icn3d 3.36.3 → 3.37.0

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 +522 -327
  2. package/icn3d.min.js +4 -4
  3. package/icn3d.module.js +522 -327
  4. package/package.json +1 -1
package/icn3d.module.js CHANGED
@@ -9818,102 +9818,119 @@ class ClickMenu {
9818
9818
  ic.bRunRefnumAgain = false;
9819
9819
  }
9820
9820
 
9821
+ setClashedResidues() { let me = this.icn3dui, ic = me.icn3d;
9822
+ // check contacts between all chains
9823
+ let chainidArray = Object.keys(ic.chains);
9824
+ let radius = 4, bSphereCalc = false, bInteraction = true;
9825
+ for(let i = 0, il = chainidArray.length; i < il; ++i) {
9826
+ let chainid1 = chainidArray[i];
9827
+ for(let j = i + 1, jl = chainidArray.length; j < jl; ++j) {
9828
+ let chainid2 = chainidArray[j];
9829
+ ic.showInterCls.pickCustomSphere_base(radius, ic.chains[chainid1], ic.chains[chainid2], bSphereCalc, bInteraction);
9830
+ }
9831
+ }
9832
+
9833
+ // use domains to determine which one to hide
9834
+ let bNotShowDomain = true;
9835
+ ic.annoDomainCls.showDomainAll(bNotShowDomain);
9836
+ }
9837
+
9821
9838
  clickMenu1() { let me = this.icn3dui; me.icn3d;
9822
9839
  if(me.bNode) return;
9823
9840
 
9824
9841
  let thisClass = this;
9825
9842
  //mn 1
9826
9843
  // clkMn1_mmtfid: function() {
9827
- me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; e.preventDefault();
9844
+ me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; //e.preventDefault();
9828
9845
  me.htmlCls.dialogCls.openDlg('dl_vastplus', 'Please input PDB ID for VAST+');
9829
9846
  });
9830
9847
 
9831
- me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; e.preventDefault();
9848
+ me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; //e.preventDefault();
9832
9849
  me.htmlCls.dialogCls.openDlg('dl_vast', 'Please input chain or PDB file for VAST');
9833
9850
  });
9834
9851
 
9835
- me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; e.preventDefault();
9852
+ me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; //e.preventDefault();
9836
9853
  me.htmlCls.dialogCls.openDlg('dl_foldseek', 'Submit your selection to Foldseek');
9837
9854
  });
9838
9855
 
9839
- me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; e.preventDefault();
9856
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; //e.preventDefault();
9840
9857
  me.htmlCls.dialogCls.openDlg('dl_mmtfid', 'Please input BCIF/MMTF ID');
9841
9858
  });
9842
9859
 
9843
9860
  // clkMn1_pdbid: function() {
9844
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; e.preventDefault();
9861
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; //e.preventDefault();
9845
9862
  me.htmlCls.dialogCls.openDlg('dl_pdbid', 'Please input PDB ID');
9846
9863
  });
9847
9864
 
9848
- me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; e.preventDefault();
9865
+ me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; //e.preventDefault();
9849
9866
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
9850
9867
  });
9851
9868
 
9852
- me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
9869
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; //e.preventDefault();
9853
9870
  me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI Protein Accession');
9854
9871
  });
9855
9872
 
9856
- me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
9873
+ me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; //e.preventDefault();
9857
9874
  me.htmlCls.dialogCls.openDlg('dl_opmid', 'Please input OPM PDB ID');
9858
9875
  });
9859
9876
 
9860
- me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; e.preventDefault();
9877
+ me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; //e.preventDefault();
9861
9878
  me.htmlCls.dialogCls.openDlg('dl_align', 'Align two PDB structures');
9862
9879
  });
9863
9880
 
9864
- me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; e.preventDefault();
9881
+ me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; //e.preventDefault();
9865
9882
  me.htmlCls.dialogCls.openDlg('dl_alignaf', 'Align two AlphaFold structures');
9866
9883
  });
9867
9884
 
9868
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; e.preventDefault();
9885
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; //e.preventDefault();
9869
9886
  me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
9870
9887
  });
9871
9888
 
9872
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; e.preventDefault();
9889
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; //e.preventDefault();
9873
9890
  me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
9874
9891
  });
9875
9892
 
9876
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; e.preventDefault();
9893
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; //e.preventDefault();
9877
9894
  me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
9878
9895
  });
9879
9896
 
9880
- me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; e.preventDefault();
9897
+ me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; //e.preventDefault();
9881
9898
  me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
9882
9899
  });
9883
9900
 
