atom.select.RdReturn the ‘atom’ and ‘xyz’ coordinate indices of ‘pdb’ or ‘prmtop’ structure objects corresponding to the intersection of a hierarchical selection.
atom.select(...) # S3 method for pdb 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, ...) # S3 method for pdbs atom.select(pdbs, string = NULL, resno = NULL, chain = NULL, resid = NULL, operator="AND", inverse = FALSE, value = FALSE, verbose=FALSE, ...) # S3 method for mol2 atom.select(mol, string=NULL, eleno = NULL, elena = NULL, elety = NULL, resid = NULL, chain = NULL, resno = NULL, statbit = NULL, operator = "AND", inverse = FALS"AND"FALSE value = FALSE, verbose=FALSE, ...) # S3 method for prmtop atom.select(prmtop, ...) # S3 method for select print(x, ...)
| ... | arguments passed to |
|---|---|
| pdb | a structure object of class |
| pdbs | a numeric matrix of aligned C-alpha xyz Cartesian
coordinates as obtained with |
| string | a single selection keyword from |
| 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 |
| segid | a character vector of segment identifiers. Empty segid
values can be selected with |
| 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 |
| mol | a structure object of class |
| statbit | a character vector of statbit identifiers. |
| prmtop | a structure object of class |
| x | a atom.select object as obtained from
|
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.
Protein atoms are defined as any atom in a residue matching the
residue name in the attached aa.table data frame. See
aa.table$aa3 for a complete list of residue names.
Nucleic atoms are defined as all atoms found in residues with names A, U, G, C, T, I, DA, DU, DG, DC, DT, or DI.
Water atoms/residues are defined as those with residue names H2O, OH2, HOH, HHO, OHH, SOL, WAT, TIP, TIP, TIP3, or TIP4.
Returns a list of class "select" with the following components:
a numeric matrix of atomic indices.
a numeric matrix of xyz indices.
the matched call.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Barry Grant, Lars Skjaerven
read.pdb, as.select,
combine.select, trim.pdb,
write.pdb, read.prmtop,
read.crd, read.dcd,
read.ncdf.
##- PDB example # Read a PDB file pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) # Select protein atoms of chain A atom.select(pdb, "protein", chain="A")#> #> Call: atom.select.pdb(pdb = pdb, string = "protein", chain = "A") #> #> Atom Indices#: 1001 ($atom) #> XYZ Indices#: 3003 ($xyz) #> #> + attr: atom, xyz, call# Select all atoms except from the protein atom.select(pdb, "protein", inverse=TRUE, verbose=TRUE)#> #> .. 00001001 atom(s) from 'string' selection #> .. 00001001 atom(s) in final combined selection #> .. 00000000 atom(s) in inversed selection #>#> #> Call: atom.select.pdb(pdb = pdb, string = "protein", inverse = TRUE, #> verbose = TRUE) #> #> Atom Indices#: 0 ($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)#> #> .. 00000129 atom(s) from 'string' selection #> .. 00000090 atom(s) from 'resno' selection #> .. 00000012 atom(s) in final combined selection #>#> [1] "THR" "ASN" "ARG" "ASN" "THR" "ASP" "GLY" "SER" "THR" "ASP" "TYR" "GLY"#> [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) if (FALSE) { ##- PRMTOP example prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d")) ## Atom selection ca.inds <- atom.select(prmtop, "calpha") }