> me again:) we're still working on our molecular dynamics library. the
> idea is to make large trajectories (1000 or 10.000 snapshots) available=
> to the user. the problem is of course how to transfer this amount of
> data efficiently through the web and we have come up with a new way of
> comrpessing trajectories. we calculate the number of eigenvectors
> reauired to explain some 95 or 99% of the systems variance (usually
> =7E100vecs). we then extract the projection of each eigenvector over th=
> trajectory. the two files together occupy <2MB and can reproduce a
> >100MB trajectory at <0.1Ang. recovering the xyz trajectory from evecs=
> and proj is fairly easy, <50 lines in perl. however since we generally
> use jmol for visualisations it would of course be wonderfull if jmol
> could read and interpret these files directly and on the fly:)
You lost me with most of this stuff ...
but I understand that you want to add support for a new file format.
> i looked
> in the code AtomSetCollectionReader.java and
> PdbReader.java/XyzReader.java but can't find an entry point (have
> strictly speaking no idea of java)
> could you give me a hint what files i have to edit to define a new inpu=
You need to add a new class under org/jmol/adapter/smarter
Basicly, copy XyzReader.java to TimReader.java ... then modify
TimReader.java so that it supports your format.
Then modify Resolver.java so that it can uniquely distinguish your file
format. Resolver reads in the head of the file, figures out the file
format, then calls the appropriate *Reader.java
Join the jmol-developers mailing list and post questions on the list so
that others can learn too.
Open Source Molecular Visualization
Get latest updates about Open Source Projects, Conferences and News.