icn3d 3.35.0 → 3.36.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/icn3d.js +477 -368
  2. package/icn3d.min.js +4 -4
  3. package/icn3d.module.js +477 -368
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -9824,96 +9824,96 @@ class ClickMenu {
9824
9824
  let thisClass = this;
9825
9825
  //mn 1
9826
9826
  // clkMn1_mmtfid: function() {
9827
- me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; //e.preventDefault();
9827
+ me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; e.preventDefault();
9828
9828
  me.htmlCls.dialogCls.openDlg('dl_vastplus', 'Please input PDB ID for VAST+');
9829
9829
  });
9830
9830
 
9831
- me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; //e.preventDefault();
9831
+ me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; e.preventDefault();
9832
9832
  me.htmlCls.dialogCls.openDlg('dl_vast', 'Please input chain or PDB file for VAST');
9833
9833
  });
9834
9834
 
9835
- me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; //e.preventDefault();
9835
+ me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; e.preventDefault();
9836
9836
  me.htmlCls.dialogCls.openDlg('dl_foldseek', 'Submit your selection to Foldseek');
9837
9837
  });
9838
9838
 
9839
- me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; //e.preventDefault();
9839
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; e.preventDefault();
9840
9840
  me.htmlCls.dialogCls.openDlg('dl_mmtfid', 'Please input BCIF/MMTF ID');
9841
9841
  });
9842
9842
 
9843
9843
  // clkMn1_pdbid: function() {
9844
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; //e.preventDefault();
9844
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; e.preventDefault();
9845
9845
  me.htmlCls.dialogCls.openDlg('dl_pdbid', 'Please input PDB ID');
9846
9846
  });
9847
9847
 
9848
- me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; //e.preventDefault();
9848
+ me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; e.preventDefault();
9849
9849
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
9850
9850
  });
9851
9851
 
9852
- me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; //e.preventDefault();
9852
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
9853
9853
  me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI Protein Accession');
9854
9854
  });
9855
9855
 
9856
- me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; //e.preventDefault();
9856
+ me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
9857
9857
  me.htmlCls.dialogCls.openDlg('dl_opmid', 'Please input OPM PDB ID');
9858
9858
  });
9859
9859
 
9860
- me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; //e.preventDefault();
9860
+ me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; e.preventDefault();
9861
9861
  me.htmlCls.dialogCls.openDlg('dl_align', 'Align two PDB structures');
9862
9862
  });
9863
9863
 
9864
- me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; //e.preventDefault();
9864
+ me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; e.preventDefault();
9865
9865
  me.htmlCls.dialogCls.openDlg('dl_alignaf', 'Align two AlphaFold structures');
9866
9866
  });
9867
9867
 
9868
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; //e.preventDefault();
9868
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; e.preventDefault();
9869
9869
  me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
9870
9870
  });
9871
9871
 
9872
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; //e.preventDefault();
9872
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; e.preventDefault();
9873
9873
  me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
9874
9874
  });
9875
9875
 
9876
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; //e.preventDefault();
9876
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; e.preventDefault();
9877
9877
  me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
9878
9878
  });
9879
9879
 
9880
- me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; //e.preventDefault();
9880
+ me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; e.preventDefault();
9881
9881
  me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
9882
9882
  });
9883
9883
 
9884
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; //e.preventDefault();
9884
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; e.preventDefault();
9885
9885
  //me = me.setIcn3dui($(this).attr('id'));
9886
9886
  me.htmlCls.dialogCls.openDlg('dl_pdbfile', 'Please input PDB File');
9887
9887
  });
9888
- me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; //e.preventDefault();
9888
+ me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; e.preventDefault();
9889
9889
  //me = me.setIcn3dui($(this).attr('id'));
9890
9890
  me.htmlCls.dialogCls.openDlg('dl_pdbfile_app', 'Please append PDB Files');
9891
9891
  });
9892
9892
 
9893
- me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; //e.preventDefault();
9893
+ me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; e.preventDefault();
9894
9894
  me.htmlCls.dialogCls.openDlg('dl_mol2file', 'Please input Mol2 File');
9895
9895
  });
9896
9896
 
9897
- me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; //e.preventDefault();
9897
+ me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; e.preventDefault();
9898
9898
  me.htmlCls.dialogCls.openDlg('dl_sdffile', 'Please input SDF File');
9899
9899
  });
9900
9900
 
9901
- me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; //e.preventDefault();
9901
+ me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; e.preventDefault();
9902
9902
  me.htmlCls.dialogCls.openDlg('dl_xyzfile', 'Please input XYZ File');
9903
9903
  });
9904
9904
 
9905
- me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; //e.preventDefault();
9905
+ me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; e.preventDefault();
9906
9906
  me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold PAE File');
9907
9907
  });
9908
9908
 
9909
- me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; //e.preventDefault();
9909
+ me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; e.preventDefault();
9910
9910
  me.htmlCls.dialogCls.openDlg('dl_urlfile', 'Load data by URL');
9911
9911
  });
9912
9912
 
9913
- me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; //e.preventDefault();
9913
+ me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
9914
9914
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
9915
9915
  });
9916
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9916
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9917
9917
  let url = $("#" + me.pre + "sharelinkurl").val();
9918
9918
  thisClass.setLogCmd("open " + url, false);
9919
9919
  localStorage.setItem('fixedversion', '1');
@@ -9921,73 +9921,73 @@ class ClickMenu {
9921
9921
  window.open(url, urlTarget);
9922
9922
  });
9923
9923
 
9924
- me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; //e.preventDefault();
9924
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; e.preventDefault();
9925
9925
  me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please append mmCIF File');
9926
9926
  });
9927
9927
 
9928
- me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
9928
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; e.preventDefault();
9929
9929
  me.htmlCls.dialogCls.openDlg('dl_mmcifid', 'Please input mmCIF ID');
9930
9930
  });
9931
9931
 
9932
- me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; //e.preventDefault();
9932
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; e.preventDefault();
9933
9933
  me.htmlCls.dialogCls.openDlg('dl_mmdbid', 'Please input MMDB or PDB ID');
9934
9934
  });
9935
9935
 
9936
- me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; //e.preventDefault();
9936
+ me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; e.preventDefault();
9937
9937
  me.htmlCls.dialogCls.openDlg('dl_mmdbafid', 'Please input PDB/MMDB/AlphaFold UniProt IDs');
9938
9938
  });
9939
9939
 
9940
- me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; //e.preventDefault();
9940
+ me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; e.preventDefault();
9941
9941
  me.htmlCls.dialogCls.openDlg('dl_blast_rep_id', 'Align sequence to structure');
9942
9942
  });
9943
9943
 
9944
- me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; //e.preventDefault();
9944
+ me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; e.preventDefault();
9945
9945
  me.htmlCls.dialogCls.openDlg('dl_esmfold', 'Sequence to structure prediction with ESMFold');
9946
9946
  });
9947
9947
 
9948
- me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; //e.preventDefault();
9948
+ me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; e.preventDefault();
9949
9949
  me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein or gene name');
9950
9950
  });
9951
9951
 
9952
- me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; //e.preventDefault();
9952
+ me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
9953
9953
  me.htmlCls.dialogCls.openDlg('dl_cid', 'Please input PubChem Compound');
9954
9954
  });
9955
9955
 
9956
- me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; //e.preventDefault();
9957
- me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please input the PNG image');
9956
+ me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; e.preventDefault();
9957
+ me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please append PNG images');
9958
9958
  });
9959
9959
 
9960
- me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; //e.preventDefault();
9960
+ me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; e.preventDefault();
9961
9961
  me.htmlCls.dialogCls.openDlg('dl_state', 'Please input the state file');
9962
9962
  });
9963
9963
 
9964
- me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; //e.preventDefault();
9964
+ me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; e.preventDefault();
9965
9965
  me.htmlCls.dialogCls.openDlg('dl_selection', 'Please input the selection file');
9966
9966
  });
9967
9967
 
9968
- me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; //e.preventDefault();
9968
+ me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; e.preventDefault();
9969
9969
  me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
9970
9970
  });
9971
9971
 
9972
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
9972
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; e.preventDefault();
9973
9973
  me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
9974
9974
  });
9975
9975
 
9976
9976
 
9977
- me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9977
+ me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9978
9978
  ic.loadPhiFrom = 'delphi';
9979
9979
  $("#" + me.pre + "dl_delphi_tabs").tabs();
9980
9980
  me.htmlCls.dialogCls.openDlg('dl_delphi', 'Please set parameters to display DelPhi potential map');
9981
9981
  });
9982
9982
 
9983
- me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9983
+ me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9984
9984
  ic.loadPhiFrom = 'phi';
9985
9985
  $("#" + me.pre + "dl_phi_tabs").tabs();
9986
9986
  $("#" + me.pre + "phitab1_tabs").tabs();
9987
9987
  $("#" + me.pre + "phitab2_tabs").tabs();
9988
9988
  me.htmlCls.dialogCls.openDlg('dl_phi', 'Please input local phi or cube file to display DelPhi potential map');
9989
9989
  });
9990
- me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9990
+ me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9991
9991
  ic.loadPhiFrom = 'phiurl';
9992
9992
  $("#" + me.pre + "dl_phiurl_tabs").tabs();
9993
9993
  $("#" + me.pre + "phiurltab1_tabs").tabs();
@@ -9996,11 +9996,11 @@ class ClickMenu {
9996
9996
  });
9997
9997
 
9998
9998
 
9999
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
9999
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; e.preventDefault();
10000
10000
  me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the map file to display electron density map');
10001
10001
  });
10002
10002
 
10003
- me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10003
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10004
10004
  thisClass.setLogCmd("export state file", false);
10005
10005
  let file_pref = Object.keys(ic.structures).join(',');
10006
10006
 
@@ -10008,19 +10008,19 @@ class ClickMenu {
10008
10008
  });
10009
10009
 
10010
10010
 
10011
- me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; //e.preventDefault();
10011
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; e.preventDefault();
10012
10012
  me.htmlCls.setHtmlCls.exportPdb();
10013
10013
 
10014
10014
  thisClass.setLogCmd("export pdb", true);
10015
10015
  });
10016
10016
 
10017
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; //e.preventDefault();
10017
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; e.preventDefault();
10018
10018
  me.htmlCls.setHtmlCls.exportSecondary();
10019
10019
 
10020
10020
  thisClass.setLogCmd("export secondary structure", true);
10021
10021
  });
10022
10022
 
10023
- me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10023
+ me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10024
10024
  let pdbStr = ic.saveFileCls.getSelectedResiduePDB();
10025
10025
 
10026
10026
  thisClass.setLogCmd("export PDB of selected residues", false);
@@ -10029,57 +10029,57 @@ class ClickMenu {
10029
10029
  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pdb', 'text', [pdbStr]);
10030
10030
  });
10031
10031
 
10032
- me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
10032
+ me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; e.preventDefault();
10033
10033
  await me.htmlCls.setHtmlCls.exportPqr();
10034
10034
  thisClass.setLogCmd("export pqr", true);
10035
10035
  });
10036
10036
 
10037
- // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10037
+ // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10038
10038
  // let bPdb = true;
10039
10039
  // await me.htmlCls.setHtmlCls.exportPqr(bPdb);
10040
10040
  // thisClass.setLogCmd("export pdbh", false);
10041
10041
  // });
10042
10042
 
10043
- me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10043
+ me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10044
10044
  let bHydrogen = false;
10045
10045
  await ic.scapCls.exportPdbProfix(bHydrogen);
10046
10046
  thisClass.setLogCmd("export pdb missing atoms", true);
10047
10047
  });
10048
10048
 
10049
- me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10049
+ me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10050
10050
  let bHydrogen = true;
10051
10051
  await ic.scapCls.exportPdbProfix(bHydrogen);
10052
10052
  thisClass.setLogCmd("export pdb hydrogen", true);
10053
10053
  });
10054
10054
 
10055
- me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10055
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10056
10056
  ic.refnumCls.exportRefnum('igstrand');
10057
10057
  thisClass.setLogCmd("export refnum igstrand", true);
10058
10058
  });
10059
10059
 
10060
- me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10060
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10061
10061
  ic.refnumCls.exportRefnum('kabat');
10062
10062
  thisClass.setLogCmd("export refnum kabat", true);
10063
10063
  });
10064
10064
 
10065
- me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10065
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10066
10066
  ic.refnumCls.exportRefnum('imgt');
10067
10067
  thisClass.setLogCmd("export refnum imgt", true);
10068
10068
  });
10069
10069
 
10070
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10070
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10071
10071
  thisClass.setLogCmd("export stl file", false);
10072
10072
  //ic.threeDPrintCls.hideStabilizer();
10073
10073
  ic.export3DCls.exportStlFile('');
10074
10074
  });
10075
10075
 
10076
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10076
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10077
10077
  thisClass.setLogCmd("export vrml file", false);
10078
10078
  //ic.threeDPrintCls.hideStabilizer();
10079
10079
  ic.export3DCls.exportVrmlFile('');
10080
10080
  });
10081
10081
 
10082
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10082
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10083
10083
  thisClass.setLogCmd("export stl stabilizer file", false);
10084
10084
  //ic.bRender = false;
10085
10085
  ic.threeDPrintCls.hideStabilizer();
@@ -10088,7 +10088,7 @@ class ClickMenu {
10088
10088
  ic.export3DCls.exportStlFile('_stab');
10089
10089
  });
10090
10090
 
10091
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10091
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10092
10092
  thisClass.setLogCmd("export vrml stabilizer file", false);
10093
10093
  //ic.bRender = false;
10094
10094
  ic.threeDPrintCls.hideStabilizer();
@@ -10097,13 +10097,13 @@ class ClickMenu {
10097
10097
  ic.export3DCls.exportVrmlFile('_stab');
10098
10098
  });
10099
10099
 
