" parameters.
>>
>> Tim
>>
>>
>> On 26/01/2016 16:17, John M wrote:
>>
>> Yep - I'll add a better error message to reflect this.
>>
>> Regards,
>> John W May
>> john.wilkinson...@gmail.com
>>
>> On 26 January 2016 at 16:03, Tim Dudgeon < <tdudgeon...@gmail.com>
>> tdudgeon...@gmail.com> wrote:
>>
>>> So this means that options like this can't be used with
>>> DepictionGenerator?
>>>
>>>
>>> On 26/01/2016 14:53, John M wrote:
>>>
>>> There are about three different generators which have separate
>>> parameters - the depiction generator is intended to hide this, here the
>>> withParam is really an expert mode... I should give a better error message
>>> though. The depiction generator uses the StandardGenerator and and
>>> BasicSceneGenerator so you can only use parameters from their.
>>>
>>> Regards,
>>> John W May
>>> john.wilkinson...@gmail.com
>>>
>>> On 26 January 2016 at 14:36, Tim Dudgeon < <tdudgeon...@gmail.com>
>>> tdudgeon...@gmail.com> wrote:
>>>
>>>> When I try to use the low level DepictionGenerator.withParam(Class<T>,
>>>> U) method to set a parameter depiction blows up.
>>>> e.g. I try:
>>>>
>>>> withParam(BasicAtomGenerator.ShowExplicitHydrogens.class, true)
>>>>
>>>> and then try to depict I get:
>>>>
>>>> java.lang.IllegalAccessError: You requested the active parameter of
>>>> type
>>>> org.openscience.cdk.renderer.generators.BasicAtomGenerator$ShowExplicitHydrogens,
>>>> but it has not been registered yet. Did you make sure the
>>>> IGeneratorParameter is registered, by registring the appropriate
>>>> IGenerator? Alternatively, you can use getDefault() to query the default
>>>> value for any parameter on the classpath.
>>>>
>>>> at
>>>> org.openscience.cdk.renderer.RendererModel.getParameter(RendererModel.java:209)
>>>> at
>>>> org.openscience.cdk.renderer.RendererModel.set(RendererModel.java:249)
>>>> at
>>>> org.openscience.cdk.depict.DepictionGenerator.getModel(DepictionGenerator.java:284)
>>>> at
>>>> org.openscience.cdk.depict.DepictionGenerator.depict(DepictionGenerator.java:348)
>>>> at
>>>> org.openscience.cdk.depict.DepictionGenerator.depict(DepictionGenerator.java:296)
>>>>
>>>>
>>>> How is it supposed to register these?
>>>>
>>>> Tim
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> Cdk-user mailing list
>>>> Cdk-user@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>>
>>>>
>>>
>>>
>>
>>
>
>
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
