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License: GNU General Public License v3.0
JEDi: Java Essential Dynamics Inspector
License: GNU General Public License v3.0
I have made a number of changes to JEDi and fixed a number of bugs:
JEDi has been running well as most bugs have been found and squashed.
Things to think about for this year:
We were comparing the AA and HPCA results on the small subsets of residues as discussed and we noticed for a single residue the (taking all modes for both PCAs) the eigenvectors were different. We did not expect this as for a single residue taking all modes (we used subsets of glycine becasue it was the smallest) Of course the whole space was equal, but the working guess as to why the individual vectors were different was because there was an alignment discrepancy between the two PCA types.
We were wondering if you knew off the top of your head how the alignment works for them. Is the whole stucture globally aligned in the pre-processing run, and then the same alignment is used in each PCA type, or is there another alignment in each PCA which is unique to the PCA. For example do you align all the residues locally and individually for HPCA?
Giving users the ability to output the aligned A matrix for post processing use
The manual states that only Jama is needed as dependency to compile the source code. I found that several other packages are needed, JFree, and bits.fft.FastCosineTransform2d. Providing links to these packages may be useful.
Let's think about how this should work. I envision this feature to be part of the production running of JEDi, so the entire coordinates matrix will be available. Need to specifically address the syntax for selecting COLUMS of the matrix, compatible with Jama getMatrix methods.
Large numbers in text files such as eigenvalues have commas separating them, making them difficult to use with other software.
I'm dealing with a big system, part of a virus capside. It has more then 99999 atoms, so the pdb numeration for the atom field (limited to 5 characters) goes up to 99999 and then goes back to 1.
The problem arises when running doATOM_LIST, that reads the atoms list from the file specified at ATOMS_LIST variable. The format of that file is:
A 1
A 2
A 3
but the program is ignoring the chain and keeps the coordinates of the last atom with the specified atom number.
For example, in my ATOMS_LIST I have:
A 1419
At the reference pdb with atom number 1419, I have:
ATOM 1419 CA PRO A 93 102,561 103,879 248,131 1,00 63,18 C
ATOM 1419 CA VAL c6504 71,255 177,935 91,271 1,00 26,11 C
But from the application log, the selected atom is:
ATOM 1419 CA VAL c 6504 71,255 177,935 91,271 0,00 C
Could it be fixed, please?
The top Eigenvalues for Hierarchical PCA are very large in comparison with the other types in JEDi. Code is being checked for this issue.
I am requesting a code review of the formulae used to compute the reduced c-matrices and reduced dynamical matrices. The two methods are in the class PCA.java: static Matrix get_reduced_C_matrix(Matrix Q), and static Matrix get_reduced_DYN_matrix(Matrix DYN).
The key lines of code are:
double cov = (Q.get(a1, b1) + Q.get(a2, b2) + Q.get(a3, b3));
double dyn = -(DYN.get(a1, b1) + DYN.get(a2, b2) + DYN.get(a3, b3));
The original formulae were written in a vectorized form for Matlab, so I want to be sure that the conversion to the component version here is correct.
Possible bug... can't turn off kPCA...
Now that JEDi can perform so many tasks, it seems we should be thinking about parallelization. This would require implementing multi-threading and serialization of the java code. Thoughts?
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