10100
- me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10100
+ me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10101
10101
  thisClass.setLogCmd("export interactions", false);
10102
10102
  if(me.cfg.mmdbid !== undefined) await ic.viewInterPairsCls.retrieveInteractionData();
10103
10103
  ic.viewInterPairsCls.exportInteractions();
10104
10104
  });
10105
10105
 
10106
- me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10106
+ me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10107
10107
  // do not record the export command
10108
10108
  //thisClass.setLogCmd("export canvas", true);
10109
10109
  thisClass.setLogCmd("export canvas", false);
@@ -10112,28 +10112,28 @@ class ClickMenu {
10112
10112
  let bPngHtml = true;
10113
10113
  await ic.shareLinkCls.shareLink(bPngHtml);
10114
10114
  });
10115
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10115
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10116
10116
  thisClass.setLogCmd("export canvas 1", true);
10117
10117
  ic.scaleFactor = 1;
10118
10118
  await ic.shareLinkCls.shareLink(true, true);
10119
10119
  });
10120
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10120
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10121
10121
  thisClass.setLogCmd("export canvas 2", true);
10122
10122
  ic.scaleFactor = 2;
10123
10123
  await ic.shareLinkCls.shareLink(true, true);
10124
10124
  });
10125
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10125
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10126
10126
  thisClass.setLogCmd("export canvas 4", true);
10127
10127
  ic.scaleFactor = 4;
10128
10128
  await ic.shareLinkCls.shareLink(true, true);
10129
10129
  });
10130
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10130
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10131
10131
  thisClass.setLogCmd("export canvas 8", true);
10132
10132
  ic.scaleFactor = 8;
10133
10133
  await ic.shareLinkCls.shareLink(true, true);
10134
10134
  });
10135
10135
 
10136
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10136
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10137
10137
  thisClass.setLogCmd("export counts", false);
10138
10138
  let text = '<html><body><div style="text-align:center"><br><b>Total Count for atoms with coordinates</b>:<br/><table align=center border=1 cellpadding=10 cellspacing=0><tr><th>Structure Count</th><th>Chain Count</th><th>Residue Count</th><th>Atom Count</th></tr>';
10139
10139
  text += '<tr><td>' + Object.keys(ic.structures).length + '</td><td>' + Object.keys(ic.chains).length + '</td><td>' + Object.keys(ic.residues).length + '</td><td>' + Object.keys(ic.atoms).length + '</td></tr>';
@@ -10160,7 +10160,7 @@ class ClickMenu {
10160
10160
  ic.saveFileCls.saveFile(file_pref + '_counts.html', 'html', text);
10161
10161
  });
10162
10162
 
10163
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10163
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10164
10164
  thisClass.setLogCmd("export all selections", false);
10165
10165
 
10166
10166
  thisClass.SetChainsAdvancedMenu();
@@ -10170,7 +10170,7 @@ class ClickMenu {
10170
10170
  ic.saveFileCls.saveFile(file_pref + '_selections.txt', 'text', [text]);
10171
10171
  });
10172
10172
 
10173
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10173
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10174
10174
  thisClass.setLogCmd("export all selections with details", false);
10175
10175
 
10176
10176
  thisClass.SetChainsAdvancedMenu();
@@ -10181,32 +10181,32 @@ class ClickMenu {
10181
10181
  ic.saveFileCls.saveFile(file_pref + '_sel_details.txt', 'text', [text]);
10182
10182
  });
10183
10183
 
10184
- me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10184
+ me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10185
10185
  await ic.shareLinkCls.shareLink();
10186
10186
  });
10187
10187
 
10188
- me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10188
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10189
10189
  await ic.resizeCanvasCls.replayon();
10190
10190
  thisClass.setLogCmd("replay on", true);
10191
10191
  });
10192
- me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10192
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10193
10193
  await ic.resizeCanvasCls.replayoff();
10194
10194
  thisClass.setLogCmd("replay off", true);
10195
10195
  });
10196
10196
 
10197
- me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; //e.preventDefault();
10197
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; e.preventDefault();
10198
10198
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
10199
10199
 
10200
10200
  thisClass.applyShownMenus();
10201
10201
  });
10202
10202
 
10203
- me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; //e.preventDefault();
10203
+ me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; e.preventDefault();
10204
10204
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
10205
10205
 
10206
10206
  thisClass.applyShownMenus();
10207
10207
  });
10208
10208
 
10209
- me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; //e.preventDefault();
10209
+ me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; e.preventDefault();
10210
10210
  me.htmlCls.dialogCls.openDlg('dl_menupref', 'Select Menus');
10211
10211
 
10212
10212
  thisClass.getHiddenMenusFromCache();
@@ -10214,7 +10214,7 @@ class ClickMenu {
10214
10214
  thisClass.displayShownMenus();
10215
10215
  });
10216
10216
 
10217
- me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
10217
+ me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
10218
10218
  var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
10219
10219
  me.htmlCls.shownMenus = {};
10220
10220
  for (var checkbox of checkboxes) {
@@ -10224,21 +10224,21 @@ class ClickMenu {
10224
10224
  thisClass.applyShownMenus();
10225
10225
  });
10226
10226
 
10227
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
10227
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
10228
10228
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
10229
10229
 
10230
10230
  thisClass.applyShownMenus();
10231
10231
  thisClass.displayShownMenus();
10232
10232
  });
10233
10233
 
10234
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; //e.preventDefault();
10234
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; e.preventDefault();
10235
10235
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
10236
10236
 
10237
10237
  thisClass.applyShownMenus();
10238
10238
  thisClass.displayShownMenus();
10239
10239
  });
10240
10240
 
10241
- me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10241
+ me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10242
10242
  let menuStr = '[';
10243
10243
 
10244
10244
  //var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
@@ -10287,30 +10287,30 @@ class ClickMenu {
10287
10287
  }
10288
10288
  });
10289
10289
 
10290
- me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; //e.preventDefault();
10290
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; e.preventDefault();
10291
10291
  me.htmlCls.dialogCls.openDlg('dl_menuloadpref', 'Please input the menu preference file');
10292
10292
  });
10293
10293
 
10294
10294
 
10295
- me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10295
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10296
10296
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
10297
10297
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
10298
10298
  window.open(url, urlTarget);
10299
10299
  });
10300
10300
 
10301
- me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; //e.preventDefault();
10301
+ me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; e.preventDefault();
10302
10302
  let url = 'https://github.com/sokrypton/ColabFold';
10303
10303
  window.open(url, '_blank');
10304
10304
  });
10305
10305
 
10306
- me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10306
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10307
10307
  let url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
10308
10308
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
10309
10309
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
10310
10310
  window.open(url, urlTarget);
10311
10311
  });
10312
10312
 
10313
- me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10313
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10314
10314
  let url;
10315
10315
  if(ic.inputid === undefined) {
10316
10316
  url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
@@ -10339,7 +10339,7 @@ class ClickMenu {
10339
10339
  window.open(url, urlTarget);
10340
10340
  });
10341
10341
 
10342
- me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10342
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10343
10343
  let url;
10344
10344
  if(ic.inputid === undefined) {
10345
10345
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
@@ -10383,7 +10383,7 @@ class ClickMenu {
10383
10383
  }
10384
10384
  });
10385
10385
 
10386
- me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10386
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10387
10387
  //ic.saveFileCls.setEntrezLinks('protein');
10388
10388
  let structArray = Object.keys(ic.structures);
10389
10389
  let chainArray = Object.keys(ic.chains);
@@ -10408,19 +10408,19 @@ class ClickMenu {
10408
10408
 
10409
10409
  let thisClass = this;
10410
10410
 
10411
- me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10411
+ me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10412
10412
  await ic.showAnnoCls.showAnnotations();
10413
10413
  thisClass.setLogCmd("view annotations", true);
10414
10414
  //thisClass.setLogCmd("window annotations", true);
10415
10415
  });
10416
10416
 
10417
- me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10417
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10418
10418
  thisClass.setLogCmd("select all", true);
10419
10419
  ic.selectionCls.selectAll();
10420
10420
  ic.hlUpdateCls.removeHlAll();
10421
10421
  ic.drawCls.draw();
10422
10422
  });
10423
- me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10423
+ me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10424
10424
  thisClass.setLogCmd("clear all", true);
10425
10425
  ic.bSelectResidue = false;
10426
10426
  ic.selectionCls.selectAll();
@@ -10428,7 +10428,7 @@ class ClickMenu {
10428
10428
  ic.drawCls.draw();
10429
10429
  });
10430
10430
 
10431
- me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10431
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10432
10432
  thisClass.setLogCmd("select displayed set", true);
10433
10433
  //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
10434
10434
  ic.hAtoms = me.hashUtilsCls.cloneHash(ic.viewSelectionAtoms);
@@ -10436,106 +10436,106 @@ class ClickMenu {
10436
10436
  //ic.drawCls.draw();
10437
10437
  });
10438
10438
 
10439
- me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10439
+ me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10440
10440
  thisClass.setLogCmd("show all", true);
10441
10441
  ic.selectionCls.showAll();
10442
10442
  });
10443
10443
 
10444
- me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10444
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10445
10445
  if(Object.keys(ic.hAtoms).length < Object.keys(ic.atoms).length) {
10446
10446
  thisClass.setLogCmd("select complement", true);
10447
10447
  ic.resid2specCls.selectComplement();
10448
10448
  }
10449
10449
  });
10450
10450
 
10451
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10451
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10452
10452
  thisClass.setLogCmd("select main chains", true);
10453
10453
  ic.selectionCls.selectMainChains();
10454
10454
  });
10455
10455
 
10456
- me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10456
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10457
10457
  thisClass.setLogCmd("select side chains", true);
10458
10458
  ic.selectionCls.selectSideChains();
10459
10459
  });
10460
10460
 
10461
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10461
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10462
10462
  thisClass.setLogCmd("select main side chains", true);
10463
10463
  ic.selectionCls.selectMainSideChains();
10464
10464
  });
10465
10465
 
10466
- me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10466
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10467
10467
  thisClass.setLogCmd("select prop positive", true);
10468
10468
  ic.resid2specCls.selectProperty('positive');
10469
10469
  });
10470
- me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10470
+ me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10471
10471
  thisClass.setLogCmd("select prop negative", true);
10472
10472
  ic.resid2specCls.selectProperty('negative');
10473
10473
  });
10474
- me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10474
+ me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10475
10475
  thisClass.setLogCmd("select prop hydrophobic", true);
10476
10476
  ic.resid2specCls.selectProperty('hydrophobic');
10477
10477
  });
10478
- me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10478
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10479
10479
  thisClass.setLogCmd("select prop polar", true);
10480
10480
  ic.resid2specCls.selectProperty('polar');
10481
10481
  });
10482
- me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; //e.preventDefault();
10482
+ me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; e.preventDefault();
10483
10483
  me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor/pLDDT');
10484
10484
  });
10485
- me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; //e.preventDefault();
10485
+ me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; e.preventDefault();
10486
10486
  me.htmlCls.dialogCls.openDlg('dl_propbypercentout', 'Select residue based on the percentage of solvent accessilbe surface area');
10487
10487
  });
10488
- me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10488
+ me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10489
10489
  let from = $("#" + me.pre + "minbfactor").val();
10490
10490
  let to = $("#" + me.pre + "maxbfactor").val();
10491
10491
  thisClass.setLogCmd("select prop b factor | " + from + '_' + to, true);
10492
10492
  ic.resid2specCls.selectProperty('b factor', from, to);
10493
10493
  });
10494
- me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10494
+ me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10495
10495
  let from = $("#" + me.pre + "minpercentout").val();
10496
10496
  let to = $("#" + me.pre + "maxpercentout").val();
10497
10497
  thisClass.setLogCmd("select prop percent out | " + from + '_' + to, true);
10498
10498
  ic.resid2specCls.selectProperty('percent out', from, to);
10499
10499
  });
10500
10500
 
10501
- me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; //e.preventDefault();
10501
+ me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; e.preventDefault();
10502
10502
  me.htmlCls.dialogCls.openDlg('dl_alignment', 'Select residues in aligned sequences');
10503
10503
  thisClass.setLogCmd("window aligned sequences", true);
10504
10504
  });
10505
10505
 
10506
- me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; //e.preventDefault();
10506
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; e.preventDefault();
10507
10507
  me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
10508
10508
  thisClass.setLogCmd("window interaction table", true);
10509
10509
  });
10510
- me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; //e.preventDefault();
10510
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; e.preventDefault();
10511
10511
  me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
10512
10512
  thisClass.setLogCmd("window interaction graph", true);
10513
10513
  });
10514
- me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; //e.preventDefault();
10514
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; e.preventDefault();
10515
10515
  me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as map');
10516
10516
  thisClass.setLogCmd("window interaction scatterplot", true);
10517
10517
  });
10518
- me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; //e.preventDefault();
10518
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; e.preventDefault();
10519
10519
  me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
10520
10520
  thisClass.setLogCmd("window force-directed graph", true);
10521
10521
  });
10522
10522
 
10523
- me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; //e.preventDefault();
10523
+ me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; e.preventDefault();
10524
10524
  me.htmlCls.dialogCls.openDlg('dl_yournote', 'Your note about the current display');
10525
10525
  });
10526
10526
 
10527
- me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10527
+ me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10528
10528
  ic.yournote = $("#" + me.pre + "yournote").val();
10529
10529
  if(me.cfg.shownote) document.title = ic.yournote;
10530
10530
  if(!me.cfg.notebook) dialog.dialog( "close" );
10531
10531
  thisClass.setLogCmd('your note | ' + ic.yournote, true);
10532
10532
  });
10533
10533
 
10534
- me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; //e.preventDefault();
10534
+ me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; e.preventDefault();
10535
10535
  me.htmlCls.dialogCls.openDlg('dl_advanced2', 'Select by specification');
10536
10536
  });
10537
10537
 
