Inverse process of the funciton pdb2sse.

bounds.sse(x, pdb = NULL)

Arguments

x

a character vector indicating SSE for each amino acid residue.

pdb

an object of class pdb as obtained from function read.pdb. Can be ignored if x has 'names' attribute for residue labels.

Value

a 'sse' object.

Details

call for its effects.

Note

In both $helix and $sheet, an additional $id component is added to indicate the original numbering of the sse. This is particularly useful in e.g. trim.pdb() function.

Author

Xin-Qiu Yao & Barry Grant

See also

pdb2sse

Examples

# \donttest{ # PDB server connection required - testing excluded pdb <- read.pdb("1a7l")
#> Note: Accessing on-line PDB file
sse <- pdb2sse(pdb) sse.ind <- bounds.sse(sse) sse.ind
#> #> Call: #> NULL #> #> Class: #> sse #> #> Helices: 49 #> 17-31 (A) 43-53 (A) 64-72 (A) 83-88 (A) 91-97 (A) #> 132-142 (A) 154-163 (A) 186-200 (A) 210-218 (A) 229-238 (A) #> 273-282 (A) 287-296 (A) 305-313 (A) 315-326 (A) 334-351 (A) #> 357-365 (A) 134-137 (A) 17-31 (B) 43-50 (B) 64-73 (B) #> 83-88 (B) 91-97 (B) 132-142 (B) 154-163 (B) 186-200 (B) #> 210-219 (B) 229-238 (B) 273-282 (B) 287-296 (B) 305-313 (B) #> 315-326 (B) 334-351 (B) 357-132 (B) 17-31 (C) 43-53 (C) #> 64-72 (C) 83-88 (C) 91-97 (C) 132-142 (C) 154-163 (C) #> 186-200 (C) 210-218 (C) 229-238 (C) 273-282 (C) 287-296 (C) #> 305-313 (C) 315-326 (C) 334-352 (C) 357-363 (C) #> #> Sheets: 24 #> 7-10 (A) 35-38 (A) 59-63 (A) 260-266 (A) 106-111 (A) #> 224-227 (A) 114-118 (A) 242-245 (A) 6-10 (B) 34-38 (B) #> 59-63 (B) 260-266 (B) 106-111 (B) 224-227 (B) 114-118 (B) #> 242-245 (B) 7-10 (C) 35-38 (C) 59-63 (C) 260-266 (C) #> 106-111 (C) 224-227 (C) 114-118 (C) 242-245 (C) #> #> Turns: 0 #> #> Output is provided in residue numbers #>
# }