Residue distances to coordinates

Given a distance matrix D, we can define a Gram matrix M by classical multidimensional scaling (MDS) (Young, Gale, and Aiston S. Householder. Psychometrika 3, no. 1 (1938): 19-22.),

$$\mathbf{M}_{ij} = \frac{\mathbf{D}_{1j}^2+\mathbf{D}_{i1}^2-\mathbf{D}_{ij}^2}{2}$$

Using the following code, one can generate a set of coordinates for a given distance matrix.

amo dist2coord \
-jobname [JOB_NAME] \
-type 1 \
-fastx <INPUT_FASTA_FILE> \
-mat <DISTANCE_MAP_FILE> \
-output [OUTPUT_DIRECTORY] \
-hlog