Mask a Subset of Atoms in a DCCM Object.
mask.dccm.RdProduce a new DCCM object with selected atoms masked.
mask(...) # S3 method for dccm mask(dccm, pdb = NULL, a.inds = NULL, b.inds = NULL, ...)
Arguments
| dccm | a DCCM structure object obtained from function
|
|---|---|
| pdb | a PDB structure object obtained from
|
| a.inds | a numeric vector containing the indices of the elements
of the DCCM matrix in which should not be masked. Alternatively, if
|
| b.inds | a numeric vector containing the indices of the elements of the DCCM matrix in which should not be masked. |
| ... | arguments not passed anywhere. |
Details
This is a basic utility function for masking a DCCM object matrix to highlight user-selected regions in the correlation network.
When both a.inds and b.inds are provided only their
intersection is retained. When only a.inds is provided then
the corresponding region to everything else is retained.
Note: The current version assumes that the input PDB corresponds to the input DCCM. In many cases this will correspond to a PDB object containing only CA atoms.
Value
Returns a matrix list of class "dccm" with the indices/atoms
not corresponding to the selection masked.
References
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Author
Lars Skjaerven
See also
Examples
## Calculate DCCM pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) cij <- dccm(nma(pdb))#> Building Hessian... Done in 0.011 seconds. #> Diagonalizing Hessian... Done in 0.079 seconds. #> | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================= | 94% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100%## Mask DCCM matrix according to matrix indices cijm <- mask(cij, a.inds=40:50, b.inds=80:90) plot(cijm)## Mask DCCM matrix according PDB selection pdb.ca <- trim(pdb, "calpha") a.inds <- atom.select(pdb.ca, resno=40:50) b.inds <- atom.select(pdb.ca, resno=80:90) # Provide pdb object correspoding to input dccm cijm <- mask(cij, pdb.ca, a.inds, b.inds) plot(cijm)