10538
- me.myEventCls.onIds(["#" + me.pre + "mn2_definedsets", "#" + me.pre + "definedsets", "#" + me.pre + "definedsets2", "#" + me.pre + "tool_definedsets"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10538
+ me.myEventCls.onIds(["#" + me.pre + "mn2_definedsets", "#" + me.pre + "definedsets", "#" + me.pre + "definedsets2", "#" + me.pre + "tool_definedsets"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10539
10539
  ic.definedSetsCls.showSets();
10540
10540
  thisClass.setLogCmd('defined sets', true);
10541
10541
  //thisClass.setLogCmd('window defined sets', true);
@@ -10554,7 +10554,7 @@ class ClickMenu {
10554
10554
  });
10555
10555
 
10556
10556
 
10557
- me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10557
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10558
10558
  ic.pk = 0;
10559
10559
  ic.opts['pk'] = 'no';
10560
10560
  thisClass.setLogCmd('set pk off', true);
@@ -10562,50 +10562,50 @@ class ClickMenu {
10562
10562
  ic.hlObjectsCls.removeHlObjects();
10563
10563
  });
10564
10564
 
10565
- me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10565
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10566
10566
  ic.pk = 1;
10567
10567
  ic.opts['pk'] = 'atom';
10568
10568
  thisClass.setLogCmd('set pk atom', true);
10569
10569
  });
10570
10570
 
10571
- me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10571
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10572
10572
  ic.pk = 2;
10573
10573
  ic.opts['pk'] = 'residue';
10574
10574
  thisClass.setLogCmd('set pk residue', true);
10575
10575
  });
10576
10576
 
10577
- me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10577
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10578
10578
  ic.pk = 3;
10579
10579
  ic.opts['pk'] = 'strand';
10580
10580
  thisClass.setLogCmd('set pk strand', true);
10581
10581
  });
10582
10582
 
10583
- me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10583
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10584
10584
  ic.pk = 4;
10585
10585
  ic.opts['pk'] = 'domain';
10586
10586
  thisClass.setLogCmd('set pk domain', true);
10587
10587
  });
10588
10588
 
10589
- me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10589
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10590
10590
  ic.pk = 5;
10591
10591
  ic.opts['pk'] = 'chain';
10592
10592
  thisClass.setLogCmd('set pk chain', true);
10593
10593
  });
10594
10594
 
10595
- me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; //e.preventDefault();
10595
+ me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; e.preventDefault();
10596
10596
  me.htmlCls.dialogCls.openDlg('dl_adjustmem', 'Adjust the Z-axis positions of the membrane');
10597
10597
  });
10598
10598
 
10599
- me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10599
+ me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10600
10600
  ic.selectionCls.toggleMembrane();
10601
10601
  thisClass.setLogCmd('toggle membrane', true);
10602
10602
  });
10603
10603
 
10604
- me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; //e.preventDefault();
10604
+ me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; e.preventDefault();
10605
10605
  me.htmlCls.dialogCls.openDlg('dl_selectplane', 'Select a region between two planes');
10606
10606
  });
10607
10607
 
10608
- me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10608
+ me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10609
10609
  thisClass.SetChainsAdvancedMenu();
10610
10610
 
10611
10611
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -10622,7 +10622,7 @@ class ClickMenu {
10622
10622
  $("#" + me.pre + "atomsCustomSphere2").resizable();
10623
10623
  });
10624
10624
 
10625
- me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; //e.preventDefault();
10625
+ me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; e.preventDefault();
10626
10626
  me.htmlCls.dialogCls.openDlg('dl_select_chain', 'Select Structure/Chain/Custom Selection');
10627
10627
  });
10628
10628
 
@@ -10633,242 +10633,242 @@ class ClickMenu {
10633
10633
 
10634
10634
  let thisClass = this;
10635
10635
  // mn 3
10636
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10636
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10637
10637
  ic.setOptionCls.setStyle('proteins', 'ribbon');
10638
10638
  thisClass.setLogCmd('style proteins ribbon', true);
10639
10639
  });
10640
10640
 
10641
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10641
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10642
10642
  ic.setOptionCls.setStyle('proteins', 'strand');
10643
10643
  thisClass.setLogCmd('style proteins strand', true);
10644
10644
  });
10645
10645
 
10646
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10646
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10647
10647
  ic.setOptionCls.setStyle('proteins', 'cylinder and plate');
10648
10648
  thisClass.setLogCmd('style proteins cylinder and plate', true);
10649
10649
  });
10650
10650
 
10651
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10651
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10652
10652
  ic.setOptionCls.setStyle('proteins', 'schematic');
10653
10653
  thisClass.setLogCmd('style proteins schematic', true);
10654
10654
  });
10655
10655
 
10656
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10656
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10657
10657
  ic.setOptionCls.setStyle('proteins', 'c alpha trace');
10658
10658
  thisClass.setLogCmd('style proteins c alpha trace', true);
10659
10659
  });
10660
10660
 
10661
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10661
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10662
10662
  ic.setOptionCls.setStyle('proteins', 'backbone');
10663
10663
  thisClass.setLogCmd('style proteins backbone', true);
10664
10664
  });
10665
10665
 
10666
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10666
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10667
10667
  ic.setOptionCls.setStyle('proteins', 'b factor tube');
10668
10668
  thisClass.setLogCmd('style proteins b factor tube', true);
10669
10669
  });
10670
10670
 
10671
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10671
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10672
10672
  ic.setOptionCls.setStyle('proteins', 'lines');
10673
10673
  thisClass.setLogCmd('style proteins lines', true);
10674
10674
  });
10675
10675
 
10676
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10676
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10677
10677
  ic.setOptionCls.setStyle('proteins', 'stick');
10678
10678
  thisClass.setLogCmd('style proteins stick', true);
10679
10679
  });
10680
10680
 
10681
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10681
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10682
10682
  ic.setOptionCls.setStyle('proteins', 'ball and stick');
10683
10683
  thisClass.setLogCmd('style proteins ball and stick', true);
10684
10684
  });
10685
10685
 
10686
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10686
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10687
10687
  ic.setOptionCls.setStyle('proteins', 'sphere');
10688
10688
  thisClass.setLogCmd('style proteins sphere', true);
10689
10689
  });
10690
10690
 
10691
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10691
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10692
10692
  ic.setOptionCls.setStyle('proteins', 'nothing');
10693
10693
  thisClass.setLogCmd('style proteins nothing', true);
10694
10694
  });
10695
10695
 
10696
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10696
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10697
10697
  ic.setOptionCls.setStyle('sidec', 'lines2');
10698
10698
  thisClass.setLogCmd('style sidec lines2', true);
10699
10699
  });
10700
10700
 
10701
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10701
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10702
10702
  ic.setOptionCls.setStyle('sidec', 'stick2');
10703
10703
  thisClass.setLogCmd('style sidec stick2', true);
10704
10704
  });
10705
10705
 
10706
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10706
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10707
10707
  ic.setOptionCls.setStyle('sidec', 'ball and stick2');
10708
10708
  thisClass.setLogCmd('style sidec ball and stick2', true);
10709
10709
  });
10710
10710
 
10711
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10711
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10712
10712
  ic.setOptionCls.setStyle('sidec', 'sphere2');
10713
10713
  thisClass.setLogCmd('style sidec sphere2', true);
10714
10714
  });
10715
10715
 
10716
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10716
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10717
10717
  ic.setOptionCls.setStyle('sidec', 'nothing');
10718
10718
  thisClass.setLogCmd('style sidec nothing', true);
10719
10719
  });
10720
10720
 
10721
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10721
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10722
10722
  ic.setOptionCls.setStyle('ntbase', 'lines2');
10723
10723
  thisClass.setLogCmd('style ntbase lines2', true);
10724
10724
  });
10725
10725
 
10726
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10726
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10727
10727
  ic.setOptionCls.setStyle('ntbase', 'stick2');
10728
10728
  thisClass.setLogCmd('style ntbase stick2', true);
10729
10729
  });
10730
10730
 
10731
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10731
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10732
10732
  ic.setOptionCls.setStyle('ntbase', 'ball and stick2');
10733
10733
  thisClass.setLogCmd('style ntbase ball and stick2', true);
10734
10734
  });
10735
10735
 
10736
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10736
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10737
10737
  ic.setOptionCls.setStyle('ntbase', 'sphere2');
10738
10738
  thisClass.setLogCmd('style ntbase sphere2', true);
10739
10739
  });
10740
10740
 
10741
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10741
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10742
10742
  ic.setOptionCls.setStyle('ntbase', 'nothing');
10743
10743
  thisClass.setLogCmd('style ntbase nothing', true);
10744
10744
  });
10745
10745
 
10746
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10746
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10747
10747
  ic.setOptionCls.setStyle('nucleotides', 'nucleotide cartoon');
10748
10748
  thisClass.setLogCmd('style nucleotides nucleotide cartoon', true);
10749
10749
  });
10750
10750
 
10751
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10751
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10752
10752
  ic.setOptionCls.setStyle('nucleotides', 'backbone');
10753
10753
  thisClass.setLogCmd('style nucleotides backbone', true);
10754
10754
  });
10755
10755
 
10756
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10756
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10757
10757
  ic.setOptionCls.setStyle('nucleotides', 'schematic');
10758
10758
  thisClass.setLogCmd('style nucleotides schematic', true);
10759
10759
  });
10760
10760
 
10761
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10761
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10762
10762
  ic.setOptionCls.setStyle('nucleotides', 'o3 trace');
10763
10763
  thisClass.setLogCmd('style nucleotides o3 trace', true);
10764
10764
  });
10765
10765
 
10766
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10766
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10767
10767
  ic.setOptionCls.setStyle('nucleotides', 'lines');
10768
10768
  thisClass.setLogCmd('style nucleotides lines', true);
10769
10769
  });
10770
10770
 
10771
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10771
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10772
10772
  ic.setOptionCls.setStyle('nucleotides', 'stick');
10773
10773
  thisClass.setLogCmd('style nucleotides stick', true);
10774
10774
  });
10775
10775
 
10776
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10776
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10777
10777
  ic.setOptionCls.setStyle('nucleotides', 'ball and stick');
10778
10778
  thisClass.setLogCmd('style nucleotides ball and stick', true);
10779
10779
  });
10780
10780
 
10781
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10781
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10782
10782
  ic.setOptionCls.setStyle('nucleotides', 'sphere');
10783
10783
  thisClass.setLogCmd('style nucleotides sphere', true);
10784
10784
  });
10785
10785
 
10786
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10786
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10787
10787
  ic.setOptionCls.setStyle('nucleotides', 'nothing');
10788
10788
  thisClass.setLogCmd('style nucleotides nothing', true);
10789
10789
  });
10790
10790
 
10791
- me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10791
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10792
10792
  ic.setOptionCls.setStyle('chemicals', 'lines');
10793
10793
  thisClass.setLogCmd('style chemicals lines', true);
10794
10794
  });
10795
10795
 
10796
- me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10796
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10797
10797
  ic.setOptionCls.setStyle('chemicals', 'stick');
10798
10798
  thisClass.setLogCmd('style chemicals stick', true);
10799
10799
  });
10800
10800
 
10801
- me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10801
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10802
10802
  ic.setOptionCls.setStyle('chemicals', 'ball and stick');
10803
10803
  thisClass.setLogCmd('style chemicals ball and stick', true);
10804
10804
  });
10805
10805
 
10806
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10806
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10807
10807
  ic.setOptionCls.setStyle('chemicals', 'schematic');
10808
10808
  thisClass.setLogCmd('style chemicals schematic', true);
10809
10809
  });
10810
10810
 
10811
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10811
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10812
10812
  ic.setOptionCls.setStyle('chemicals', 'sphere');
10813
10813
  thisClass.setLogCmd('style chemicals sphere', true);
10814
10814
  });
10815
10815
 
10816
- me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10816
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10817
10817
  ic.setOptionCls.setStyle('chemicals', 'nothing');
10818
10818
  thisClass.setLogCmd('style chemicals nothing', true);
10819
10819
  });
10820
10820
 
10821
10821
 
10822
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10822
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10823
10823
  ic.bGlycansCartoon = true;
10824
10824
  ic.drawCls.draw();
10825
10825
  thisClass.setLogCmd('glycans cartoon yes', true);
10826
10826
  });
10827
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10827
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10828
10828
  ic.bGlycansCartoon = false;
10829
10829
  ic.drawCls.draw();
10830
10830
  thisClass.setLogCmd('glycans cartoon no', true);
10831
10831
  });
10832
10832
 
10833
10833
 
10834
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10834
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10835
10835
  ic.showInterCls.showHydrogens();
10836
10836
  ic.drawCls.draw();
10837
10837
  thisClass.setLogCmd('hydrogens', true);
10838
10838
  });
10839
10839
 
10840
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10840
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10841
10841
  ic.showInterCls.hideHydrogens();
10842
10842
  ic.drawCls.draw();
10843
10843
  thisClass.setLogCmd('set hydrogens off', true);
10844
10844
  });
10845
10845
 
10846
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10846
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10847
10847
  ic.setOptionCls.setStyle('ions', 'sphere');
10848
10848
  thisClass.setLogCmd('style ions sphere', true);
10849
10849
  });
10850
10850
 
10851
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10851
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10852
10852
  ic.setOptionCls.setStyle('ions', 'dot');
10853
10853
  thisClass.setLogCmd('style ions dot', true);
10854
10854
  });
10855
10855
 
10856
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10856
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10857
10857
  ic.setOptionCls.setStyle('ions', 'nothing');
10858
10858
  thisClass.setLogCmd('style ions nothing', true);
10859
10859
  });
10860
10860
 
10861
- me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10861
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10862
10862
  ic.setOptionCls.setStyle('water', 'sphere');
10863
10863
  thisClass.setLogCmd('style water sphere', true);
10864
10864
  });
10865
10865
 
10866
- me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10866
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10867
10867
  ic.setOptionCls.setStyle('water', 'dot');
10868
10868
  thisClass.setLogCmd('style water dot', true);
10869
10869
  });
10870
10870
 
10871
- me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10871
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10872
10872
  ic.setOptionCls.setStyle('water', 'nothing');
10873
10873
  thisClass.setLogCmd('style water nothing', true);
10874
10874
  });
@@ -10880,16 +10880,16 @@ class ClickMenu {
10880
10880
 
