I'll take a look at this - can you resend the SD files as attachments?
Thanks,
On Sep 13, 2007, at 6:25 AM, Alexander Klenner wrote:
> Hello Rajarshi
>
> since u are the author of the KabschAlignment class maybe you can
> help me again.
>
> There are two attached moleculs in this email which I am trying to
> aling with KabschAligment. What happens is, that two axis' seem to
> be correct but the rotation of another axis does not work correctly
> as the molecule seems to rotate 'too far' or not far enough arround
> this axis.
>
> I figured this problem out aligning much bigger molecules but its
> always the same effect, the superimposition of the two aligned
> structures seems bad due to a wrong rotation of one axis. You can
> easily see, that there's a better aligment ( which can also be
> found for the two attached structures with MOE ).
>
> But on the other hand the aligment works just fine for many
> different structures, thus if there's an error it does not occur
> everytime you use KabschAlignment.
>
> Im using plain CDK code to do this aligment at the moment, thus you
> should see the same effect if you try to align the attached
> structures with KabschAlignment.
>
> Just in case there was a big fix or this has been a known issue
> before and its now fixed I am using CDK Version 20060714.
>
> Thanks a lot in advance!
>
> Alex Klenner
>
> PS 2171.mol is my ac1 2172.mol is ac2 and 2171_vs_2172.sdf
> consists of both the rotated 2172.mol and 2171.mol
>
>
>
>
> Rajarshi Guha schrieb:
>>
>> On Sep 10, 2007, at 5:14 AM, Alexander Klenner wrote:
>>
>>> Hi,
>>>
>>> I am trying to to do an aligment of two structures ( mol1 and
>>> mol2 ) and
>>> I want to superimpose both structures on the original position
>>> of mol1
>>> ( thus I do not want the translation of the center of mass to the
>>> origin! ).
>>>
>>> I just deleted the translation part where all the atoms of mol2
>>> become
>>> translated arround the origin depending on the center of mass. The
>>> strange thing is, that doesn't seem to change anything for me.
>>>
>>> Do I overlook anything here?
>>
>> Do you mean that the coordinates after rotation do not change?
>>
>> Can you send example structures and code that give the problem?
>>
>> One (crude) way to get around this is to use rotateAtomContainer
>> (with translation) and just translate the rotated structure back
>> to the CoM of mol1, since you can get the CoM via getCenterofMass()
>>
>> -------------------------------------------------------------------
>> Rajarshi Guha <[EMAIL PROTECTED]>
>> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
>> -------------------------------------------------------------------
>> The way to love anything is to realize that it might be lost.
>>
>>
>
>
> MOE2006 3D
>
> 7 7 0 0 0 0 0 0 0 0999 V2000
> -0.9970 -2.8680 1.1060 N 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0830 -3.0480 1.3660 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7430 -2.4240 1.4050 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.9300 -1.2700 0.6190 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3840 -1.1070 -0.2050 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1790 -1.5940 -0.7700 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7420 -2.8920 0.8020 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 3 1 0 0 0 0
> 1 7 2 0 0 0 0
> 2 7 1 0 0 0 0
> 3 4 2 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 6 7 1 0 0 0 0
> M END
>
> CDK 9/13/07,11:47
>
> 7 7 0 0 0 0 0 0 0 0999 V2000
> -0.9970 -2.8680 1.1060 N 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0830 -3.0480 1.3660 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7430 -2.4240 1.4050 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.9300 -1.2700 0.6190 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3840 -1.1070 -0.2050 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1790 -1.5940 -0.7700 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7420 -2.8920 0.8020 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 3 1 0 0 0 0
> 1 7 2 0 0 0 0
> 2 7 1 0 0 0 0
> 3 4 2 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 6 7 1 0 0 0 0
> M END
> $$$$
>
> CDK 9/13/07,11:47
>
> 7 7 0 0 0 0 0 0 0 0999 V2000
> 0.0706 -1.9849 -1.2990 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5224 -3.0319 2.0394 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7367 -2.3283 2.0045 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0448 -1.5139 0.9028 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1388 -1.4021 -0.1640 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.9235 -2.1067 -0.1292 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7624 -2.8352 0.9685 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1 6 1 0 0 0 0
> 2 3 1 0 0 0 0
> 2 7 2 0 0 0 0
> 3 4 2 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 6 7 1 0 0 0 0
> M END
> $$$$
>
> MOE2006 3D
>
> 7 7 0 0 0 0 0 0 0 0999 V2000
> 0.0650 -1.9870 -1.2960 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5280 -3.0320 2.0430 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7420 -2.3280 2.0080 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0500 -1.5140 0.9060 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1440 -1.4030 -0.1610 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.9290 -2.1080 -0.1260 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7680 -2.8360 0.9720 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1 6 1 0 0 0 0
> 2 3 1 0 0 0 0
> 2 7 2 0 0 0 0
> 3 4 2 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 6 7 1 0 0 0 0
> M END
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
...but there was no one in it.......
- RG
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