9884
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; e.preventDefault();
9901
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; //e.preventDefault();
9885
9902
  //me = me.setIcn3dui($(this).attr('id'));
9886
9903
  me.htmlCls.dialogCls.openDlg('dl_pdbfile', 'Please input PDB File');
9887
9904
  });
9888
- me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; e.preventDefault();
9905
+ me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; //e.preventDefault();
9889
9906
  //me = me.setIcn3dui($(this).attr('id'));
9890
9907
  me.htmlCls.dialogCls.openDlg('dl_pdbfile_app', 'Please append PDB Files');
9891
9908
  });
9892
9909
 
9893
- me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; e.preventDefault();
9910
+ me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; //e.preventDefault();
9894
9911
  me.htmlCls.dialogCls.openDlg('dl_mol2file', 'Please input Mol2 File');
9895
9912
  });
9896
9913
 
9897
- me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; e.preventDefault();
9914
+ me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; //e.preventDefault();
9898
9915
  me.htmlCls.dialogCls.openDlg('dl_sdffile', 'Please input SDF File');
9899
9916
  });
9900
9917
 
9901
- me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; e.preventDefault();
9918
+ me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; //e.preventDefault();
9902
9919
  me.htmlCls.dialogCls.openDlg('dl_xyzfile', 'Please input XYZ File');
9903
9920
  });
9904
9921
 
9905
- me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; e.preventDefault();
9922
+ me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; //e.preventDefault();
9906
9923
  me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold PAE File');
9907
9924
  });
9908
9925
 
9909
- me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; e.preventDefault();
9926
+ me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; //e.preventDefault();
9910
9927
  me.htmlCls.dialogCls.openDlg('dl_urlfile', 'Load data by URL');
9911
9928
  });
9912
9929
 
9913
- me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
9930
+ me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; //e.preventDefault();
9914
9931
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
9915
9932
  });
9916
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9933
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9917
9934
  let url = $("#" + me.pre + "sharelinkurl").val();
9918
9935
  thisClass.setLogCmd("open " + url, false);
9919
9936
  localStorage.setItem('fixedversion', '1');
@@ -9921,73 +9938,73 @@ class ClickMenu {
9921
9938
  window.open(url, urlTarget);
9922
9939
  });
9923
9940
 
9924
- me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; e.preventDefault();
9941
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; //e.preventDefault();
9925
9942
  me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please append mmCIF File');
9926
9943
  });
9927
9944
 
9928
- me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; e.preventDefault();
9945
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
9929
9946
  me.htmlCls.dialogCls.openDlg('dl_mmcifid', 'Please input mmCIF ID');
9930
9947
  });
9931
9948
 
9932
- me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; e.preventDefault();
9949
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; //e.preventDefault();
9933
9950
  me.htmlCls.dialogCls.openDlg('dl_mmdbid', 'Please input MMDB or PDB ID');
9934
9951
  });
9935
9952
 
9936
- me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; e.preventDefault();
9953
+ me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; //e.preventDefault();
9937
9954
  me.htmlCls.dialogCls.openDlg('dl_mmdbafid', 'Please input PDB/MMDB/AlphaFold UniProt IDs');
9938
9955
  });
9939
9956
 
9940
- me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; e.preventDefault();
9957
+ me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; //e.preventDefault();
9941
9958
  me.htmlCls.dialogCls.openDlg('dl_blast_rep_id', 'Align sequence to structure');
9942
9959
  });
9943
9960
 
9944
- me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; e.preventDefault();
9961
+ me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; //e.preventDefault();
9945
9962
  me.htmlCls.dialogCls.openDlg('dl_esmfold', 'Sequence to structure prediction with ESMFold');
9946
9963
  });
9947
9964
 
9948
- me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; e.preventDefault();
9965
+ me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; //e.preventDefault();
9949
9966
  me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein or gene name');
9950
9967
  });
9951
9968
 
9952
- me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
9969
+ me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; //e.preventDefault();
9953
9970
  me.htmlCls.dialogCls.openDlg('dl_cid', 'Please input PubChem Compound');
9954
9971
  });
9955
9972
 
9956
- me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; e.preventDefault();
9973
+ me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; //e.preventDefault();
9957
9974
  me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please append PNG images');
9958
9975
  });
9959
9976
 
9960
- me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; e.preventDefault();
9977
+ me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; //e.preventDefault();
9961
9978
  me.htmlCls.dialogCls.openDlg('dl_state', 'Please input the state file');
9962
9979
  });
9963
9980
 
9964
- me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; e.preventDefault();
9981
+ me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; //e.preventDefault();
9965
9982
  me.htmlCls.dialogCls.openDlg('dl_selection', 'Please input the selection file');
9966
9983
  });
9967
9984
 