10881
10881
  let thisClass = this;
10882
10882
  // mn 4
10883
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10883
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10884
10884
  ic.setOptionCls.setOption('color', 'spectrum');
10885
10885
  thisClass.setLogCmd('color spectrum', true);
10886
10886
  });
10887
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10887
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10888
10888
  ic.setOptionCls.setOption('color', 'spectrum for chains');
10889
10889
  thisClass.setLogCmd('color spectrum for chains', true);
10890
10890
  });
10891
10891
 
10892
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10892
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10893
10893
  thisClass.SetChainsAdvancedMenu();
10894
10894
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10895
10895
  if($("#" + me.pre + "atomsCustomColorSpectrumAcross").length) {
@@ -10900,7 +10900,7 @@ class ClickMenu {
10900
10900
  $("#" + me.pre + "atomsCustomColorSpectrumAcross").resizable();
10901
10901
  });
10902
10902
 
10903
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10903
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10904
10904
  thisClass.SetChainsAdvancedMenu();
10905
10905
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10906
10906
  if($("#" + me.pre + "atomsCustomColorSpectrum").length) {
@@ -10911,7 +10911,7 @@ class ClickMenu {
10911
10911
  $("#" + me.pre + "atomsCustomColorSpectrum").resizable();
10912
10912
  });
10913
10913
 
10914
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10914
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10915
10915
  thisClass.SetChainsAdvancedMenu();
10916
10916
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10917
10917
  if($("#" + me.pre + "atomsCustomColorRainbowAcross").length) {
@@ -10922,7 +10922,7 @@ class ClickMenu {
10922
10922
  $("#" + me.pre + "atomsCustomColorRainbowAcross").resizable();
10923
10923
  });
10924
10924
 
10925
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10925
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10926
10926
  thisClass.SetChainsAdvancedMenu();
10927
10927
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10928
10928
  if($("#" + me.pre + "atomsCustomColorRainbow").length) {
@@ -10933,59 +10933,60 @@ class ClickMenu {
10933
10933
  $("#" + me.pre + "atomsCustomColorRainbow").resizable();
10934
10934
  });
10935
10935
 
10936
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10936
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10937
10937
  ic.setOptionCls.setOption('color', 'rainbow');
10938
+
10938
10939
  thisClass.setLogCmd('color rainbow', true);
10939
10940
  });
10940
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10941
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10941
10942
  ic.setOptionCls.setOption('color', 'rainbow for chains');
10942
10943
  thisClass.setLogCmd('color rainbow for chains', true);
10943
10944
  });
10944
10945
 
10945
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10946
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10946
10947
  ic.setOptionCls.setOption('color', 'chain');
10947
10948
  thisClass.setLogCmd('color chain', true);
10948
10949
  });
10949
- me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10950
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10950
10951
  ic.setOptionCls.setOption('color', 'structure');
10951
10952
  thisClass.setLogCmd('color structure', true);
10952
10953
  });
10953
10954
 
10954
- me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10955
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10955
10956
  ic.setOptionCls.setOption('color', 'domain');
10956
10957
  thisClass.setLogCmd('color domain', true);
10957
10958
  });
10958
10959
 
10959
- me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10960
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10960
10961
  ic.setOptionCls.setOption('color', 'defined sets');
10961
10962
  thisClass.setLogCmd('color defined sets', true);
10962
10963
  });
10963
10964
 
10964
10965
 
10965
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10966
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10966
10967
  ic.sheetcolor = 'green';
10967
10968
  ic.setOptionCls.setOption('color', 'secondary structure green');
10968
10969
  thisClass.setLogCmd('color secondary structure green', true);
10969
10970
  });
10970
10971
 
10971
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10972
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10972
10973
  ic.sheetcolor = 'yellow';
10973
10974
  ic.setOptionCls.setOption('color', 'secondary structure yellow');
10974
10975
  thisClass.setLogCmd('color secondary structure yellow', true);
10975
10976
  });
10976
10977
 
10977
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10978
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10978
10979
  ic.setOptionCls.setOption('color', 'secondary structure spectrum');
10979
10980
  thisClass.setLogCmd('color secondary structure spectrum', true);
10980
10981
  });
10981
10982
 
10982
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10983
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10983
10984
  //ic.legendClick = 2;
10984
10985
  ic.setOptionCls.setOption('color', 'residue');
10985
10986
  thisClass.setLogCmd('color residue', true);
10986
10987
  });
10987
10988
 
10988
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; //e.preventDefault();
10989
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; e.preventDefault();
10989
10990
  //ic.legendClick = 2;
10990
10991
  me.htmlCls.dialogCls.openDlg('dl_rescolorfile', 'Please input the file on residue colors');
10991
10992
  });
@@ -11031,12 +11032,12 @@ class ClickMenu {
11031
11032
  ic.addTrackCls.setCustomFile('color', ic.startColor, ic.midColor, ic.endColor);
11032
11033
  });
11033
11034
 
11034
- me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; //e.preventDefault();
11035
+ me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; e.preventDefault();
11035
11036
 
11036
11037
  me.htmlCls.dialogCls.openDlg('dl_customref', 'Set custom reference numbers');
11037
11038
  });
11038
11039
 
11039
- me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11040
+ me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11040
11041
 
11041
11042
  if(!me.cfg.notebook) dialog.dialog( "close" );
11042
11043
 
@@ -11073,82 +11074,82 @@ class ClickMenu {
11073
11074
  ic.addTrackCls.setCustomFile('tube');
11074
11075
  });
11075
11076
 
11076
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11077
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11077
11078
  //ic.legendClick = 3;
11078
11079
  ic.setOptionCls.setOption('color', 'charge');
11079
11080
  thisClass.setLogCmd('color charge', true);
11080
11081
  });
11081
11082
 
11082
- me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11083
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11083
11084
  //ic.legendClick = 4;
11084
11085
  ic.setOptionCls.setOption('color', 'hydrophobic');
11085
11086
  thisClass.setLogCmd('color hydrophobic', true);
11086
11087
  });
11087
11088
 
11088
- me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11089
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11089
11090
  //ic.legendClick = 4;
11090
11091
  ic.setOptionCls.setOption('color', 'normalized hydrophobic');
11091
11092
  thisClass.setLogCmd('color normalized hydrophobic', true);
11092
11093
  });
11093
11094
 
11094
11095
 
11095
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11096
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11096
11097
  //ic.legendClick = 1;
11097
11098
  ic.setOptionCls.setOption('color', 'atom');
11098
11099
  thisClass.setLogCmd('color atom', true);
11099
11100
  });
11100
11101
 
11101
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11102
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11102
11103
  //ic.legendClick = 5;
11103
11104
  ic.setOptionCls.setOption('color', 'b factor');
11104
11105
  thisClass.setLogCmd('color b factor', true);
11105
11106
  });
11106
11107
 
11107
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11108
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11108
11109
  //ic.legendClick = 6;
11109
11110
  ic.setOptionCls.setOption('color', 'confidence');
11110
11111
  thisClass.setLogCmd('color confidence', true);
11111
11112
  });
11112
11113
 
11113
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11114
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11114
11115
  //ic.legendClick = 6;
11115
11116
  ic.setOptionCls.setOption('color', 'ig strand');
11116
11117
  thisClass.setLogCmd('color ig strand', true);
11117
11118
  });
11118
11119
 
11119
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11120
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11120
11121
  //ic.legendClick = 6;
11121
11122
  ic.setOptionCls.setOption('color', 'ig protodomain');
11122
11123
  thisClass.setLogCmd('color ig protodomain', true);
11123
11124
  });
11124
11125
 
11125
11126
 
11126
- me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; //e.preventDefault();
11127
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; e.preventDefault();
11127
11128
  me.htmlCls.dialogCls.openDlg('dl_colorbyarea', "Color based on residue's solvent accessibility");
11128
11129
  });
11129
- me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11130
+ me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11130
11131
  ic.midpercent = $("#" + me.pre + 'midpercent').val();
11131
11132
  ic.setOptionCls.setOption('color', 'area');
11132
11133
  thisClass.setLogCmd('color area | ' + ic.midpercent, true);
11133
11134
 
11134
11135
  });
11135
11136
 
11136
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11137
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11137
11138
  ic.setOptionCls.setOption('color', 'b factor percentile');
11138
11139
  thisClass.setLogCmd('color b factor percentile', true);
11139
11140
  });
11140
11141
 
11141
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11142
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11142
11143
  ic.setOptionCls.setOption('color', 'identity');
11143
11144
  thisClass.setLogCmd('color identity', true);
11144
11145
  });
11145
11146
 
11146
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11147
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11147
11148
  ic.setOptionCls.setOption('color', 'conservation');
11148
11149
  thisClass.setLogCmd('color conservation', true);
11149
11150
  });
11150
11151
 
11151
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; //e.preventDefault();
11152
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; e.preventDefault();
11152
11153
  me.htmlCls.dialogCls.openDlg('dl_clr', 'Color picker');
11153
11154
  });
11154
11155
 
@@ -11157,25 +11158,26 @@ class ClickMenu {
11157
11158
  //e.preventDefault();
11158
11159
  let color = $(this).attr('color');
11159
11160
  ic.setOptionCls.setOption("color", color);
11161
+
11160
11162
  thisClass.setLogCmd("color " + color, true);
11161
11163
  });
11162
11164
 
11163
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11165
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11164
11166
  ic.setOptionCls.saveColor();
11165
11167
  thisClass.setLogCmd('save color', true);
11166
11168
  });
11167
11169
 
11168
- me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11170
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11169
11171
  ic.setOptionCls.applySavedColor();
11170
11172
  thisClass.setLogCmd('apply saved color', true);
11171
11173
  });
11172
11174
 
11173
- me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11175
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11174
11176
  ic.setOptionCls.saveStyle();
11175
11177
  thisClass.setLogCmd('save style', true);
11176
11178
  });
11177
11179
 
11178
- me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11180
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11179
11181
  ic.setOptionCls.applySavedStyle();
11180
11182
  thisClass.setLogCmd('apply saved style', true);
11181
11183
  });
@@ -11187,7 +11189,7 @@ class ClickMenu {
11187
11189
 
11188
11190
  let thisClass = this;
11189
11191
  // mn 5
11190
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11192
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11191
11193
  ic.bConsiderNeighbors = true;
11192
11194
  ic.applyMapCls.removeLastSurface();
11193
11195
  ic.applyMapCls.applySurfaceOptions();
@@ -11195,7 +11197,7 @@ class ClickMenu {
11195
11197
  thisClass.setLogCmd('set surface neighbors on', true);
11196
11198
  });
11197
11199
 
11198
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11200
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11199
11201
  ic.bConsiderNeighbors = false;
11200
11202
  ic.applyMapCls.removeLastSurface();
11201
11203
  ic.applyMapCls.applySurfaceOptions();
@@ -11203,48 +11205,48 @@ class ClickMenu {
11203
11205
  thisClass.setLogCmd('set surface neighbors off', true);
11204
11206
  });
11205
11207
 
11206
- me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11208
+ me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11207
11209
  ic.bConsiderNeighbors = false;
11208
11210
  ic.setOptionCls.setOption('surface', 'Van der Waals surface');
11209
11211
  thisClass.setLogCmd('set surface Van der Waals surface', true);
11210
11212
  });
11211
11213
 
11212
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11214
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11213
11215
  ic.bConsiderNeighbors = false;
11214
11216
  ic.setOptionCls.setOption('surface', 'solvent accessible surface');
11215
11217
  thisClass.setLogCmd('set surface solvent accessible surface', true);
11216
11218
  });
11217
11219
 
11218
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11220
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11219
11221
  ic.bConsiderNeighbors = false;
11220
11222
  ic.setOptionCls.setOption('surface', 'molecular surface');
11221
11223
  thisClass.setLogCmd('set surface molecular surface', true);
11222
11224
  });
11223
11225
 
11224
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11226
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11225
11227
  ic.bConsiderNeighbors = true;
11226
11228
  ic.setOptionCls.setOption('surface', 'Van der Waals surface with context');
11227
11229
  thisClass.setLogCmd('set surface Van der Waals surface with context', true);
11228
11230
  });
11229
11231
 
11230
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11232
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11231
11233
  ic.bConsiderNeighbors = true;
11232
11234
  ic.setOptionCls.setOption('surface', 'solvent accessible surface with context');
11233
11235
  thisClass.setLogCmd('set surface solvent accessible surface with context', true);
11234
11236
  });
11235
11237
 
11236
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11238
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11237
11239
  ic.bConsiderNeighbors = true;
11238
11240
  ic.setOptionCls.setOption('surface', 'molecular surface with context');
11239
11241
  thisClass.setLogCmd('set surface molecular surface with context', true);
11240
11242
  });
11241
11243
 
11242
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11244
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11243
11245
  ic.setOptionCls.setOption('surface', 'nothing');
11244
11246
  thisClass.setLogCmd('set surface nothing', true);
11245
11247
  });
11246
11248
 
11247
- $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; //e.preventDefault();
11249
+ $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; e.preventDefault();
11248
11250
  ic.transparentRenderOrder = false;
11249
11251
 
11250
11252
  let value = $(this).attr('v');
@@ -11252,7 +11254,7 @@ class ClickMenu {
11252
11254
  thisClass.setLogCmd('set surface opacity ' + value, true);
11253
11255
  });
11254
11256
 
11255
- $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; //e.preventDefault();
11257
+ $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; e.preventDefault();
11256
11258
  ic.transparentRenderOrder = true;
11257
11259
 
11258
11260
  let value = $(this).attr('v');
@@ -11260,35 +11262,35 @@ class ClickMenu {
11260
11262
  thisClass.setLogCmd('set surface2 opacity ' + value, true);
11261
11263
  });
11262
11264
 
11263
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11265
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11264
11266
  ic.setOptionCls.setOption('wireframe', 'yes');
11265
11267
  thisClass.setLogCmd('set surface wireframe on', true);
11266
11268
  });
11267
11269
 
