com. bio3d 2.3-0

Usage

com(...)
"com"(pdb, inds=NULL, use.mass=TRUE, ...)
"com"(xyz, mass=NULL, ...)

Arguments

pdb: an object of class pdb as obtained from function read.pdb.
inds: atom and xyz coordinate indices obtained from atom.select that selects the elements of pdb upon which the calculation should be based.
use.mass: logical, if TRUE the calculation will be mass weighted (center of mass).
...: additional arguments to atom2mass.
xyz: a numeric vector or matrix of Cartesian coordinates (e.g. an object of type xyz).
mass: a numeric vector containing the masses of each atom in xyz.

Description

Calculate the center of mass of a PDB object.

Details

This function calculates the center of mass of the provided PDB structure / Cartesian coordiantes. Atom names found in standard amino acids in the PDB are mapped to atom elements and their corresponding relative atomic masses.

In the case of an unknown atom name elety.custom and mass.custom can be used to map an atom to the correct atomic mass. See examples for more details.

Alternatively, the atom name will be mapped automatically to the element corresponding to the first character of the atom name. Atom names starting with character H will be mapped to hydrogen atoms.

Value

Returns the Cartesian coordinates at the center of mass.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples


# PDB server connection required - testing excluded

## Stucture of PKA:
pdb <- read.pdb("3dnd")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE


## Center of mass:
com(pdb)

Warning message:

	unknown element: mapped O1P to O
	unknown element: mapped O2P to O
	unknown element: mapped O3P to O
	unknown element: mapped O1P to O
	unknown element: mapped O2P to O
	unknown element: mapped O3P to O
	unknown element: mapped C8 to C
	unknown element: mapped C11 to C
	unknown element: mapped C13 to C
	unknown element: mapped C12 to C
	unknown element: mapped C9 to C
	unknown element: mapped C5 to C
	unknown element: mapped C2 to C
	unknown element: mapped C1 to C
	unknown element: mapped S4 to S
	unknown element: mapped C3 to C
	unknown element: mapped N6 to N
	unknown element: mapped C7 to C
	unknown element: mapped N10 to N
            x        y         z
[1,] 9.760781 2.455901 -2.076182


## Center of mass of a selection
inds <- atom.select(pdb, chain="I")
com(pdb, inds)

            x          y        z
[1,] 22.72468 -0.6884178 8.571269


## using XYZ Cartesian coordinates
xyz <- pdb$xyz[, inds$xyz]
com.xyz(xyz)

            x          y        z
[1,] 22.68164 -0.7530328 8.586634


## with mass weighting
com.xyz(xyz, mass=atom2mass(pdb$atom[inds$atom, "elety"]) )

            x          y        z
[1,] 22.72468 -0.6884178 8.571269




## Unknown atom names
pdb <- read.pdb("3dnd")

  Note: Accessing on-line PDB file

Warning message:
/tmp/RtmpTDihxb/3dnd.pdb  exists. Skipping download
   PDB has ALT records, taking A only, rm.alt=TRUE

inds <- atom.select(pdb, resid="LL2")
mycom <- com(pdb, inds, rescue=TRUE)

Warning message:

	unknown element: mapped C8 to C
	unknown element: mapped C11 to C
	unknown element: mapped C13 to C
	unknown element: mapped C12 to C
	unknown element: mapped C9 to C
	unknown element: mapped C5 to C
	unknown element: mapped C2 to C
	unknown element: mapped C1 to C
	unknown element: mapped S4 to S
	unknown element: mapped C3 to C
	unknown element: mapped N6 to N
	unknown element: mapped C7 to C
	unknown element: mapped N10 to N
#warnings()


## Map atom names manually
pdb <- read.pdb("3RE0")

  Note: Accessing on-line PDB file
   PDB has ALT records, taking A only, rm.alt=TRUE

inds <- atom.select(pdb, resno=201)

myelety  <- data.frame(name = c("CL2","PT1","N1","N2"), symb = c("Cl","Pt","N","N"))
mymasses <- data.frame(symb = c("Cl","Pt"), mass = c(35.45, 195.08))
mycom    <- com(pdb, inds, elety.custom=myelety, mass.custom=mymasses)

Author

Lars Skjaerven

Center of Mass