extractDescScales: Scales-Based Descriptors with 20+ classes of Molecular Descriptors
Description
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.
A length lag * p^2 named vector,
p is the number of scales selected.
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.