9968
- me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; e.preventDefault();
9985
+ me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; //e.preventDefault();
9969
9986
  me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
9970
9987
  });
9971
9988
 
9972
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; e.preventDefault();
9989
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
9973
9990
  me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
9974
9991
  });
9975
9992
 
9976
9993
 
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();
9994
+ 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
9995
  ic.loadPhiFrom = 'delphi';
9979
9996
  $("#" + me.pre + "dl_delphi_tabs").tabs();
9980
9997
  me.htmlCls.dialogCls.openDlg('dl_delphi', 'Please set parameters to display DelPhi potential map');
9981
9998
  });
9982
9999
 
9983
- me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10000
+ me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9984
10001
  ic.loadPhiFrom = 'phi';
9985
10002
  $("#" + me.pre + "dl_phi_tabs").tabs();
9986
10003
  $("#" + me.pre + "phitab1_tabs").tabs();
9987
10004
  $("#" + me.pre + "phitab2_tabs").tabs();
9988
10005
  me.htmlCls.dialogCls.openDlg('dl_phi', 'Please input local phi or cube file to display DelPhi potential map');
9989
10006
  });
9990
- me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10007
+ me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9991
10008
  ic.loadPhiFrom = 'phiurl';
9992
10009
  $("#" + me.pre + "dl_phiurl_tabs").tabs();
9993
10010
  $("#" + me.pre + "phiurltab1_tabs").tabs();
@@ -9996,11 +10013,11 @@ class ClickMenu {
9996
10013
  });
9997
10014
 
9998
10015
 
9999
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; e.preventDefault();
10016
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
10000
10017
  me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the map file to display electron density map');
10001
10018
  });
10002
10019
 
10003
- me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10020
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10004
10021
  thisClass.setLogCmd("export state file", false);
10005
10022
  let file_pref = Object.keys(ic.structures).join(',');
10006
10023
 
@@ -10008,19 +10025,19 @@ class ClickMenu {
10008
10025
  });
10009
10026
 
10010
10027
 
10011
- me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; e.preventDefault();
10028
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; //e.preventDefault();
10012
10029
  me.htmlCls.setHtmlCls.exportPdb();
10013
10030
 
10014
10031
  thisClass.setLogCmd("export pdb", true);
10015
10032
  });
10016
10033
 
10017
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; e.preventDefault();
10034
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; //e.preventDefault();
10018
10035
  me.htmlCls.setHtmlCls.exportSecondary();
10019
10036
 
10020
10037
  thisClass.setLogCmd("export secondary structure", true);
10021
10038
  });
10022
10039
 
10023
- me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10040
+ me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10024
10041
  let pdbStr = ic.saveFileCls.getSelectedResiduePDB();
10025
10042
 
10026
10043
  thisClass.setLogCmd("export PDB of selected residues", false);
@@ -10029,57 +10046,57 @@ class ClickMenu {
10029
10046
  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pdb', 'text', [pdbStr]);
10030
10047
  });
10031
10048
 
10032
- me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; e.preventDefault();
10049
+ me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
10033
10050
  await me.htmlCls.setHtmlCls.exportPqr();
10034
10051
  thisClass.setLogCmd("export pqr", true);
10035
10052
  });
10036
10053
 
10037
- // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10054
+ // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10038
10055
  // let bPdb = true;
10039
10056
  // await me.htmlCls.setHtmlCls.exportPqr(bPdb);
10040
10057
  // thisClass.setLogCmd("export pdbh", false);
10041
10058
  // });
10042
10059
 
10043
- me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10060
+ me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10044
10061
  let bHydrogen = false;
10045
10062
  await ic.scapCls.exportPdbProfix(bHydrogen);
10046
10063
  thisClass.setLogCmd("export pdb missing atoms", true);
10047
10064
  });
10048
10065
 
10049
- me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10066
+ me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10050
10067
  let bHydrogen = true;
10051
10068
  await ic.scapCls.exportPdbProfix(bHydrogen);
10052
10069
  thisClass.setLogCmd("export pdb hydrogen", true);
10053
10070
  });
10054
10071
 
10055
- me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10072
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10056
10073
  ic.refnumCls.exportRefnum('igstrand');
10057
10074
  thisClass.setLogCmd("export refnum igstrand", true);
10058
10075
  });
10059
10076
 
10060
- me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10077
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10061
10078
  ic.refnumCls.exportRefnum('kabat');
10062
10079
  thisClass.setLogCmd("export refnum kabat", true);
10063
10080
  });
10064
10081
 
10065
- me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10082
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10066
10083
  ic.refnumCls.exportRefnum('imgt');
10067
10084
  thisClass.setLogCmd("export refnum imgt", true);
10068
10085
  });
10069
10086
 