11268
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11270
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11269
11271
  ic.setOptionCls.setOption('wireframe', 'no');
11270
11272
  thisClass.setLogCmd('set surface wireframe off', true);
11271
11273
  });
11272
11274
 
11273
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; //e.preventDefault();
11275
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; e.preventDefault();
11274
11276
  me.htmlCls.dialogCls.openDlg('dl_elecmap2fofc', '2Fo-Fc Electron Density Map');
11275
11277
  });
11276
11278
 
11277
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; //e.preventDefault();
11279
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; e.preventDefault();
11278
11280
  me.htmlCls.dialogCls.openDlg('dl_elecmapfofc', 'Fo-Fc Electron Density Map');
11279
11281
  });
11280
11282
 
11281
- me.myEventCls.onIds(["#" + me.pre + "mn5_elecmapNo", "#" + me.pre + "elecmapNo2", "#" + me.pre + "elecmapNo3", "#" + me.pre + "elecmapNo4", "#" + me.pre + "elecmapNo5"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11283
+ me.myEventCls.onIds(["#" + me.pre + "mn5_elecmapNo", "#" + me.pre + "elecmapNo2", "#" + me.pre + "elecmapNo3", "#" + me.pre + "elecmapNo4", "#" + me.pre + "elecmapNo5"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11282
11284
  ic.setOptionCls.setOption('map', 'nothing');
11283
11285
  thisClass.setLogCmd('setoption map nothing', true);
11284
11286
  });
11285
11287
 
11286
- me.myEventCls.onIds(["#" + me.pre + "delphimapNo", "#" + me.pre + "phimapNo", "#" + me.pre + "phiurlmapNo", "#" + me.pre + "mn1_phimapNo"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11288
+ me.myEventCls.onIds(["#" + me.pre + "delphimapNo", "#" + me.pre + "phimapNo", "#" + me.pre + "phiurlmapNo", "#" + me.pre + "mn1_phimapNo"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11287
11289
  ic.setOptionCls.setOption('phimap', 'nothing');
11288
11290
  thisClass.setLogCmd('setoption phimap nothing', true);
11289
11291
  });
11290
11292
 
11291
- me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11293
+ me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11292
11294
  //ic.setOptionCls.setOption('surface', 'nothing');
11293
11295
  //thisClass.setLogCmd('set surface nothing', true);
11294
11296
  ic.setOptionCls.setOption('phisurface', 'nothing');
@@ -11320,22 +11322,22 @@ class ClickMenu {
11320
11322
  thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
11321
11323
  });
11322
11324
 
11323
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11325
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11324
11326
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
11325
11327
  ic.setOptionCls.setOption('mapwireframe', 'yes');
11326
11328
  thisClass.setLogCmd('set map wireframe on', true);
11327
11329
  });
11328
11330
 
11329
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11331
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11330
11332
  ic.setOptionCls.setOption('mapwireframe', 'no');
11331
11333
  thisClass.setLogCmd('set map wireframe off', true);
11332
11334
  });
11333
11335
 
11334
- me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; //e.preventDefault();
11336
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; e.preventDefault();
11335
11337
  me.htmlCls.dialogCls.openDlg('dl_emmap', 'EM Density Map');
11336
11338
  });
11337
11339
 
11338
- me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11340
+ me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11339
11341
  ic.setOptionCls.setOption('emmap', 'nothing');
11340
11342
  thisClass.setLogCmd('setoption emmap nothing', true);
11341
11343
  });
@@ -11352,13 +11354,13 @@ class ClickMenu {
11352
11354
  thisClass.setLogCmd('set emmap percentage ' + empercentage, true);
11353
11355
  });
11354
11356
 
11355
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11357
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11356
11358
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
11357
11359
  ic.setOptionCls.setOption('emmapwireframe', 'yes');
11358
11360
  thisClass.setLogCmd('set emmap wireframe on', true);
11359
11361
  });
11360
11362
 
11361
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11363
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11362
11364
  ic.setOptionCls.setOption('emmapwireframe', 'no');
11363
11365
  thisClass.setLogCmd('set emmap wireframe off', true);
11364
11366
  });
@@ -11370,19 +11372,19 @@ class ClickMenu {
11370
11372
 
11371
11373
  let thisClass = this;
11372
11374
  // mn 6
11373
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11375
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11374
11376
  ic.bAssembly = true;
11375
11377
  thisClass.setLogCmd('set assembly on', true);
11376
11378
  ic.drawCls.draw();
11377
11379
  });
11378
11380
 
11379
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11381
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11380
11382
  ic.bAssembly = false;
11381
11383
  thisClass.setLogCmd('set assembly off', true);
11382
11384
  ic.drawCls.draw();
11383
11385
  });
11384
11386
 
11385
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11387
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11386
11388
  ic.bRunRefnumAgain = true;
11387
11389
 
11388
11390
  thisClass.setLogCmd('ig refnum on', true);
@@ -11405,11 +11407,11 @@ class ClickMenu {
11405
11407
  ic.bRunRefnumAgain = false;
11406
11408
  });
11407
11409
 
11408
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
11410
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
11409
11411
  me.htmlCls.dialogCls.openDlg('dl_igrefTpl', 'Choose an Ig template');
11410
11412
  });
11411
11413
 
11412
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; //e.preventDefault();
11414
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; e.preventDefault();
11413
11415
  if(!me.cfg.notebook) dialog.dialog( "close" );
11414
11416
 
11415
11417
  let template = $("#" + me.pre + "refTpl").val();
@@ -11419,11 +11421,11 @@ class ClickMenu {
11419
11421
  thisClass.setLogCmd('ig template ' + template, true);
11420
11422
  });
11421
11423
 
11422
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
11424
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
11423
11425
  me.htmlCls.dialogCls.openDlg('dl_alignrefTpl', 'Align with an Ig template');
11424
11426
  });
11425
11427
 
11426
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11428
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11427
11429
  if(!me.cfg.notebook) dialog.dialog( "close" );
11428
11430
 
11429
11431
  let template = $("#" + me.pre + "refTpl2").val();
@@ -11447,7 +11449,7 @@ class ClickMenu {
11447
11449
  thisClass.setLogCmd('realign on tmalign', true);
11448
11450
  });
11449
11451
 
11450
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11452
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11451
11453
  thisClass.setLogCmd('ig refnum off', true);
11452
11454
  await ic.refnumCls.hideIgRefNum();
11453
11455
 
@@ -11457,14 +11459,14 @@ class ClickMenu {
11457
11459
  // ic.drawCls.draw();
11458
11460
  });
11459
11461
 
11460
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11462
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11461
11463
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
11462
11464
  ic.selectionCls.saveSelectionIfSelected();
11463
11465
  thisClass.setLogCmd('add atom labels', true);
11464
11466
  ic.drawCls.draw();
11465
11467
  });
11466
11468
 
11467
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11469
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11468
11470
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms, true);
11469
11471
  ic.selectionCls.saveSelectionIfSelected();
11470
11472
  thisClass.setLogCmd('add element labels', true);
@@ -11472,49 +11474,49 @@ class ClickMenu {
11472
11474
  });
11473
11475
 
11474
11476
 
11475
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11477
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11476
11478
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms);
11477
11479
  ic.selectionCls.saveSelectionIfSelected();
11478
11480
  thisClass.setLogCmd('add residue labels', true);
11479
11481
  ic.drawCls.draw();
11480
11482
  });
11481
11483
 
11482
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11484
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11483
11485
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, true);
11484
11486
  ic.selectionCls.saveSelectionIfSelected();
11485
11487
  thisClass.setLogCmd('add residue number labels', true);
11486
11488
  ic.drawCls.draw();
11487
11489
  });
11488
11490
 
11489
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11491
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11490
11492
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
11491
11493
  ic.selectionCls.saveSelectionIfSelected();
11492
11494
  thisClass.setLogCmd('add reference number labels', true);
11493
11495
  ic.drawCls.draw();
11494
11496
  });
11495
11497
 
11496
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11498
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11497
11499
  ic.residueLabelsCls.addIgLabels(ic.hAtoms);
11498
11500
  ic.selectionCls.saveSelectionIfSelected();
11499
11501
  thisClass.setLogCmd('add ig labels', true);
11500
11502
  ic.drawCls.draw();
11501
11503
  });
11502
11504
 
11503
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11505
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11504
11506
  ic.analysisCls.addChainLabels(ic.hAtoms);
11505
11507
  ic.selectionCls.saveSelectionIfSelected();
11506
11508
  thisClass.setLogCmd('add chain labels', true);
11507
11509
  ic.drawCls.draw();
11508
11510
  });
11509
11511
 
11510
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11512
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11511
11513
  ic.analysisCls.addTerminiLabels(ic.hAtoms);
11512
11514
  ic.selectionCls.saveSelectionIfSelected();
11513
11515
  thisClass.setLogCmd('add terminal labels', true);
11514
11516
  ic.drawCls.draw();
11515
11517
  });
11516
11518
 
11517
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11519
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11518
11520
  me.htmlCls.dialogCls.openDlg('dl_addlabel', 'Add custom labels by selection');
11519
11521
  ic.pk = 1;
11520
11522
  ic.opts['pk'] = 'atom';
@@ -11522,19 +11524,19 @@ class ClickMenu {
11522
11524
  ic.pAtomNum = 0;
11523
11525
  });
11524
11526
 
11525
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; //e.preventDefault();
11527
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; e.preventDefault();
11526
11528
  me.htmlCls.dialogCls.openDlg('dl_addlabelselection', 'Add custom labels by the selected');
11527
11529
  });
11528
11530
 
11529
- me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; //e.preventDefault();
11531
+ me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; e.preventDefault();
11530
11532
  me.htmlCls.dialogCls.openDlg('dl_labelColor', 'Change color for all labels');
11531
11533
  });
11532
11534
 
11533
- me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; //e.preventDefault();
11535
+ me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; e.preventDefault();
11534
11536
  me.htmlCls.dialogCls.openDlg('dl_saveselection', 'Save the selected');
11535
11537
  });
11536
11538
 
11537
- me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11539
+ me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11538
11540
  ic.labelcolor = undefined;
11539
11541
  ic.pickpair = false;
11540
11542
  //ic.labels['residue'] = [];
@@ -11549,14 +11551,14 @@ class ClickMenu {
11549
11551
  ic.drawCls.draw();
11550
11552
  });
11551
11553
 
11552
- $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; //e.preventDefault();
11554
+ $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; e.preventDefault();
11553
11555
  let value = $(this).attr('v');
11554
11556
  ic.labelScale = value;
11555
11557
  ic.drawCls.draw();
11556
11558
  thisClass.setLogCmd('set label scale ' + value, true);
11557
11559
  });
11558
11560
 
11559
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11561
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11560
11562
  me.htmlCls.dialogCls.openDlg('dl_distance', 'Measure the distance of atoms');
11561
11563
  ic.pk = 1;
11562
11564
  ic.opts['pk'] = 'atom';
@@ -11566,7 +11568,7 @@ class ClickMenu {
11566
11568
  });
11567
11569
 
11568
11570
 
11569
- me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11571
+ me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11570
11572
  me.htmlCls.dialogCls.openDlg('dl_disttwosets', 'Measure the distance between two sets');
11571
11573
 
11572
11574
  thisClass.setSetsMenus('atomsCustomDist');
@@ -11574,7 +11576,7 @@ class ClickMenu {
11574
11576
  ic.bMeasureDistance = true;
11575
11577
  });
11576
11578
 
11577
- me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11579
+ me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11578
11580
  me.htmlCls.dialogCls.openDlg('dl_distmanysets', 'Measure the pairwise distances among many sets');
11579
11581
 
11580
11582
  thisClass.setSetsMenus('atomsCustomDistTable');
@@ -11582,7 +11584,7 @@ class ClickMenu {
11582
11584
  ic.bMeasureDistance = true;
11583
11585
  });
11584
11586
 
11585
- me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11587
+ me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11586
11588
  me.htmlCls.dialogCls.openDlg('dl_anglemanysets', 'Measure the pairwise angles among many sets');
11587
11589
 
11588
11590
  thisClass.setSetsMenus('atomsCustomAngleTable');
@@ -11590,7 +11592,7 @@ class ClickMenu {
11590
11592
  ic.bMeasureAngle = true;
11591
11593
  });
11592
11594
 
11593
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11595
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11594
11596
  ic.pickpair = false;
11595
11597
  let select = "set lines off";
11596
11598
  thisClass.setLogCmd(select, true);
@@ -11601,7 +11603,7 @@ class ClickMenu {
11601
11603
  ic.drawCls.draw();
11602
11604
  });
11603
11605
 
11604
- me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11606
+ me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11605
11607
  me.htmlCls.dialogCls.openDlg('dl_cartoonshape', 'Draw cartoon for a set');
11606
11608
 
11607
11609
  let bOneset = true;
@@ -11610,7 +11612,7 @@ class ClickMenu {
11610
11612
  ic.bCartoonshape = true;
11611
11613
  });
11612
11614
 
11613
- me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11615
+ me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11614
11616
  me.htmlCls.dialogCls.openDlg('dl_linebtwsets', 'Draw a line between two sets');
11615
11617
 
11616
11618
  thisClass.setSetsMenus('linebtwsets');
@@ -11619,21 +11621,21 @@ class ClickMenu {
11619
11621
  });
11620
11622
 
11621
11623
 
11622
- me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11624
+ me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11623
11625
  //thisClass.setLogCmd('zoom selection', true);
11624
11626
  ic.transformCls.zoominSelection();
11625
11627
  ic.drawCls.draw();
11626
11628
  thisClass.setLogCmd('zoom selection', true);
11627
11629
  });
11628
11630
 
11629
- me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11631
+ me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11630
11632
  //thisClass.setLogCmd('center selection', true);
11631
11633
  ic.applyCenterCls.centerSelection();
11632
11634
  ic.drawCls.draw();
11633
11635
  thisClass.setLogCmd('center selection', true);
11634
11636
  });
11635
11637
 
