bio3d (version 2.3-4)

trim.mol2: Trim a MOL2 Object To A Subset of Atoms.

Description

Produce a new smaller MOL2 object, containing a subset of atoms, from a given larger MOL2 object.

Usage

# S3 method for mol2
trim(mol, …, inds = NULL)

Arguments

mol

a MOL2 structure object obtained from read.mol2.

…

additional arguments passed to atom.select. If inds is also provided, these arguments will be ignored.

inds

a list object of ATOM and XYZ indices as obtained from atom.select. If NULL, atom selection will be obtained from calling atom.select(mol, …).

Value

Returns a list of class "mol2".

Details

This is a basic utility function for creating a new MOL2 object based on a selection of atoms.

References

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

See Also

read.mol2, atom.select.mol2, as.pdb.mol2, write.mol2,

Examples

# NOT RUN {
## Read a MOL2 file from those included with the package
mol <- read.mol2( system.file("examples/aspirin.mol2", package="bio3d"))

## Trim away H-atoms
mol <- trim(mol, "noh")

# }