10070
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10087
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10071
10088
  thisClass.setLogCmd("export stl file", false);
10072
10089
  //ic.threeDPrintCls.hideStabilizer();
10073
10090
  ic.export3DCls.exportStlFile('');
10074
10091
  });
10075
10092
 
10076
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10093
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10077
10094
  thisClass.setLogCmd("export vrml file", false);
10078
10095
  //ic.threeDPrintCls.hideStabilizer();
10079
10096
  ic.export3DCls.exportVrmlFile('');
10080
10097
  });
10081
10098
 
10082
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10099
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10083
10100
  thisClass.setLogCmd("export stl stabilizer file", false);
10084
10101
  //ic.bRender = false;
10085
10102
  ic.threeDPrintCls.hideStabilizer();
@@ -10088,7 +10105,7 @@ class ClickMenu {
10088
10105
  ic.export3DCls.exportStlFile('_stab');
10089
10106
  });
10090
10107
 
10091
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10108
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10092
10109
  thisClass.setLogCmd("export vrml stabilizer file", false);
10093
10110
  //ic.bRender = false;
10094
10111
  ic.threeDPrintCls.hideStabilizer();
@@ -10097,13 +10114,13 @@ class ClickMenu {
10097
10114
  ic.export3DCls.exportVrmlFile('_stab');
10098
10115
  });
10099
10116
 
10100
- me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10117
+ me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10101
10118
  thisClass.setLogCmd("export interactions", false);
10102
10119
  if(me.cfg.mmdbid !== undefined) await ic.viewInterPairsCls.retrieveInteractionData();
10103
10120
  ic.viewInterPairsCls.exportInteractions();
10104
10121
  });
10105
10122
 
10106
- me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10123
+ me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10107
10124
  // do not record the export command
10108
10125
  //thisClass.setLogCmd("export canvas", true);
10109
10126
  thisClass.setLogCmd("export canvas", false);
@@ -10112,28 +10129,28 @@ class ClickMenu {
10112
10129
  let bPngHtml = true;
10113
10130
  await ic.shareLinkCls.shareLink(bPngHtml);
10114
10131
  });
10115
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10132
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10116
10133
  thisClass.setLogCmd("export canvas 1", true);
10117
10134
  ic.scaleFactor = 1;
10118
10135
  await ic.shareLinkCls.shareLink(true, true);
10119
10136
  });
10120
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10137
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10121
10138
  thisClass.setLogCmd("export canvas 2", true);
10122
10139
  ic.scaleFactor = 2;
10123
10140
  await ic.shareLinkCls.shareLink(true, true);
10124
10141
  });
10125
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10142
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10126
10143
  thisClass.setLogCmd("export canvas 4", true);
10127
10144
  ic.scaleFactor = 4;
10128
10145
  await ic.shareLinkCls.shareLink(true, true);
10129
10146
  });
10130
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10147
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10131
10148
  thisClass.setLogCmd("export canvas 8", true);
10132
10149
  ic.scaleFactor = 8;
10133
10150
  await ic.shareLinkCls.shareLink(true, true);
10134
10151
  });
10135
10152
 
10136
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10153
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10137
10154
  thisClass.setLogCmd("export counts", false);
10138
10155
  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
10156
  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 +10177,7 @@ class ClickMenu {
10160
10177
  ic.saveFileCls.saveFile(file_pref + '_counts.html', 'html', text);
10161
10178
  });
10162
10179
 
10163
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10180
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10164
10181
  thisClass.setLogCmd("export all selections", false);
10165
10182
 
10166
10183
  thisClass.SetChainsAdvancedMenu();
@@ -10170,7 +10187,7 @@ class ClickMenu {
10170
10187
  ic.saveFileCls.saveFile(file_pref + '_selections.txt', 'text', [text]);
10171
10188
  });
10172
10189
 
10173
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10190
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10174
10191
  thisClass.setLogCmd("export all selections with details", false);
10175
10192
 
10176
10193
  thisClass.SetChainsAdvancedMenu();
@@ -10181,32 +10198,32 @@ class ClickMenu {
10181
10198
  ic.saveFileCls.saveFile(file_pref + '_sel_details.txt', 'text', [text]);
10182
10199
  });
10183
10200
 
10184
- me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10201
+ me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10185
10202
  await ic.shareLinkCls.shareLink();
10186
10203
  });
10187
10204
 
10188
- me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10205
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10189
10206
  await ic.resizeCanvasCls.replayon();
10190
10207
  thisClass.setLogCmd("replay on", true);
10191
10208
  });
10192
- me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10209
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10193
10210
  await ic.resizeCanvasCls.replayoff();
10194
10211
  thisClass.setLogCmd("replay off", true);
10195
10212
  });
10196
10213
 