11636
- me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11638
+ me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11637
11639
  //thisClass.setLogCmd('reset orientation', true);
11638
11640
  ic.transformCls.resetOrientation();
11639
11641
  //ic.setColorCls.applyOriginalColor();
@@ -11641,17 +11643,17 @@ class ClickMenu {
11641
11643
  thisClass.setLogCmd('reset orientation', true);
11642
11644
  });
11643
11645
 
11644
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11646
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11645
11647
  ic.setOptionCls.setOption('chemicalbinding', 'show');
11646
11648
  thisClass.setLogCmd('set chemicalbinding show', true);
11647
11649
  });
11648
11650
 
11649
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11651
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11650
11652
  ic.setOptionCls.setOption('chemicalbinding', 'hide');
11651
11653
  thisClass.setLogCmd('set chemicalbinding hide', true);
11652
11654
  });
11653
11655
 
11654
- me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11656
+ me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11655
11657
  if(ic.bInputfile) {
11656
11658
  alert("Side-by-Side does NOT work when the input is from a local file.");
11657
11659
  return;
@@ -11670,19 +11672,19 @@ class ClickMenu {
11670
11672
  //}
11671
11673
  });
11672
11674
 
11673
- $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; //e.preventDefault();
11675
+ $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; e.preventDefault();
11674
11676
  me.htmlCls.dialogCls.openDlg('dl_translate', 'Translate the X,Y,Z coordinates of the structure');
11675
11677
  });
11676
11678
 
11677
- $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; //e.preventDefault();
11679
+ $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; e.preventDefault();
11678
11680
  me.htmlCls.dialogCls.openDlg('dl_angle', 'Measure the angle between two vectors');
11679
11681
  });
11680
11682
 
11681
- $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; //e.preventDefault();
11683
+ $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; e.preventDefault();
11682
11684
  me.htmlCls.dialogCls.openDlg('dl_matrix', 'Apply matrix to the X,Y,Z coordinates of the structure');
11683
11685
  });
11684
11686
 
11685
- $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; //e.preventDefault();
11687
+ $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; e.preventDefault();
11686
11688
  let value = $(this).attr('v').toLowerCase();
11687
11689
  let direction = value.split(' ')[1];
11688
11690
 
@@ -11694,7 +11696,7 @@ class ClickMenu {
11694
11696
  ic.resizeCanvasCls.rotStruc(direction);
11695
11697
  });
11696
11698
 
11697
- $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; //e.preventDefault();
11699
+ $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; e.preventDefault();
11698
11700
  let value = $(this).attr('v').toLowerCase();
11699
11701
  let direction = value.split(' ')[1];
11700
11702
 
@@ -11713,21 +11715,21 @@ class ClickMenu {
11713
11715
  ic.transformCls.setRotation(axis, angle);
11714
11716
  });
11715
11717
 
11716
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11718
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11717
11719
  ic.setOptionCls.setOption('camera', 'perspective');
11718
11720
  thisClass.setLogCmd('set camera perspective', true);
11719
11721
  });
11720
11722
 
11721
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11723
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11722
11724
  ic.setOptionCls.setOption('camera', 'orthographic');
11723
11725
  thisClass.setLogCmd('set camera orthographic', true);
11724
11726
  });
11725
11727
 
11726
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11728
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11727
11729
  ic.setStyleCls.setBackground('black');
11728
11730
  });
11729
11731
 
11730
- me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11732
+ me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11731
11733
  if(ic.opts['background'] == 'black') {
11732
11734
  ic.setStyleCls.setBackground('white');
11733
11735
  }
@@ -11736,19 +11738,19 @@ class ClickMenu {
11736
11738
  }
11737
11739
  });
11738
11740
 
11739
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11741
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11740
11742
  ic.setStyleCls.setBackground('grey');
11741
11743
  });
11742
11744
 
11743
- me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11745
+ me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11744
11746
  ic.setStyleCls.setBackground('white');
11745
11747
  });
11746
11748
 
11747
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11749
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11748
11750
  ic.setStyleCls.setBackground('transparent');
11749
11751
  });
11750
11752
 
11751
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11753
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11752
11754
  //ic.setOptionCls.setOption('fog', 'yes');
11753
11755
  ic.opts['fog'] = 'yes';
11754
11756
  ic.fogCls.setFog(true);
@@ -11756,7 +11758,7 @@ class ClickMenu {
11756
11758
  thisClass.setLogCmd('set fog on', true);
11757
11759
  });
11758
11760
 
11759
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11761
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11760
11762
  //ic.setOptionCls.setOption('fog', 'no');
11761
11763
  ic.opts['fog'] = 'no';
11762
11764
  ic.fogCls.setFog(true);
@@ -11764,22 +11766,22 @@ class ClickMenu {
11764
11766
  thisClass.setLogCmd('set fog off', true);
11765
11767
  });
11766
11768
 
11767
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11769
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11768
11770
  ic.setOptionCls.setOption('slab', 'yes');
11769
11771
  thisClass.setLogCmd('set slab on', true);
11770
11772
  });
11771
11773
 
11772
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11774
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11773
11775
  ic.setOptionCls.setOption('slab', 'no');
11774
11776
  thisClass.setLogCmd('set slab off', true);
11775
11777
  });
11776
11778
 
11777
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11779
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11778
11780
  ic.setOptionCls.setOption('axis', 'yes');
11779
11781
  thisClass.setLogCmd('set axis on', true);
11780
11782
  });
11781
11783
 
11782
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11784
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11783
11785
  ic.pc1 = true;
11784
11786
 
11785
11787
  ic.axesCls.setPc1Axes();
@@ -11787,7 +11789,7 @@ class ClickMenu {
11787
11789
  });
11788
11790
 
11789
11791
 
11790
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11792
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11791
11793
  ic.pc1 = false;
11792
11794
  ic.axes = [];
11793
11795
 
@@ -11796,37 +11798,37 @@ class ClickMenu {
11796
11798
  thisClass.setLogCmd('set axis off', true);
11797
11799
  });
11798
11800
 
11799
- me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11801
+ me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11800
11802
  ic.bAxisOnly = false;
11801
11803
  await ic.symdCls.retrieveSymmetry(Object.keys(ic.structures)[0]);
11802
11804
  //me.htmlCls.dialogCls.openDlg('dl_symmetry', 'Symmetry');
11803
11805
  });
11804
11806
 
11805
- me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11807
+ me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11806
11808
  ic.bAxisOnly = false;
11807
11809
  await ic.symdCls.retrieveSymd();
11808
11810
  ic.bSymd = true;
11809
11811
 
11810
11812
  thisClass.setLogCmd('symd symmetry', true);
11811
11813
  });
11812
- me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11814
+ me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11813
11815
  ic.symdArray = [];
11814
11816
  ic.drawCls.draw();
11815
11817
  thisClass.setLogCmd('clear symd symmetry', true);
11816
11818
  });
11817
- me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11819
+ me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11818
11820
  ic.bAxisOnly = true;
11819
11821
  ic.drawCls.draw();
11820
11822
  thisClass.setLogCmd('show axis', true);
11821
11823
  });
11822
11824
 
11823
11825
 
11824
- me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11826
+ me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11825
11827
  ic.analysisCls.calculateArea();
11826
11828
  thisClass.setLogCmd('area', true);
11827
11829
  });
11828
11830
 
11829
- me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11831
+ me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11830
11832
  ic.bAxisOnly = false;
11831
11833
 
11832
11834
  let title = $("#" + me.pre + "selectSymmetry" ).val();
@@ -11836,14 +11838,14 @@ class ClickMenu {
11836
11838
  ic.drawCls.draw();
11837
11839
  thisClass.setLogCmd('symmetry ' + title, true);
11838
11840
  });
11839
- me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11841
+ me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11840
11842
  let title = 'none';
11841
11843
  ic.symmetrytitle = undefined;
11842
11844
  ic.drawCls.draw();
11843
11845
  thisClass.setLogCmd('symmetry ' + title, true);
11844
11846
  });
11845
11847
 
11846
- me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11848
+ me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11847
11849
  thisClass.SetChainsAdvancedMenu();
11848
11850
 
11849
11851
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -11860,11 +11862,11 @@ class ClickMenu {
11860
11862
  $("#" + me.pre + "atomsCustomHbond2").resizable();
11861
11863
  });
11862
11864
 
11863
- me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; //e.preventDefault();
11865
+ me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; e.preventDefault();
11864
11866
  me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
11865
11867
  });
11866
11868
 
11867
- me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11869
+ me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11868
11870
  thisClass.setLogCmd('set dssp sse', true);
11869
11871
  await ic.pdbParserCls.applyCommandDssp();
11870
11872
  ic.bResetAnno = true;
@@ -11877,12 +11879,12 @@ class ClickMenu {
11877
11879
  });
11878
11880
 
11879
11881
 
11880
- me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11882
+ me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11881
11883
  ic.showInterCls.hideHbondsContacts();
11882
11884
  ic.drawCls.draw();
11883
11885
  });
11884
11886
 
11885
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11887
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11886
11888
  let select = "stabilizer";
11887
11889
  ic.threeDPrintCls.addStabilizer();
11888
11890
  ic.threeDPrintCls.prepareFor3Dprint();
@@ -11890,14 +11892,14 @@ class ClickMenu {
11890
11892
  thisClass.setLogCmd(select, true);
11891
11893
  });
11892
11894
 
11893
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11895
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11894
11896
  let select = "set stabilizer off";
11895
11897
  thisClass.setLogCmd(select, true);
11896
11898
  ic.threeDPrintCls.hideStabilizer();
11897
11899
  ic.drawCls.draw();
11898
11900
  });
11899
11901
 
11900
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11902
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11901
11903
  me.htmlCls.dialogCls.openDlg('dl_stabilizer', 'Add One Stabilizer');
11902
11904
  ic.pk = 1;
11903
11905
  ic.opts['pk'] = 'atom';
@@ -11905,7 +11907,7 @@ class ClickMenu {
11905
11907
  ic.pAtomNum = 0;
11906
11908
  });
11907
11909
 
11908
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11910
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11909
11911
  me.htmlCls.dialogCls.openDlg('dl_stabilizer_rm', 'Remove One Stabilizer');
11910
11912
  ic.pk = 1;
11911
11913
  ic.opts['pk'] = 'atom';
@@ -11913,27 +11915,27 @@ class ClickMenu {
11913
11915
  ic.pAtomNum = 0;
11914
11916
  });
11915
11917
 
11916
- me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; //e.preventDefault();
11918
+ me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; e.preventDefault();
11917
11919
  me.htmlCls.dialogCls.openDlg('dl_thickness', 'Set Thickness for 3D Printing');
11918
11920
  });
11919
11921
 
11920
- me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; //e.preventDefault();
11922
+ me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; e.preventDefault();
11921
11923
  me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Style Preferences');
11922
11924
  });
11923
11925
 
11924
11926
 
11925
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11927
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11926
11928
  let select = "disulfide bonds";
11927
11929
  thisClass.setLogCmd(select, true);
11928
11930
  ic.showInterCls.showSsbonds();
11929
11931
  });
11930
11932
 
11931
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11933
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11932
11934
  ic.viewInterPairsCls.exportSsbondPairs();
11933
11935
  thisClass.setLogCmd("export disulfide bond pairs", false);
11934
11936
  });
11935
11937
 
11936
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11938
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11937
11939
  ic.opts["ssbonds"] = "no";
11938
11940
  let select = "set disulfide bonds off";
11939
11941
  thisClass.setLogCmd(select, true);
@@ -11941,7 +11943,7 @@ class ClickMenu {
11941
11943
  ic.setOptionCls.setStyle('sidec', 'nothing');
11942
11944
  });
11943
11945
 
11944
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11946
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11945
11947
  let select = "cross linkage";
11946
11948
  thisClass.setLogCmd(select, true);
11947
11949
  //ic.bShowCrossResidueBond = true;
@@ -11949,12 +11951,12 @@ class ClickMenu {
11949
11951
  ic.showInterCls.showClbonds();
11950
11952
  });
11951
11953
 
11952
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11954
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11953
11955
  ic.viewInterPairsCls.exportClbondPairs();
11954
11956
  thisClass.setLogCmd("export cross linkage pairs", false);
11955
11957
  });
11956
11958
 
11957
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11959
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11958
11960
  ic.opts["clbonds"] = "no";
11959
11961
  let select = "set cross linkage off";
11960
11962
  thisClass.setLogCmd(select, true);
@@ -12002,7 +12004,7 @@ class ClickMenu {
12002
12004
  });
12003
12005
  });
12004
12006
 
12005
- me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; //e.preventDefault();
12007
+ me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; e.preventDefault();
12006
12008
  let text = $("#" + me.pre + "jn_commands").val();
12007
12009
  navigator.clipboard.writeText(text);
12008
12010
  });
@@ -12628,7 +12630,7 @@ class SetMenu {
12628
12630
 
12629
12631
  html += this.getLink('mn1_urlfile', 'URL(CORS) ' + me.htmlCls.wifiStr, undefined, 2);
12630
12632
  html += this.getMenuSep();
12631
- html += this.getLink('mn1_pngimage', 'iCn3D PNG Image', 1, 2);
12633
+ html += this.getLink('mn1_pngimage', 'iCn3D PNG (appendable)', 1, 2);
12632
12634
  html += this.getLink('mn1_state', 'State/Script File', undefined, 2);
12633
12635
  html += this.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr, undefined, 2);
12634
12636
  html += this.getLink('mn1_selection', 'Selection File', undefined, 2);
@@ -15067,9 +15069,9 @@ class SetDialog {
15067
15069
  html += "</div>";
15068
15070
 
