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
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