10197
- me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; e.preventDefault();
10214
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; //e.preventDefault();
10198
10215
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
10199
10216
 
10200
10217
  thisClass.applyShownMenus();
10201
10218
  });
10202
10219
 
10203
- me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; e.preventDefault();
10220
+ me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; //e.preventDefault();
10204
10221
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
10205
10222
 
10206
10223
  thisClass.applyShownMenus();
10207
10224
  });
10208
10225
 
10209
- me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; e.preventDefault();
10226
+ me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; //e.preventDefault();
10210
10227
  me.htmlCls.dialogCls.openDlg('dl_menupref', 'Select Menus');
10211
10228
 
10212
10229
  thisClass.getHiddenMenusFromCache();
@@ -10214,7 +10231,7 @@ class ClickMenu {
10214
10231
  thisClass.displayShownMenus();
10215
10232
  });
10216
10233
 
10217
- me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
10234
+ me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
10218
10235
  var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
10219
10236
  me.htmlCls.shownMenus = {};
10220
10237
  for (var checkbox of checkboxes) {
@@ -10224,21 +10241,21 @@ class ClickMenu {
10224
10241
  thisClass.applyShownMenus();
10225
10242
  });
10226
10243
 
10227
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
10244
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
10228
10245
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
10229
10246
 
10230
10247
  thisClass.applyShownMenus();
10231
10248
  thisClass.displayShownMenus();
10232
10249
  });
10233
10250
 
10234
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; e.preventDefault();
10251
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; //e.preventDefault();
10235
10252
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
10236
10253
 
10237
10254
  thisClass.applyShownMenus();
10238
10255
  thisClass.displayShownMenus();
10239
10256
  });
10240
10257
 
10241
- me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10258
+ me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10242
10259
  let menuStr = '[';
10243
10260
 
10244
10261
  //var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
@@ -10287,30 +10304,30 @@ class ClickMenu {
10287
10304
  }
10288
10305
  });
10289
10306
 
10290
- me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; e.preventDefault();
10307
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; //e.preventDefault();
10291
10308
  me.htmlCls.dialogCls.openDlg('dl_menuloadpref', 'Please input the menu preference file');
10292
10309
  });
10293
10310
 
10294
10311
 
10295
- me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10312
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10296
10313
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
10297
10314
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
10298
10315
  window.open(url, urlTarget);
10299
10316
  });
10300
10317
 
10301
- me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; e.preventDefault();
10318
+ me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; //e.preventDefault();
10302
10319
  let url = 'https://github.com/sokrypton/ColabFold';
10303
10320
  window.open(url, '_blank');
10304
10321
  });
10305
10322
 
10306
- me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10323
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10307
10324
  let url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
10308
10325
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
10309
10326
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
10310
10327
  window.open(url, urlTarget);
10311
10328
  });
10312
10329
 
10313
- me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10330
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10314
10331
  let url;
10315
10332
  if(ic.inputid === undefined) {
10316
10333
  url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
@@ -10339,7 +10356,7 @@ class ClickMenu {
10339
10356
  window.open(url, urlTarget);
10340
10357
  });
10341
10358
 
10342
- me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10359
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10343
10360
  let url;
10344
10361
  if(ic.inputid === undefined) {
10345
10362
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
@@ -10383,7 +10400,7 @@ class ClickMenu {
10383
10400
  }
10384
10401
  });
10385
10402
 
10386
- me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10403
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10387
10404
  //ic.saveFileCls.setEntrezLinks('protein');
10388
10405
  let structArray = Object.keys(ic.structures);
10389
10406
  let chainArray = Object.keys(ic.chains);
@@ -10408,19 +10425,19 @@ class ClickMenu {
10408
10425
 
10409
10426
  let thisClass = this;
10410
10427
 
10411
- me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10428
+ me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10412
10429
  await ic.showAnnoCls.showAnnotations();
10413
10430
  thisClass.setLogCmd("view annotations", true);
10414
10431
  //thisClass.setLogCmd("window annotations", true);
10415
10432
  });
10416
10433
 
10417
- me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10434
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10418
10435
  thisClass.setLogCmd("select all", true);
10419
10436
  ic.selectionCls.selectAll();
10420
10437
  ic.hlUpdateCls.removeHlAll();
10421
10438
  ic.drawCls.draw();
10422
10439
  });
10423
- me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10440
+ me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10424
10441
  thisClass.setLogCmd("clear all", true);
10425
10442
  ic.bSelectResidue = false;
10426
10443
  ic.selectionCls.selectAll();
@@ -10428,7 +10445,7 @@ class ClickMenu {
10428
10445
  ic.drawCls.draw();
10429
10446
  });
10430
10447
 
