Hello all,
Very nice piece of work! Coincidence has it that I'll be needing
exactly this functionality in a few weeks. Thank you for saving me a
few hours of future coding :-)
One thing I did notice when looking at your (otherwise excellent) code
was that your removeZeroEntries() function is unnecessarily complex.
You can safely remove from a collection you are looping over, but you
have to use an Iterator to do it.
Here is the simplified version (tested: compiles and works).
-----------
protected static void removeZeroEntries(Map<String, Double> hash) {
for (Iterator<String> it = hash.keySet().iterator(); it.hasNext(); )
if (hash.get(it.next())==0.0) {
it.remove();
}
return;
}
-----------
Thanks for sharing!
Regards, Jules
On 8 July 2010 04:04, gilleain torrance <[email protected]> wrote:
> Ok, I was being lazy about all the Hashtables being thrown around.
> Here is a more strongly-typed version:
>
> http://gist.github.com/466912/c578bb2c41c0cd2906fe3556e973d4ba8785ed55
>
> There were lots of casts of the type
> ((Double)map.get(key)).doubleValue(); that are unnecessary with java
> 1.6's generics and unboxing. However, be sure to test to make sure I
> haven't caused some subtle Integer/Double casting error.
>
> I'm guessing that the use of doubles everywhere is because reactions
> can have fractional stoichiometries? Like 1.5*benzene + 2.3 HOH = ?
>
> Well, anyway, hope it now works...
>
> gilleain
>
> On 7/7/10, wateriestfire <[email protected]> wrote:
>>
>> Hey,
>>
>> Thanks for replying, you have been very helpful, however Java gave me this
>> error when I tried to run your modification:
>>
>> Exception in thread "main" java.lang.ClassCastException:
>> org.openscience.cdk.Atom cannot be cast to java.lang.String
>> at ReactionBalancer.removeZeroEntries(ReactionBalancer.java:430)
>> at ReactionBalancer.makeDiffHashtable(ReactionBalancer.java:187)
>> at ReactionBalancer.balance(ReactionBalancer.java:140)
>> at Tester.main(Tester.java:81)
>>
>> on line 430, and at 263 specifically... I tried casting them as Objects and
>> as Atoms, but then it only gave the answer "false" when I did it on known
>> equations.
>>
>> thanks, I feel we are on the verge of solving this. :)
>>
>>
>>
>> gilleain torrance wrote:
>>>
>>> Hi,
>>>
>>> I know very little about the reaction code in the cdk, but I've made
>>> some small changes to the ReactionBalancer class you posted:
>>>
>>> http://gist.github.com/466912
>>>
>>> which also now needs this class:
>>>
>>> http://gist.github.com/466913
>>>
>>> to replace the old cdk.math.PermutationGenerator class (there is an
>>> AtomContainerPermutor class, but that isn't suitable for permuting a
>>> Double[]).
>>>
>>> Now, it might be that the functionality of the ReactionBalancer has
>>> been moved, but this should work ... although I only know that it
>>> compiles, not that it works :)
>>>
>>> gilleain
>>>
>>> On Wed, Jul 7, 2010 at 3:24 PM, wateriestfire <[email protected]>
>>> wrote:
>>>>
>>>> Here is the original source code for ReactionBalancer.java, it is
>>>> incompatible with the newest version of the CDK, I don't know if it
>>>> helps, I
>>>> have tried converting it myself to work with the newest versions, but I
>>>> haven't been able to get it right.
>>>>
>>>> Thanks again!
>>>> http://old.nabble.com/file/p29096830/ReactionBalancer.java
>>>> ReactionBalancer.java
>>>>
>>>>
>>>> wateriestfire wrote:
>>>>>
>>>>> ReactionBalancer used to be a class in the CDK, and what it did was
>>>>> check
>>>>> to see if a reaction could be balanced, It was then removed... Now I
>>>>> have
>>>>> a list of reactions, and while I am parsing them, I need to know if they
>>>>> can be balanced, or to actually balance them would be nice too.
>>>>>
>>>>> Is there a class in the CDK that can do this?
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://old.nabble.com/Balancing-Chemical-Reactions--tp29095305p29096830.html
>>>> Sent from the cdk-user mailing list archive at Nabble.com.
>>>>
>>>>
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