The most flexible way is to use
jmolViewer.getProperty(returnType, infoType, paramInfo);
You would specify:
returnType = null
infoType = "PolymerInfo"
paramInfo = "*" // or whatever subset you want, for instance
"*:A"
This will return a Java object that lists all groups in that set of atoms
and indicates if they are in helix, sheet, etc. To see the structure of this
object, use
print getProperty("polymerInfo")
It is a Vector of Vector of Vector of Hashtable:
models Vector[1]
polymers Vector[1]
monomers Vector[46]
chain "A"
atomInfo2 "[THR]1:A.CG2 #7"
monomerIndex 0
shapeVisibilityFlags 0
atomInfo1 "[THR]1:A.N #1"
_apt2 6
_apt1 0
structureType "sheet"
structureId 1
sequenceNumber 1
psi 147.66006
atomIndex2 6
atomIndex1 0
...(45 more of these)
Alternatively, if you just want the PDB file header info, use
jmolViewer.evalString("script(\"show structure\")")
and parse the information yourself. For example:
HELIX 1 H1 SER A 164 ILE A 176
HELIX 2 H2 LYS A 230 VAL A 235
HELIX 3 H3 SER A 236 ASN A 245
SHEET 1 S1 2 TYR A 20 THR A 21
SHEET 2 S2 2 GLN A 30 ASN A 34
SHEET 3 S3 2 HIS A 40 ASN A 48
SHEET 4 S4 2 TRP A 51 SER A 54
SHEET 5 S5 2 GLN A 64 LEU A 67
SHEET 6 S6 2 GLN A 81 VAL A 90
SHEET 7 S7 2 MET A 104 LEU A 108
SHEET 8 S8 2 GLN A 135 GLY A 140
SHEET 9 S9 2 LYS A 156 PRO A 161
SHEET 10 S10 2 MET A 180 ALA A 183
SHEET 11 S11 2 PRO A 198 CYS A 201
SHEET 12 S12 2 LYS A 204 TRP A 215
SHEET 13 S13 2 GLY A 226 THR A 229
Bob Hanson
On Thu, Aug 6, 2009 at 11:17 AM, Charles Shubert <[email protected]> wrote:
> How does my Java application get a list of secondary structures from
> JmolViewer that duplicates the information in a pdb file?
>
> For a HELIX this would be: the helix id, init residue, end residue.
> For a SHEET STRAND this would be: the strand#, sheet id, number of
> strands, init residue, end residue.
>
> Thanks, Chuck
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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