Hi,
On Fri, Mar 4, 2022 at 9:11 AM wangjianing_mail
<wangjianing_mail.163.com> wrote:
> I hope to read/load in another artificial covariance matrix in PCA analysis of cpptraj，But I didn't know how it word in cpptraj.
You can read in matrix data from an ASCII file formatted in two ways.
The first is <column <row> <value>, e.g.:
1.000 1.000 0.000
2.000 1.000 3.822
3.000 1.000 5.736
4.000 1.000 7.081
This is accomplished using the 'read2d nosquare2d' keywords with the
'readdata' command, e.g. 'readdata matrix.dat read2d name MyMatrix
nosquare2d'
You can also read the matrix formatted in rows, e.g.
0.000 3.822 5.736 7.081
This is accomplished using just the 'read2d' keyword with the
'readdata' command, e.g. 'readdata squarematrix.dat name MyMatrix
read2d'
> Because I want to do a weighted PCA analysis, that is, each point in the trajectory has an additional weighted. This leads to the covariance matrix I want to use is not the most straightforward version.
There is currently no way to assign weights to individual frames.
Contributions to the code are welcome!
-Dan
>
>
> Can someone give me a suggestion, or tell me that there is no direct command/options in cpptraj.
>
>
>
>
> Regards,
> JN Wang
>
>
>
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Received on Fri Mar 04 2022 - 07:00:02 PST
