Just to clarify, the delete command is clearly running because the atoms do
disappear from the view of the molecule. But I'd like to understand why
interrogating the JmolViewer instance reveals them as still present in the
first model.
2014-09-27 18:30 GMT+01:00 N David Brown <hubd...@gmail.com>:
> I use Jmol embedded within a custom Java application.
>
> I’m deleting some bonds then atoms by running a command like this:
>
> JmolViewer viewer; // Gets defined.// ...
> String script = "connect (Rh1) (B155) delete;connect (Rh1) (B93)
> delete;connect (B155) (Rh1) delete;connect (B155) (B101) delete;connect
> (B155) (C3) delete;connect (B155) (B140) delete;connect (B155) (B154)
> delete;connect (B155) (B159) delete;connect (B155) (B156) delete;connect
> (B155) (B33) delete;connect (B155) (B45) delete;connect (C2) (B159)
> delete;connect (C2) (C1) delete;connect (C3) (S2) delete;connect (C3) (S3)
> delete;connect (C3) (C1) delete;connect (C3) (B159) delete;connect (C3)
> (B157) delete;connect (C3) (B156) delete;connect (C3) (B155) delete;connect
> (C3) (B154) delete;connect (C3) (B140) delete;connect (C3) (B135)
> delete;connect (C3) (B133) delete;connect (C3) (B45) delete;connect (B33)
> (S3) delete;connect (B33) (B155) delete;connect (B33) (B38) delete;connect
> (B45) (S3) delete;connect (B45) (S4) delete;connect (B45) (C3) delete;connect
> (B45) (B159) delete;connect (B45) (B157) delete;connect (B45) (B155)
> delete;connect (B45) (B154) delete;connect (B45) (B140) delete;connect (B45)
> (B135) delete;connect (B45) (B133) delete;connect (B45) (B101) delete;connect
> (B101) (S2) delete;connect (B101) (S3) delete;connect (B101) (B159)
> delete;connect (B101) (B157) delete;connect (B101) (B156) delete;connect
> (B101) (B155) delete;connect (B101) (B140) delete;connect (B101) (B135)
> delete;connect (B101) (B133) delete;connect (B101) (C1) delete;connect (B101)
> (B45) delete;connect (B101) (B85) delete;connect (B133) (S4) delete;connect
> (B133) (S5) delete;connect (B133) (B101) delete;connect (B133) (C3)
> delete;connect (B133) (B159) delete;connect (B133) (B157) delete;connect
> (B133) (B156) delete;connect (B133) (B154) delete;connect (B133) (B135)
> delete;connect (B133) (B45) delete;connect (B135) (S3) delete;connect (B135)
> (S4) delete;connect (B135) (B101) delete;connect (B135) (C1) delete;connect
> (B135) (C3) delete;connect (B135) (B133) delete;connect (B135) (B159)
> delete;connect (B135) (B157) delete;connect (B135) (B156) delete;connect
> (B135) (B154) delete;connect (B135) (B140) delete;connect (B135) (B45)
> delete;connect (B140) (S4) delete;connect (B140) (S5) delete;connect (B140)
> (B101) delete;connect (B140) (C3) delete;connect (B140) (B159) delete;connect
> (B140) (B157) delete;connect (B140) (B156) delete;connect (B140) (B155)
> delete;connect (B140) (B154) delete;connect (B140) (B135) delete;connect
> (B140) (B45) delete;connect (B154) (S2) delete;connect (B154) (S5)
> delete;connect (B154) (C1) delete;connect (B154) (C3) delete;connect (B154)
> (B140) delete;connect (B154) (B133) delete;connect (B154) (B135)
> delete;connect (B154) (B157) delete;connect (B154) (B156) delete;connect
> (B154) (B155) delete;connect (B154) (B45) delete;connect (B154) (B93)
> delete;connect (B156) (S2) delete;connect (B156) (S5) delete;connect (B156)
> (B101) delete;connect (B156) (C3) delete;connect (B156) (B140) delete;connect
> (B156) (B133) delete;connect (B156) (B135) delete;connect (B156) (B159)
> delete;connect (B156) (B157) delete;connect (B156) (B154) delete;connect
> (B156) (B155) delete;connect (B157) (S4) delete;connect (B157) (S5)
> delete;connect (B157) (B101) delete;connect (B157) (C1) delete;connect (B157)
> (C3) delete;connect (B157) (B140) delete;connect (B157) (B133) delete;connect
> (B157) (B135) delete;connect (B157) (B156) delete;connect (B157) (B154)
> delete;connect (B157) (B45) delete;connect (B159) (S4) delete;connect (B159)
> (B101) delete;connect (B159) (C2) delete;connect (B159) (C1) delete;connect
> (B159) (C3) delete;connect (B159) (B140) delete;connect (B159) (B133)
> delete;connect (B159) (B135) delete;connect (B159) (B156) delete;connect
> (B159) (B155) delete;connect (B159) (B45) delete;connect (Rh2) (B87)
> delete;connect (C4) (B158) delete;connect (C4) (B4) delete;connect (B15) (S1)
> delete;connect (B15) (P3) delete;connect (B15) (B4) delete;connect (B15)
> (B160) delete;connect (B15) (B158) delete;connect (B15) (B152) delete;connect
> (B15) (B137) delete;connect (B15) (B73) delete;connect (B73) (P1)
> delete;connect (B73) (P5) delete;connect (B73) (B15) delete;connect (B73)
> (B158) delete;connect (B73) (B152) delete;connect (B73) (B137) delete;connect
> (B137) (P1) delete;connect (B137) (P3) delete;connect (B137) (B4)
> delete;connect (B137) (B160) delete;connect (B137) (B158) delete;connect
> (B137) (B152) delete;connect (B137) (B15) delete;connect (B137) (B73)
> delete;connect (B152) (S1) delete;connect (B152) (P5) delete;connect (B152)
> (B137) delete;connect (B152) (B15) delete;connect (B152) (B158)
> delete;connect (B152) (B73) delete;connect (B158) (P1) delete;connect (B158)
> (C4) delete;connect (B158) (B4) delete;connect (B158) (B137) delete;connect
> (B158) (B15) delete;connect (B158) (B160) delete;connect (B158) (B152)
> delete;connect (B158) (B73) delete;connect (B158) (B87) delete;connect (B160)
> (S1) delete;connect (B160) (P1) delete;connect (B160) (P5) delete;connect
> (B160) (B137) delete;connect (B160) (B15) delete;connect (B160) (B158)
> delete;delete B155;delete C2;delete C3;delete B33;delete B45;delete
> B101;delete B133;delete B135;delete B140;delete B154;delete B156;delete
> B157;delete B159;delete C4;delete B15;delete B73;delete B137;delete
> B152;delete B158;delete B160;"
>
> viewer.scriptWaitStatus(script, null);
> // I've also tried this:
> viewer.getProperty(null, "evaluate", "script(' "+script+ "; refresh ')");
>
> After this has run I inspect the first viewer model:
>
> final short nAtoms = (short) viewer.getAtomCountInModel(0);for (short id = 0;
> id < nAtoms; ++id) {
> org.jmol.modelset.Atom atom = (org.jmol.modelset.Atom)
> viewer.getAtomPoint3f(id);
> System.out.println(atom.getAtomName());
> }
>
> The atoms I’ve deleted are listed as still in the model. Why?
>
> If I try to manipulate these deleted atoms in the Jmol console, the output
> suggests they don’t exist.
>
> How can I get the viewer model to update so the atoms really are deleted?
>
> Cheers,
>
> Dave
>
>
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