Just to be more clear:I store the AminoAcides as HashMap where 1
group contains 1AA, and the String is the name of the AA. (I prefer 1 letter
code there)
To shift the desired AA in place, I'd match the Cb atomsThen rotate the AA so
that the Ca-Cb line would matchThen rotate the AA so that the N-
Thanks for the codes! I've noticed the methods in Calc, but my main questionis
the following. Let's say I've got a primitive library of AminoAcides.They
stored as a group, they have all the atoms. When I'm mutating thechain, I want
to keep the backbone atoms in place, so as far as your mutatemet
Hi Tamas!
If I've got a Group , which is an amino acid, and I want to shift it
by a 3D vector (or 3 2D vectors), how may I do it?
There is the org.biojava.bio.structure.Calc class that allows to do
calculations with the structure.
e.g. to shift a structure do:
double x =
If I've got a Group , which is an amino acid, and I want to shift it by a
3Dvector (or 3 2D vectors), how may I do it?Similarly, if i want to rotate the
same structure, how may I do it?If you just can show me a very short sample
code, I'd really appreciate it!Thanks!
On 12/1/05, Tamas Horvath <[
Exactly... I want to keep a backbone and replace the whole sidechain
asnecessary... I know this should be relatively easy, but I'm a bit lost intthe
documentation...
On 12/1/05, Andreas Prlic <[EMAIL PROTECTED]> wrote:>> Hi Tamas,>> it is
possible to access the content of a structure and> chan
Hi Tamas,
it is possible to access the content of a structure and
change/add/drop groups and atoms as you wish.
When talking about introducing "point mutations" I assume you want to
re-label a residue's main chain
atoms and drop the side chain atoms, but keep the Cb one? this would
take
See the addChain(), addModel() and setConnections() methods in the
Structure interface. For addChain() and addModel() also refer to the
Chain and Model interfaces in the same package.
cheers,
Richard
Richard Holland
Bioinformatics Specialist
GIS extension 8199