15069
15071
  html += me.htmlCls.divStr + "dl_pngimage' class='" + dialogClass + "'>";
15070
- html += this.addNotebookTitle('dl_pngimage', 'Please input an iCn3D PNG Image file');
15071
- html += "iCn3D PNG image: " + me.htmlCls.inputFileStr + "id='" + me.pre + "pngimage'><br/>";
15072
- html += me.htmlCls.buttonStr + "reload_pngimage' style='margin-top: 6px;'>Load</button>";
15072
+ html += this.addNotebookTitle('dl_pngimage', 'Please append iCn3D PNG Image files');
15073
+ html += "Multiple iCn3D PNG images: " + me.htmlCls.inputFileStr + " multiple id='" + me.pre + "pngimage' size=8><br/>";
15074
+ html += me.htmlCls.buttonStr + "reload_pngimage' style='margin-top: 6px;'>Append</button>";
15073
15075
  html += "</div>";
15074
15076
 
15075
15077
  html += me.htmlCls.divStr + "dl_state' class='" + dialogClass + "'>";
@@ -16325,11 +16327,18 @@ class Events {
16325
16327
  }
16326
16328
  }
16327
16329
 
16328
- async readFile(bAppend, files, index, dataStrAll, bmmCIF) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
16330
+ async readFile(bAppend, files, index, dataStrAll, bmmCIF, bPng) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
16329
16331
  let file = files[index];
16330
16332
  let commandName = (bAppend) ? 'append': 'load';
16331
- commandName += (bmmCIF) ? ' mmcif file ': ' pdb file ';
16333
+ commandName += (bmmCIF) ? ' mmcif file ' : (bPng) ? ' png file ' : ' pdb file ';
16332
16334
 
16335
+ /*
16336
+ reader.onload = async function(e) {
16337
+ let imageStr = e.target.result; // or = reader.result;
16338
+ await thisClass.loadPng(dataStr);
16339
+ }
16340
+ */
16341
+
16333
16342
  let reader = new FileReader();
16334
16343
  reader.onload = async function(e) {
16335
16344
  let dataStr = e.target.result; // or = reader.result;
@@ -16347,7 +16356,14 @@ class Events {
16347
16356
  }
16348
16357
 
16349
16358
  ic.bInputfile = true;
16350
- ic.InputfileType = (bmmCIF) ? 'mmcif' : 'pdb';
16359
+ ic.InputfileType = (bmmCIF) ? 'mmcif' : (bPng) ? 'png' : 'pdb';
16360
+ if(bPng) {
16361
+ let result = await me.htmlCls.setHtmlCls.loadPng(dataStr);
16362
+ dataStr = result.pdb;
16363
+ if(!ic.statefileArray) ic.statefileArray = [];
16364
+ ic.statefileArray.push(result.statefile);
16365
+ }
16366
+
16351
16367
  ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + dataStr : dataStr;
16352
16368
 
16353
16369
  dataStrAll = (index > 0) ? dataStrAll + '\nENDMDL\n' + dataStr : dataStr;
@@ -16367,7 +16383,7 @@ class Events {
16367
16383
  //ic.InputfileType = undefined; // reset
16368
16384
  }
16369
16385
  else {
16370
- await thisClass.readFile(bAppend, files, index + 1, dataStrAll, bmmCIF);
16386
+ await thisClass.readFile(bAppend, files, index + 1, dataStrAll, bmmCIF, bPng);
16371
16387
  }
16372
16388
 
16373
16389
  if(bAppend) {
@@ -20080,7 +20096,7 @@ class SetHtml {
20080
20096
  if(me.bNode) return;
20081
20097
 
20082
20098
  let thisClass = this;
20083
- me.myEventCls.onIds("#" + me.pre + "reload_pngimage", "click", function(e) { let ic = me.icn3d;
20099
+ me.myEventCls.onIds("#" + me.pre + "reload_pngimage", "click", async function(e) { let ic = me.icn3d;
20084
20100
  e.preventDefault();
20085
20101
  if(!me.cfg.notebook) dialog.dialog( "close" );
20086
20102
  //close all dialog
@@ -20090,50 +20106,53 @@ class SetHtml {
20090
20106
  else {
20091
20107
  ic.resizeCanvasCls.closeDialogs();
20092
20108
  }
20093
- // initialize icn3dui
20094
- //me.initUI();
20095
- ic.init();
20096
- let file = $("#" + me.pre + "pngimage")[0].files[0];
20097
- if(!file) {
20109
+
20110
+ // ic.init();
20111
+ let files = $("#" + me.pre + "pngimage")[0].files;
20112
+ if(!files[0]) {
20098
20113
  alert("Please select a file before clicking 'Load'");
20099
20114
  }
20100
20115
  else {
20101
20116
  thisClass.fileSupport();
20102
- let reader = new FileReader();
20103
- reader.onload = async function(e) {
20104
- let imageStr = e.target.result; // or = reader.result;
20105
- await thisClass.loadPng(imageStr);
20106
- };
20107
- reader.readAsText(file);
20117
+
20118
+ let bAppend = true;
20119
+ let bmmCIF = false;
20120
+ let bPng = true;
20121
+ await me.htmlCls.eventsCls.readFile(bAppend, files, 0, '', bmmCIF, bPng);
20108
20122
  }
20109
20123
  });
20110
20124
  }
20111
20125
 
20112
- async loadPng(imageStr, command) { let me = this.icn3dui, ic = me.icn3d;
20126
+ // async loadPng(imageStr, command) { let me = this.icn3dui, ic = me.icn3d;
20127
+ async loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
20113
20128
  let matchedStr = 'Share Link: ';
20114
20129
  let pos = imageStr.indexOf(matchedStr);
20115
20130
  let matchedStrState = "Start of state file======\n";
20116
20131
  let posState = imageStr.indexOf(matchedStrState);
20132
+
20133
+ let data = '', statefile = '';
20134
+
20117
20135
  if(pos == -1 && posState == -1) {
20118
20136
  alert('Please load a PNG image saved by clicking the menu "File > Save File > iCn3D PNG Image"...');
20119
20137
  }
20120
- else if(pos != -1) {
20121
- let url = imageStr.substr(pos + matchedStr.length);
20122
- me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
20123
- window.open(url, '_self');
20124
- }
20138
+ // else if(!bReturn && pos != -1) { // no need to return pdb and state files
20139
+ // let url = imageStr.substr(pos + matchedStr.length);
20140
+ // me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
20141
+ // window.open(url, '_self');
20142
+ // }
20125
20143
  else if(posState != -1) {
20126
20144
  let matchedStrData = "Start of data file======\n";
20127
20145
  let posData = imageStr.indexOf(matchedStrData);
20128
20146
  ic.bInputfile =(posData == -1) ? false : true;
20129
20147
  ic.bInputPNGWithData = ic.bInputfile;
20130
- let commandStr = (command) ? command.replace(/;/g, "\n") : '';
20148
+ // let commandStr = (command) ? command.replace(/;/g, "\n") : '';
20149
+ let commandStr = '';
20131
20150
 
20132
- let statefile;
20133
- if(ic.bInputfile) {
20151
+ // let statefile;
20152
+ // if(ic.bInputfile) {
20134
20153
  let posDataEnd = imageStr.indexOf("End of data file======\n");
20135
- let data = imageStr.substr(posData + matchedStrData.length, posDataEnd - posData - matchedStrData.length);
20136
- ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : data;
20154
+ data = imageStr.substr(posData + matchedStrData.length, posDataEnd - posData - matchedStrData.length);
20155
+ // ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : data;
20137
20156
 
20138
20157
  let matchedStrType = "Start of type file======\n";
20139
20158
  let posType = imageStr.indexOf(matchedStrType);
@@ -20147,7 +20166,8 @@ class SetHtml {
20147
20166
  statefile = imageStr.substr(posState + matchedStrState.length, posStateEnd - posState- matchedStrState.length);
20148
20167
  //statefile = decodeURIComponent(statefile);
20149
20168
  statefile = decodeURIComponent(statefile + "\n" + commandStr);
20150
-
20169
+
20170
+ /*
20151
20171
  if(type === 'pdb') {
20152
20172
  await ic.pdbParserCls.loadPdbData(data);
20153
20173
 
@@ -20186,10 +20206,13 @@ class SetHtml {
20186
20206
  //await ic.loadScriptCls.loadScript(statefile, true);
20187
20207
  }
20188
20208
 
20189
- await ic.loadScriptCls.loadScript(statefile, true);
20209
+ await ic.loadScriptCls.loadScript(statefile, true);
20190
20210
 
20191
20211
  me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
20212
+ */
20192
20213
  }
20214
+
20215
+ return {'pdb': data, 'statefile': statefile};
20193
20216
  }
20194
20217
 
20195
20218
  fileSupport() {
@@ -37775,7 +37798,7 @@ class Contact {
37775
37798
  for (let j in neighbors) {
37776
37799
  let atom = neighbors[j];
37777
37800
 
37778
- if(!ic.crossstrucinter && oriAtom.structure != atom.structure) continue;
37801
+ if(bInteraction && !ic.crossstrucinter && oriAtom.structure != atom.structure) continue;
37779
37802
 
37780
37803
  // exclude the target atoms
37781
37804
  if(!bIncludeTarget && atom.serial in atomlistTarget) continue;
@@ -38206,7 +38229,6 @@ class HBond {
38206
38229
  //"threshold" is the maximum distance of hydrogen bonds and has the unit of angstrom.
38207
38230
  calculateChemicalHbonds(startAtoms, targetAtoms, threshold, bSaltbridge, type, bInternal) { let ic = this.icn3d, me = ic.icn3dui;
38208
38231
  if(Object.keys(startAtoms).length === 0 || Object.keys(targetAtoms).length === 0) return;
38209
-
38210
38232
  ic.resid2Residhash = {};
38211
38233
 
38212
38234
  let atomHbond = {};
@@ -38300,6 +38322,7 @@ class HBond {
38300
38322
  && (atom.name === 'N' || atom.name === 'O') && (atomHbond[j].name === 'O' || atomHbond[j].name === 'N') ) {
38301
38323
 
38302
38324
  if(atom.name === atomHbond[j].name) continue;
38325
+
38303
38326
  if(atom.structure == atomHbond[j].structure && atom.chain == atomHbond[j].chain && Math.abs(atom.resi - atomHbond[j].resi) <= 1) continue; // peptide bond
38304
38327
 
38305
38328
  // protein backbone hydrogen
@@ -47717,12 +47740,14 @@ class Annotation {
47717
47740
  chainHash[chainid] = 1;
47718
47741
  }
47719
47742
  $("#" + ic.pre + "dl_annotations > .icn3d-annotation").hide();
47743
+
47720
47744
  for(let chainid in chainHash) {
47721
47745
  if($("#" + ic.pre + "anno_" + chainid).length) {
47722
47746
  $("#" + ic.pre + "anno_" + chainid).show();
47723
47747
  }
47748
+
47724
47749
  let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chainid]);
47725
- if(atom.resn !== undefined) {
47750
+ if(atom && atom.resn !== undefined) {
47726
47751
  let oneLetterRes = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
47727
47752
  $("#" + ic.pre + "anno_" + oneLetterRes).show();
47728
47753
  }
@@ -50035,6 +50060,7 @@ class HlUpdate {
50035
50060
  if(chainArray2d !== undefined) {
50036
50061
  for(let i = 0, il = chainArray2d.length; i < il; ++i) {
50037
50062
  let hlatoms = me.hashUtilsCls.intHash(ic.chains[chainArray2d[i]], ic.hAtoms);
50063
+ if(!ic.chains[chainArray2d[i]]) continue;
50038
50064
  let ratio = 1.0 * Object.keys(hlatoms).length / Object.keys(ic.chains[chainArray2d[i]]).length;
50039
50065
 
50040
50066
  let firstAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(hlatoms);
@@ -51263,6 +51289,7 @@ class GetGraph {
51263
51289
  let residLabel = '1_1_' + resid;
51264
51290
  //if(cnt > 0) nodeStr += ', ';
51265
51291
  let colorStr = (atom.color) ? atom.color.getHexString().toUpperCase() : '000';
51292
+
51266
51293
  nodeArray.push('{"id": "' + resName + '", "r": "' + residLabel + '", "s": "' + setName + '", "x": ' + atom.coord.x.toFixed(0)
51267
51294
  + ', "y": ' + atom.coord.y.toFixed(0) + ', "c": "' + colorStr + '"}');
51268
51295
  if(cnt > 0 && prevChain == atom.chain &&(ic.resid2ncbi[atom.resi] == ic.resid2ncbi[prevResi] + 1 || ic.resid2ncbi[atom.resi] == ic.resid2ncbi[prevResi]) ) {
@@ -51615,11 +51642,12 @@ class ShowInter {
51615
51642
  let firstSetAtoms, complement;
51616
51643
  firstSetAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray2);
51617
51644
  complement = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
51618
- ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
51645
+ // let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
51619
51646
 
51620
51647
  if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
51621
51648
  // let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
51622
51649
  let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
51650
+
51623
51651
  let commanddesc;
51624
51652
  if(bSaltbridge) {
51625
51653
  ic.resid2ResidhashSaltbridge = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
@@ -52057,6 +52085,7 @@ class ViewInterPairs {
52057
52085
  if(!threshold || isNaN(threshold)) threshold = ic.tsHbond;
52058
52086
  if(!bHbondCalc) {
52059
52087
  ic.hAtoms = me.hashUtilsCls.cloneHash(prevHatoms);
52088
+
52060
52089
  ic.showInterCls.showHbonds(threshold, nameArray2, nameArray, bHbondCalc, undefined, type);
52061
52090
  }
52062
52091
  hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.hAtoms);
@@ -58291,7 +58320,8 @@ class PdbParser {
58291
58320
  await ic.mmcifParserCls.loadMmcifData(data);
58292
58321
  }
58293
58322
  else if(type === 'icn3dpng') {
58294
- await me.htmlCls.setHtmlCls.loadPng(data, command);
58323
+ // await me.htmlCls.setHtmlCls.loadPng(data, command);
58324
+ await me.htmlCls.setHtmlCls.loadPng(data);
58295
58325
  }
58296
58326
  else if(type === 'pae') {
58297
58327
  me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
@@ -58320,7 +58350,7 @@ class PdbParser {
58320
58350
  if(!ic.bStatefile) ic.init(bKeepCmd);
58321
58351
  }
58322
58352
 