10431
- me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10448
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10432
10449
  thisClass.setLogCmd("select displayed set", true);
10433
10450
  //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
10434
10451
  ic.hAtoms = me.hashUtilsCls.cloneHash(ic.viewSelectionAtoms);
@@ -10436,106 +10453,123 @@ class ClickMenu {
10436
10453
  //ic.drawCls.draw();
10437
10454
  });
10438
10455
 
10439
- me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10456
+ me.myEventCls.onIds("#" + me.pre + "mn2_clashedYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10457
+ ic.bHideClashed = false;
10458
+ ic.annoDomainCls.showHideClashedResidues();
10459
+
10460
+ ic.drawCls.draw();
10461
+ thisClass.setLogCmd('clashed residues show', true);
10462
+ });
10463
+ me.myEventCls.onIds("#" + me.pre + "mn2_clashedNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10464
+ ic.bHideClashed = true;
10465
+
10466
+ thisClass.setClashedResidues();
10467
+ ic.annoDomainCls.showHideClashedResidues();
10468
+
10469
+ ic.drawCls.draw();
10470
+ thisClass.setLogCmd('clashed residues hide', true);
10471
+ });
10472
+
10473
+ me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10440
10474
  thisClass.setLogCmd("show all", true);
10441
10475
  ic.selectionCls.showAll();
10442
10476
  });
10443
10477
 
10444
- me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10478
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10445
10479
  if(Object.keys(ic.hAtoms).length < Object.keys(ic.atoms).length) {
10446
10480
  thisClass.setLogCmd("select complement", true);
10447
10481
  ic.resid2specCls.selectComplement();
10448
10482
  }
10449
10483
  });
10450
10484
 
10451
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10485
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10452
10486
  thisClass.setLogCmd("select main chains", true);
10453
10487
  ic.selectionCls.selectMainChains();
10454
10488
  });
10455
10489
 
10456
- me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10490
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10457
10491
  thisClass.setLogCmd("select side chains", true);
10458
10492
  ic.selectionCls.selectSideChains();
10459
10493
  });
10460
10494
 
10461
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10495
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10462
10496
  thisClass.setLogCmd("select main side chains", true);
10463
10497
  ic.selectionCls.selectMainSideChains();
10464
10498
  });
10465
10499
 
10466
- me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10500
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10467
10501
  thisClass.setLogCmd("select prop positive", true);
10468
10502
  ic.resid2specCls.selectProperty('positive');
10469
10503
  });
10470
- me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10504
+ me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10471
10505
  thisClass.setLogCmd("select prop negative", true);
10472
10506
  ic.resid2specCls.selectProperty('negative');
10473
10507
  });
10474
- me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10508
+ me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10475
10509
  thisClass.setLogCmd("select prop hydrophobic", true);
10476
10510
  ic.resid2specCls.selectProperty('hydrophobic');
10477
10511
  });
10478
- me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10512
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10479
10513
  thisClass.setLogCmd("select prop polar", true);
10480
10514
  ic.resid2specCls.selectProperty('polar');
10481
10515
  });
10482
- me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; e.preventDefault();
10516
+ me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; //e.preventDefault();
10483
10517
  me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor/pLDDT');
10484
10518
  });
10485
- me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; e.preventDefault();
10519
+ me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; //e.preventDefault();
10486
10520
  me.htmlCls.dialogCls.openDlg('dl_propbypercentout', 'Select residue based on the percentage of solvent accessilbe surface area');
10487
10521
  });
10488
- me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10522
+ me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10489
10523
  let from = $("#" + me.pre + "minbfactor").val();
10490
10524
  let to = $("#" + me.pre + "maxbfactor").val();
10491
10525
  thisClass.setLogCmd("select prop b factor | " + from + '_' + to, true);
10492
10526
  ic.resid2specCls.selectProperty('b factor', from, to);
10493
10527
  });
10494
- me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10528
+ me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10495
10529
  let from = $("#" + me.pre + "minpercentout").val();
10496
10530
  let to = $("#" + me.pre + "maxpercentout").val();
10497
10531
  thisClass.setLogCmd("select prop percent out | " + from + '_' + to, true);
10498
10532
  ic.resid2specCls.selectProperty('percent out', from, to);
10499
10533
  });
10500
10534
 
