# Scales-Based Descriptors with 20+ classes of Molecular Descriptors

Source:`R/pcm-02-extractDescScales.R`

`extractDescScales.Rd`

This function calculates the scales-based descriptors with molecular descriptors sets calculated by Dragon, Discovery Studio and MOE. Users can specify which molecular descriptors to select from one of these deseriptor sets by specify the numerical or character index of the molecular descriptors in the descriptor set.

## Arguments

- x
A character vector, as the input protein sequence.

- propmat
The matrix containing the descriptor set for the amino acids, which can be chosen from

`AAMOE2D`

,`AAMOE3D`

,`AACPSA`

,`AADescAll`

,`AA2DACOR`

,`AA3DMoRSE`

,`AAACF`

,`AABurden`

,`AAConn`

,`AAConst`

,`AAEdgeAdj`

,`AAEigIdx`

,`AAFGC`

,`AAGeom`

,`AAGETAWAY`

,`AAInfo`

,`AAMolProp`

,`AARandic`

,`AARDF`

,`AATopo`

,`AATopoChg`

,`AAWalk`

, and`AAWHIM`

.- index
Integer vector or character vector. Specify which molecular descriptors to select from one of these deseriptor sets by specify the numerical or character index of the molecular descriptors in the descriptor set. Default is

`NULL`

, which means selecting all the molecular descriptors in this descriptor set.- pc
Integer. The maximum dimension of the space which the data are to be represented in. Must be no greater than the number of amino acid properties provided.

- lag
The lag parameter. Must be less than the amino acids.

- scale
Logical. Should we auto-scale the property matrix (

`propmat`

) before doing MDS? Default is`TRUE`

.- silent
Logical. Whether we print the standard deviation, proportion of variance and the cumulative proportion of the selected principal components or not. Default is

`TRUE`

.

## Author

Nan Xiao <https://nanx.me>

## Examples

```
x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
descscales <- extractDescScales(
x,
propmat = "AATopo", index = c(37:41, 43:47),
pc = 5, lag = 7, silent = FALSE
)
#> Summary of the first 5 principal components:
#> PC1 PC2 PC3 PC4 PC5
#> Standard deviation 2.581537 1.754133 0.4621854 0.1918666 0.08972087
#> Proportion of Variance 0.666430 0.307700 0.0213600 0.0036800 0.00080000
#> Cumulative Proportion 0.666430 0.974130 0.9954900 0.9991700 0.99998000
```