bio3d (version 2.1-2)

read.mol2: Read MOL2 File

Description

Read a Sybyl MOL2 file

Usage

read.mol2(file, maxlines = -1L)

Arguments

file

a single element character vector containing the name of the MOL2 file to be read.

maxlines

the maximum number of lines to read before giving up with large files. Default is all lines.

Value

• Returns a list of molecules containing the following components:
• atom
  a character matrix containing all atomic coordinate ATOM data, with a row per ATOM and a column per record type. See below for details of the record type naming convention (useful for accessing columns).
• xyz
  a numeric vector or matrix of ATOM coordinate data.
• info
  a numeric vector of MOL2 info data.
• name
  a single element character vector containing the molecule name.

Details

Basic functionality to parse a MOL2 file. The current version omits bond information, and only @MOLECULE and @ATOM records are stored.

In the case of a multi-molecule MOL2 file, each molecule will be stored as an individual object in a list. Conversely, if the multi-molecule MOL2 file contains identical molecules in different conformations (typically a dockin run), then the output will be one object with an atom and xyz component (xyz in matrix representation; row-wise coordinates).

See examples for further details.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. For a description of the MOL2 format see: http://www.tripos.com/data/support/mol2.pdf.

See Also

atom.select, read.pdb

Examples

cat("")
## Read a single entry MOL2 file
## (returns a single object)
mol <- read.mol2("single.mol2")

## ATOM records
mol$atom

## Print some coordinate data
head(mol$atom[, c("x","y","z")])

## Or coordinates as a numeric vector
head(mol$xyz)

## Print atom charges
head(mol$atom[, "charge")])



## Read a multi-molecule MOL2 file
## (returns a list of objects)
multi.mol <- read.mol2("zinc.mol2")

## Number of molecules described in file
length(multi.mol)

## Access ATOM records for the first molecule
multi.mol[[1]]$atom

## Or coordinates for the second molecule
multi.mol[[2]]$xyz



## Process output from docking (e.g. DOCK)
## (typically one molecule with many conformations)
## (returns one object, but xyz in matrix format)
dock <- read.mol2("dock.mol2")

## Reference PDB file (e.g. X-ray structure)
pdb <- read.pdb("dock_ref.pdb")

## Calculate RMSD of docking modes
sele <- atom.select(dock, "noh")
rmsd(pdb$xyz, dock$xyz, b.inds=sele$xyz)