10501
- me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; e.preventDefault();
10535
+ me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; //e.preventDefault();
10502
10536
  me.htmlCls.dialogCls.openDlg('dl_alignment', 'Select residues in aligned sequences');
10503
10537
  thisClass.setLogCmd("window aligned sequences", true);
10504
10538
  });
10505
10539
 
10506
- me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; e.preventDefault();
10540
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; //e.preventDefault();
10507
10541
  me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
10508
10542
  thisClass.setLogCmd("window interaction table", true);
10509
10543
  });
10510
- me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; e.preventDefault();
10544
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; //e.preventDefault();
10511
10545
  me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
10512
10546
  thisClass.setLogCmd("window interaction graph", true);
10513
10547
  });
10514
- me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; e.preventDefault();
10548
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; //e.preventDefault();
10515
10549
  me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as map');
10516
10550
  thisClass.setLogCmd("window interaction scatterplot", true);
10517
10551
  });
10518
- me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; e.preventDefault();
10552
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; //e.preventDefault();
10519
10553
  me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
10520
10554
  thisClass.setLogCmd("window force-directed graph", true);
10521
10555
  });
10522
10556
 
10523
- me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; e.preventDefault();
10557
+ me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; //e.preventDefault();
10524
10558
  me.htmlCls.dialogCls.openDlg('dl_yournote', 'Your note about the current display');
10525
10559
  });
10526
10560
 
10527
- me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10561
+ me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10528
10562
  ic.yournote = $("#" + me.pre + "yournote").val();
10529
10563
  if(me.cfg.shownote) document.title = ic.yournote;
10530
10564
  if(!me.cfg.notebook) dialog.dialog( "close" );
10531
10565
  thisClass.setLogCmd('your note | ' + ic.yournote, true);
10532
10566
  });
10533
10567
 
10534
- me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; e.preventDefault();
10568
+ me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; //e.preventDefault();
10535
10569
  me.htmlCls.dialogCls.openDlg('dl_advanced2', 'Select by specification');
10536
10570
  });
10537
10571
 
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();
10572
+ 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
10573
  ic.definedSetsCls.showSets();
10540
10574
  thisClass.setLogCmd('defined sets', true);
10541
10575
  //thisClass.setLogCmd('window defined sets', true);
@@ -10554,7 +10588,7 @@ class ClickMenu {
10554
10588
  });
10555
10589
 
10556
10590
 
10557
- me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10591
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10558
10592
  ic.pk = 0;
10559
10593
  ic.opts['pk'] = 'no';
10560
10594
  thisClass.setLogCmd('set pk off', true);
@@ -10562,50 +10596,50 @@ class ClickMenu {
10562
10596
  ic.hlObjectsCls.removeHlObjects();
10563
10597
  });
10564
10598
 
10565
- me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10599
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10566
10600
  ic.pk = 1;
10567
10601
  ic.opts['pk'] = 'atom';
10568
10602
  thisClass.setLogCmd('set pk atom', true);
10569
10603
  });
10570
10604
 
10571
- me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10605
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10572
10606
  ic.pk = 2;
10573
10607
  ic.opts['pk'] = 'residue';
10574
10608
  thisClass.setLogCmd('set pk residue', true);
10575
10609
  });
10576
10610
 
10577
- me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10611
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10578
10612
  ic.pk = 3;
10579
10613
  ic.opts['pk'] = 'strand';
10580
10614
  thisClass.setLogCmd('set pk strand', true);
10581
10615
  });
10582
10616
 
10583
- me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10617
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10584
10618
  ic.pk = 4;
10585
10619
  ic.opts['pk'] = 'domain';
10586
10620
  thisClass.setLogCmd('set pk domain', true);
10587
10621
  });
10588
10622
 
10589
- me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10623
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10590
10624
  ic.pk = 5;
10591
10625
  ic.opts['pk'] = 'chain';
10592
10626
  thisClass.setLogCmd('set pk chain', true);
10593
10627
  });
10594
10628
 
10595
- me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; e.preventDefault();
10629
+ me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; //e.preventDefault();
10596
10630
  me.htmlCls.dialogCls.openDlg('dl_adjustmem', 'Adjust the Z-axis positions of the membrane');
10597
10631
  });
10598
10632
 
10599
- me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10633
+ me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10600
10634
  ic.selectionCls.toggleMembrane();
10601
10635
  thisClass.setLogCmd('toggle membrane', true);
10602
10636
  });
10603
10637
 
10604
- me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; e.preventDefault();
10638
+ me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; //e.preventDefault();
10605
10639
  me.htmlCls.dialogCls.openDlg('dl_selectplane', 'Select a region between two planes');
10606
10640
  });
10607
10641
 
10608
- me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10642
+ me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10609
10643
  thisClass.SetChainsAdvancedMenu();
10610
10644
 
