conMA {ChemmineR} | R Documentation |
Creates a bond matrix from SDF
and SDFset
objects. The matrix contains the atom labels in the row and column titles and the bond types are given in the data part as follows: 0 is no connection, 1 is a single bond, 2 is a double bond and 3 is a triple bond.
conMA(x, exclude = "none")
x |
|
exclude |
if |
...
If x
is of class SDF
, then a single bond matrix
is returned. If x
is of class SDFset
, then a list
of matrices is returned that has the same length as x
.
Thomas Girke
...
Functions: bonds
Class: SDF
and SDFset
## Instances of SDFset class data(sdfsample) sdfset <- sdfsample ## Create bond matrix for first two molecules in sdfset conMA(sdfset[1:2], exclude=c("H")) ## Return bond matrix for first molecule and plot its structure with atom numbering conMA(sdfset[[1]], exclude=c("H")) plot(sdfset[1], atomnum = TRUE, noHbonds=FALSE , no_print_atoms = "", atomcex=0.8) ## Return number of non-H bonds for each atom rowSums(conMA(sdfset[[1]], exclude=c("H")))