Trim a MOL2 Object To A Subset of Atoms.

Usage

"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, ...).

Description

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

Details

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

Value

Returns a list of class "mol2".

References

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

Examples

## 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")




 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..        0 atom(s) from 'string' selection 
 ..        0 atom(s) in final combined selection 

 .. number of atoms in PDB:  20 
 .. number of calphas in PDB: 0 
 .. number of residues in PDB: 1

See also

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

Author

Lars Skjaerven