58323
- let hAtoms = ic.loadPDBCls.loadPDB(data, pdbid, bOpm, undefined, undefined, bAppend, type, bEsmfold); // defined in the core library
58353
+ let hAtoms = await ic.loadPDBCls.loadPDB(data, pdbid, bOpm, undefined, undefined, bAppend, type, bEsmfold); // defined in the core library
58324
58354
 
58325
58355
  if(me.cfg.opmid === undefined) ic.ParserUtilsCls.transformToOpmOri(pdbid);
58326
58356
 
@@ -58365,9 +58395,7 @@ class PdbParser {
58365
58395
  await this.applyCommandDssp(bAppend);
58366
58396
  }
58367
58397
  else {
58368
- // could this line be removed?
58369
58398
  await this.loadPdbDataRender(bAppend);
58370
-
58371
58399
  if(!me.bNode) await ic.ParserUtilsCls.checkMemProteinAndRotate();
58372
58400
 
58373
58401
  /// if(ic.deferredOpm !== undefined) ic.deferredOpm.resolve();
@@ -58413,8 +58441,37 @@ class PdbParser {
58413
58441
  ic.definedSetsCls.setModeAndDisplay('all');
58414
58442
  }
58415
58443
 
58444
+ if(ic.struct_statefile) {
58445
+ for(let i = 0, il = ic.struct_statefile.length; i < il; ++i) {
58446
+ await this.execStatefile(ic.struct_statefile[i].structure, ic.struct_statefile[i].statefile);
58447
+ }
58448
+ }
58449
+
58416
58450
  // if(me.deferred !== undefined) me.deferred.resolve(); /// if(ic.deferred2 !== undefined) ic.deferred2.resolve();
58417
58451
  }
58452
+
58453
+ async execStatefile(structure, statefile) {let ic = this.icn3d, me = ic.icn3dui;
58454
+ // if(!statefile) return;
58455
+
58456
+ let commandArray = statefile.trim().split('\n');
58457
+ commandArray = ['select $' + structure].concat(commandArray);
58458
+ ic.STATENUMBER = commandArray.length;
58459
+ ic.CURRENTNUMBER = 0;
58460
+ let bStrict = true;
58461
+
58462
+ let hAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
58463
+ let commands = ic.commands;
58464
+
58465
+ // reset ic.hAtoms
58466
+ ic.hAtoms = {};
58467
+ ic.commands = commandArray;
58468
+
58469
+ await ic.loadScriptCls.execCommands(ic.CURRENTNUMBER, ic.STATENUMBER-1, ic.STATENUMBER, bStrict);
58470
+
58471
+ // revert back to the original set
58472
+ ic.hAtoms = me.hashUtilsCls.cloneHash(hAtoms);
58473
+ ic.commands = commands.concat(ic.commands);
58474
+ }
58418
58475
  }
58419
58476
 
58420
58477
  /**
@@ -63762,7 +63819,7 @@ class LoadPDB {
63762
63819
 
63763
63820
  // modified from iview (http://istar.cse.cuhk.edu.hk/iview/)
63764
63821
  //This PDB parser feeds the viewer with the content of a PDB file, pdbData.
63765
- loadPDB(src, pdbid, bOpm, bVector, bMutation, bAppend, type, bEsmfold) { let ic = this.icn3d, me = ic.icn3dui;
63822
+ async loadPDB(src, pdbid, bOpm, bVector, bMutation, bAppend, type, bEsmfold) { let ic = this.icn3d, me = ic.icn3dui;
63766
63823
  let hAtoms = {};
63767
63824
 
63768
63825
  let bNMR = false;
@@ -63773,6 +63830,8 @@ class LoadPDB {
63773
63830
 
63774
63831
  if(!ic.atoms) bAppend = false;
63775
63832
 
63833
+ if(ic.statefileArray) ic.struct_statefile = [];
63834
+
63776
63835
  let serial, moleculeNum;
63777
63836
  if(!bMutation && !bAppend) {
63778
63837
  ic.init();
@@ -63962,11 +64021,14 @@ class LoadPDB {
63962
64021
 
63963
64022
  ic.organism = ic.organism.substr(0, ic.organism.length - 1);
63964
64023
  } else if (record === 'ENDMDL') {
64024
+ if(ic.statefileArray) {
64025
+ ic.struct_statefile.push({'structure': structure, 'statefile': ic.statefileArray[moleculeNum - 1]});
64026
+ }
64027
+
63965
64028
  ++moleculeNum;
63966
64029
  id = ic.defaultPdbId;
63967
64030
 
63968
64031
  structure = this.getStructureId(id, moleculeNum, bMutation);
63969
-
63970
64032
  //helices = [];
63971
64033
  //sheets = [];
63972
64034
  if(!bNMR) {
@@ -64229,6 +64291,10 @@ class LoadPDB {
64229
64291
  if(ic.chains[chainNum] === undefined) ic.chains[chainNum] = {};
64230
64292
  ic.chains[chainNum] = me.hashUtilsCls.unionHash2Atoms(ic.chains[chainNum], chainsTmp, ic.atoms);
64231
64293
 
64294
+ if(ic.statefileArray) {
64295
+ ic.struct_statefile.push({'structure': structure, 'statefile': ic.statefileArray[moleculeNum - 1]});
64296
+ }
64297
+
64232
64298
  //if(!bMutation) this.adjustSeq(ic.chainMissingResidueArray);
64233
64299
  this.adjustSeq(ic.chainMissingResidueArray);
64234
64300
 
@@ -64701,6 +64767,7 @@ class LoadCIF {
64701
64767
  let id = (bcifid) ? bcifid : ic.defaultPdbId;
64702
64768
 
64703
64769
  let structure = id;
64770
+ let CSerial, prevCSerial, OSerial, prevOSerial;
64704
64771
 
64705
64772
  let bFirstAtom = true;
64706
64773
 
@@ -65150,19 +65217,23 @@ class LoadCIF {
65150
65217
  ssend: false // optional, used to show the end of secondary structures
65151
65218
  };
65152
65219
 
65153
- if(!atomDetails.het && atomDetails.name === 'C') ;
65154
- if(!atomDetails.het && atomDetails.name === 'O') ;
65220
+ if(!atomDetails.het && atomDetails.name === 'C') {
65221
+ CSerial = serial;
65222
+ }
65223
+ if(!atomDetails.het && atomDetails.name === 'O') {
65224
+ OSerial = serial;
65225
+ }
65155
65226
 
65156
65227
  // from DSSP C++ code
65157
- // if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
65158
- // let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
65228
+ if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
65229
+ let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
65159
65230
 
65160
- // let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
65161
- // let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
65162
- // let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
65231
+ let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
65232
+ let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
65233
+ let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
65163
65234
 
65164
- // atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
65165
- // }
65235
+ atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
65236
+ }
65166
65237
 
65167
65238
  ic.atoms[serial] = atomDetails;
65168
65239
 
@@ -65234,6 +65305,8 @@ class LoadCIF {
65234
65305
 
65235
65306
  // different chain
65236
65307
  if(chainNum !== prevChainNum) {
65308
+ prevCSerial = undefined;
65309
+ prevOSerial = undefined;
65237
65310
 
65238
65311
  // a chain could be separated in two sections
65239
65312
  if(serial !== 1 && prevChainNum !== '') {
@@ -65255,6 +65328,8 @@ class LoadCIF {
65255
65328
  ic.chainsSeq[chainNum].push(resObject);
65256
65329
  }
65257
65330
  else {
65331
+ prevCSerial = CSerial;
65332
+ prevOSerial = OSerial;
65258
65333
 
65259
65334
  let resObject = {};
65260
65335
  resObject.resi = resi;
@@ -69170,14 +69245,16 @@ class LoadScript {
69170
69245
  for(i=start; i <= end; ++i) {
69171
69246
  let bFinalStep =(i === steps - 1) ? true : false;
69172
69247
 
69173
- if(!ic.commands[i].trim()) continue;
69248
+ if(!ic.commands[i] || !ic.commands[i].trim()) {
69249
+ continue;
69250
+ }
69251
+
69174
69252
  let nAtoms = (ic.atoms) ? Object.keys(ic.atoms).length : 0;
69175
69253
 
69176
69254
  if(nAtoms == 0 && ic.commands[i].indexOf('load') == -1) continue;
69177
69255
 
69178
69256
  let strArray = ic.commands[i].split("|||");
69179
69257
  let command = strArray[0].trim();
69180
-
69181
69258
  // sometimes URL has an ID input, then load a structure in commands
69182
69259
  //if(ic.inputid) ic.bNotLoadStructure = true;
69183
69260
 
@@ -70532,9 +70609,11 @@ class Selection {
70532
70609
  ic.hAtoms = {};
70533
70610
  ic.dAtoms = {};
70534
70611
 
70535
- for(let i in ic.chains) {
70536
- ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[i]);
70537
- //ic.dAtoms = me.hashUtilsCls.unionHash(ic.dAtoms, ic.chains[i]);
70612
+ for(let structure in ic.structures) {
70613
+ let chainidArray = ic.structures[structure];
70614
+ for(let i = 0, il = chainidArray.length; i < il; ++i) {
70615
+ ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[chainidArray[i]]);
70616
+ }
70538
70617
  }
70539
70618
 
70540
70619
  ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
@@ -79909,7 +79988,7 @@ class ShareLink {
79909
79988
  });
79910
79989
  }
79911
79990
 
79912
- shareLinkUrl(bAllCommands, bOutputCmd) { let ic = this.icn3d, me = ic.icn3dui;
79991
+ shareLinkUrl(bAllCommands, bOutputCmd, bStatefile) { let ic = this.icn3d, me = ic.icn3dui;
79913
79992
  let url = me.htmlCls.baseUrl + "icn3d/?";
79914
79993
  let outputCmd = '';
79915
79994
  if(me.cfg.bSidebyside) url = me.htmlCls.baseUrl + "icn3d/full2.html?";
@@ -80078,7 +80157,7 @@ class ShareLink {
80078
80157
  }
80079
80158
 
80080
80159
  // keep all commands in statefile
80081
- statefile += prevCommandStr + "\n";
80160
+ if(prevCommandStr.indexOf('load ') == -1) statefile += prevCommandStr + "\n";
80082
80161
 
80083
80162
  prevCommandStr = commandStr;
80084
80163
  }
@@ -80108,14 +80187,14 @@ class ShareLink {
80108
80187
  url = url.replace(new RegExp('blast_rep_id=!','g'), 'blast_rep_id=' + id + '_');
80109
80188
  }
80110
80189
 
80111
- return (bOutputCmd) ? outputCmd : url;
80190
+ return (bStatefile) ? statefile : (bOutputCmd) ? outputCmd : url;
80112
80191
  }
80113
80192
 
80114
80193
  getPngText() { let ic = this.icn3d; ic.icn3dui;
80115
- let url; // output state file if ic.bInputfile is true or the URL is more than 4000 chars
80116
80194
  let bAllCommands = true;
80117
80195
 
80118
80196
  let text = "";
80197
+ /*
80119
80198
  if(ic.bInputfile) {
80120
80199
  url = this.shareLinkUrl(bAllCommands); // output state file if ic.bInputfile is true or the URL is more than 4000 chars
80121
80200
 
@@ -80130,7 +80209,6 @@ class ShareLink {
80130
80209
 
80131
80210
  text += "Start of data file======\n";
80132
80211
  //text += ic.InputfileData;
80133
- /// text += ic.saveFileCls.getPDBHeader();
80134
80212
  text += ic.saveFileCls.getAtomPDB(ic.atoms);
80135
80213
 
80136
80214
  text += "End of data file======\n";
@@ -80155,7 +80233,38 @@ class ShareLink {
80155
80233
  text += "\nShare Link: " + url;
80156
80234
  }
80157
80235
  }
80236
+ */
80237
+
80238
+ // always output PDB and commands
80239
+ text += "\nStart of type file======\n";
80240
+ text += "pdb\n";
80241
+ text += "End of type file======\n";
80242
+
80243
+ text += "Start of data file======\n";
80244
+ text += ic.saveFileCls.getAtomPDB(ic.atoms);
80245
+ text += "End of data file======\n";
80158
80246
 
80247
+ let bStatefile = true;
80248
+ let commands = this.shareLinkUrl(bAllCommands, undefined, bStatefile);
80249
+ text += "Start of state file======\n";
80250
+ text += commands + "\n";
80251
+ text += "End of state file======\n";
80252
+ /*
80253
+ if(ic.bInputfile) {
80254
+ url = this.shareLinkUrl(bAllCommands); // output state file if ic.bInputfile is true or the URL is more than 4000 chars
80255
+
80256
+ if(url.substr(0,4) == 'http') {
80257
+ text += "\nShare Link: " + url;
80258
+ }
80259
+ }
80260
+ else {
80261
+ url = this.shareLinkUrl();
80262
+ let bTooLong =(url.length > 4000 || url.indexOf('http') !== 0) ? true : false;
80263
+ if(!bTooLong) {
80264
+ text += "\nShare Link: " + url;
80265
+ }
80266
+ }
80267
+ */
80159
80268
  text = text.replace(/!/g, Object.keys(ic.structures)[0] + '_');
80160
80269
 
80161
80270
  return text;
@@ -82991,7 +83100,7 @@ class iCn3DUI {
82991
83100
  //even when multiple iCn3D viewers are shown together.
82992
83101
  this.pre = this.cfg.divid + "_";
82993
83102
 
82994
- this.REVISION = '3.35.0';
83103
+ this.REVISION = '3.36.0';
82995
83104
 
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83105
  // In nodejs, iCn3D defines "window = {navigator: {}}"
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83106
  this.bNode = (Object.keys(window).length < 2) ? true : false;