Atom Selection from PDB and PRMTOP Structure Objects

Usage

atom.select(...)


"atom.select"(pdb, string = NULL, type  = NULL, eleno = NULL, elety = NULL, resid = NULL, chain = NULL, resno = NULL, insert = NULL, segid = NULL,  operator = "AND", inverse = FALSE, value = FALSE, verbose=FALSE, ...)


"atom.select"(mol, string=NULL, eleno = NULL, elena = NULL, elety = NULL, resid = NULL, chain = NULL, resno = NULL, statbit = NULL,
			   operator = "AND", inverse = FALSE, value = FALSE, verbose=FALSE,  ...)


"atom.select"(prmtop, ...)


"print"(x, ...)

Arguments

...
arguments passed to atom.select.pdb, atom.select.prmtop, or print.
pdb
a structure object of class "pdb", obtained from read.pdb.
string
a single selection keyword from calpha cbeta backbone sidechain protein nucleic ligand water h or noh.
type
a single element character vector for selecting ‘ATOM’ or ‘HETATM’ record types.
eleno
a numeric vector of element numbers.
elena
a character vector of atom names.
elety
a character vector of atom names.
resid
a character vector of residue name identifiers.
chain
a character vector of chain identifiers.
resno
a numeric vector of residue numbers.
insert
a character vector of insert identifiers. Non-insert residues can be selected with NA or ‘’ values. The default value of NULL will select both insert and non-insert residues.
segid
a character vector of segment identifiers.
operator
a single element character specifying either the AND or OR operator by which individual selection components should be combined. Allowed values are ‘"AND"’ and ‘"OR"’.
verbose
logical, if TRUE details of the selection are printed.
inverse
logical, if TRUE the inversed selection is retured (i.e. all atoms NOT in the selection).
value
logical, if FALSE, vectors containing the (integer) indices of the matches determined by atom.select are returned, and if TRUE, a pdb object containing the matching atoms themselves is returned.
mol
a structure object of class "mol2", obtained from read.mol2.
statbit
a character vector of statbit identifiers.
prmtop
a structure object of class "prmtop", obtained from read.prmtop.
x
a atom.select object as obtained from atom.select.

Description

Return the ‘atom’ and ‘xyz’ coordinate indices of ‘pdb’ or ‘prmtop’ structure objects corresponding to the intersection of a hierarchical selection.

Details

This function allows for the selection of atom and coordinate data corresponding to the intersection of various input criteria.

Input selection criteria include selection string keywords (such as "calpha", "backbone", "sidechain", "protein", "nucleic", "ligand", etc.) and individual named selection components (including ‘chain’, ‘resno’, ‘resid’, ‘elety’ etc.).

For example, atom.select(pdb, "calpha") will return indices for all C-alpha (CA) atoms found in protein residues in the pdb object, atom.select(pdb, "backbone") will return indices for all protein N,CA,C,O atoms, and atom.select(pdb, "cbeta") for all protein N,CA,C,O,CB atoms.

Note that keyword string shortcuts can be combined with individual selection components, e.g. atom.select(pdb, "protein", chain="A") will select all protein atoms found in chain A.

Selection criteria are combined according to the provided operator argument. The default operator AND (or &) will combine by intersection while OR (or |) will take the union.

For example, atom.select(pdb, "protein", elety=c("N", "CA", "C"), resno=65:103) will select the N, CA, C atoms in the protein residues 65 through 103, while atom.select(pdb, "protein", resid="ATP", operator="OR") will select all protein atoms as well as any ATP residue(s).

Other string shortcuts include: "calpha", "back", "backbone", "cbeta", "protein", "notprotein", "ligand", "water", "notwater", "h", "noh", "nucleic", and "notnucleic".

In addition, the combine.select function can further combine atom selections using ‘AND’, ‘OR’, or ‘NOT’ logical operations.

Note

Protein atoms are defined as any atom in a residue matching the residue name in the attached aa.table data frame. See aa.table$aa3 for a complete list of residue names.

Nucleic atoms are defined as all atoms found in residues with names A, U, G, C, T, I, DA, DU, DG, DC, DT, or DI.

Water atoms/residues are defined as those with residue names H2O, OH2, HOH, HHO, OHH, SOL, WAT, TIP, TIP, TIP3, or TIP4.

Value

Returns a list of class "select" with the following components:
atom
a numeric matrix of atomic indices.

xyz
a numeric matrix of xyz indices.

call
the matched call.

References

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

Examples


##- PDB example
# Read a PDB file
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

# Select protein atoms of chain A
atom.select(pdb, "protein", chain="A")




 Call:  atom.select.pdb(pdb = pdb, string = "protein", chain = "A")

   Atom Indices#: 1001  ($atom)
   XYZ  Indices#: 3003  ($xyz)

+ attr: atom, xyz, call




# Select all atoms except from the protein
atom.select(pdb, "protein", inverse=TRUE, verbose=TRUE)




 ..     1001 atom(s) from 'string' selection 
 ..     1001 atom(s) in final combined selection 
 ..        0 atom(s) in inversed selection 





 Call:  atom.select.pdb(pdb = pdb, string = "protein", inverse = TRUE, 
    verbose = TRUE)

   Atom Indices#: 0  ($atom)
   XYZ  Indices#: 0  ($xyz)

+ attr: atom, xyz, call




# Select all C-alpha atoms with residues numbers between 43 and 54
sele <- atom.select(pdb, "calpha", resno=43:54, verbose=TRUE)




 ..      129 atom(s) from 'string' selection 
 ..       90 atom(s) from 'resno' selection 
 ..       12 atom(s) in final combined selection 





# Access the PDB data with the selection indices
print( pdb$atom[ sele$atom, "resid" ] )



 [1] "THR" "ASN" "ARG" "ASN" "THR" "ASP" "GLY" "SER" "THR" "ASP" "TYR" "GLY"



print( pdb$xyz[ sele$xyz ] )



 [1] 10.705 15.992 17.773 12.828 18.909 18.863 15.061 19.112 21.827 15.247
[11] 22.135 24.062 18.108 23.768 25.931 16.626 22.832 29.261 16.950 19.205
[21] 28.182 13.311 18.716 27.712 11.958 17.610 24.179  8.767 18.608 22.181
[31]  6.899 15.745 20.548  4.390 15.347 17.710




# Trim PDB to selection
ca.pdb <- trim.pdb(pdb, sele)


##- PRMTOP example
prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))

## Atom selection
ca.inds <- atom.select(prmtop, "calpha")




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

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

 .. number of atoms in PDB:  639 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46

See also

read.pdb, as.select, combine.select, trim.pdb, write.pdb, read.prmtop, read.crd, read.dcd, read.ncdf.

Author

Barry Grant, Lars Skjaerven