- xyz
numeric vector of xyz coordinates or a numeric matrix of
coordinates with a row per structure/frame.
- grpby
a vector counting connective duplicated elements that
indicate the elements of xyz
that should be considered as a group
(e.g. atoms from a particular residue).
- dcut
a cutoff distance value below which atoms are considered
in contact.
- scut
a cutoff neighbour value which has the effect of
excluding atoms that are sequentially within this value.
- pcut
a cutoff probability of structures/frames showing a contact,
above which atoms are considered in contact with respect to the ensemble.
Ignored if binary=FALSE
.
- binary
logical, if FALSE the raw matrix containing fraction of frames that
two residues are in contact is returned.
- mask.lower
logical, if TRUE the lower matrix elements
(i.e. those below the diagonal) are returned as NA.
- collapse
logical, if FALSE an array of contact maps for all frames is returned.
- gc.first
logical, if TRUE will call gc() first before calculation of
distance matrix. This is to solve the memory overload problem when ncore > 1
and xyz
has many rows, with a bit sacrifice on speed.
- ncore
number of CPU cores used to do the calculation.
ncore>1
requires package ‘parallel’ installed.
- nseg.scale
split input data into specified number of segments
prior to running multiple core calculation. See fit.xyz
.
- pdb
a structure object of class "pdb"
, obtained from
read.pdb
.
- inds
a list object of ATOM and XYZ indices as obtained from
atom.select
.
- verbose
logical, if TRUE details of the selection are
printed.
- pdbs
a ‘pdbs’ object as returned by read.fasta.pdb
,
read.all
, or pdbaln
.
- rm.gaps
logical, if TRUE gapped positions are removed in the returned value.
- all.atom
logical, if TRUE all-atom coordinates from read.all
are used.
- ...
arguments passed to and from functions.