10611
10645
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -10622,7 +10656,7 @@ class ClickMenu {
10622
10656
  $("#" + me.pre + "atomsCustomSphere2").resizable();
10623
10657
  });
10624
10658
 
10625
- me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; e.preventDefault();
10659
+ me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; //e.preventDefault();
10626
10660
  me.htmlCls.dialogCls.openDlg('dl_select_chain', 'Select Structure/Chain/Custom Selection');
10627
10661
  });
10628
10662
 
@@ -10633,242 +10667,242 @@ class ClickMenu {
10633
10667
 
10634
10668
  let thisClass = this;
10635
10669
  // mn 3
10636
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10670
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10637
10671
  ic.setOptionCls.setStyle('proteins', 'ribbon');
10638
10672
  thisClass.setLogCmd('style proteins ribbon', true);
10639
10673
  });
10640
10674
 
10641
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10675
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10642
10676
  ic.setOptionCls.setStyle('proteins', 'strand');
10643
10677
  thisClass.setLogCmd('style proteins strand', true);
10644
10678
  });
10645
10679
 
10646
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10680
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10647
10681
  ic.setOptionCls.setStyle('proteins', 'cylinder and plate');
10648
10682
  thisClass.setLogCmd('style proteins cylinder and plate', true);
10649
10683
  });
10650
10684
 
10651
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10685
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10652
10686
  ic.setOptionCls.setStyle('proteins', 'schematic');
10653
10687
  thisClass.setLogCmd('style proteins schematic', true);
10654
10688
  });
10655
10689
 
10656
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10690
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10657
10691
  ic.setOptionCls.setStyle('proteins', 'c alpha trace');
10658
10692
  thisClass.setLogCmd('style proteins c alpha trace', true);
10659
10693
  });
10660
10694
 
10661
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10695
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10662
10696
  ic.setOptionCls.setStyle('proteins', 'backbone');
10663
10697
  thisClass.setLogCmd('style proteins backbone', true);
10664
10698
  });
10665
10699
 
10666
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10700
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10667
10701
  ic.setOptionCls.setStyle('proteins', 'b factor tube');
10668
10702
  thisClass.setLogCmd('style proteins b factor tube', true);
10669
10703
  });
10670
10704
 
10671
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10705
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10672
10706
  ic.setOptionCls.setStyle('proteins', 'lines');
10673
10707
  thisClass.setLogCmd('style proteins lines', true);
10674
10708
  });
10675
10709
 
10676
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10710
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10677
10711
  ic.setOptionCls.setStyle('proteins', 'stick');
10678
10712
  thisClass.setLogCmd('style proteins stick', true);
10679
10713
  });
10680
10714
 
10681
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10715
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10682
10716
  ic.setOptionCls.setStyle('proteins', 'ball and stick');
10683
10717
  thisClass.setLogCmd('style proteins ball and stick', true);
10684
10718
  });
10685
10719
 
10686
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10720
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10687
10721
  ic.setOptionCls.setStyle('proteins', 'sphere');
10688
10722
  thisClass.setLogCmd('style proteins sphere', true);
10689
10723
  });
10690
10724
 
10691
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10725
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10692
10726
  ic.setOptionCls.setStyle('proteins', 'nothing');
10693
10727
  thisClass.setLogCmd('style proteins nothing', true);
10694
10728
  });
10695
10729
 
10696
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10730
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10697
10731
  ic.setOptionCls.setStyle('sidec', 'lines2');
10698
10732
  thisClass.setLogCmd('style sidec lines2', true);
10699
10733
  });
10700
10734
 
10701
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10735
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10702
10736
  ic.setOptionCls.setStyle('sidec', 'stick2');
10703
10737
  thisClass.setLogCmd('style sidec stick2', true);
10704
10738
  });
10705
10739
 
10706
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10740
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10707
10741
  ic.setOptionCls.setStyle('sidec', 'ball and stick2');
10708
10742
  thisClass.setLogCmd('style sidec ball and stick2', true);
10709
10743
  });
10710
10744
 
10711
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10745
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10712
10746
  ic.setOptionCls.setStyle('sidec', 'sphere2');
10713
10747
  thisClass.setLogCmd('style sidec sphere2', true);
10714
10748
  });
10715
10749
 
10716
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10750
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10717
10751
  ic.setOptionCls.setStyle('sidec', 'nothing');
10718
10752
  thisClass.setLogCmd('style sidec nothing', true);
10719
10753
  });
10720
10754
 
10721
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10755
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10722
10756
  ic.setOptionCls.setStyle('ntbase', 'lines2');
10723
10757
  thisClass.setLogCmd('style ntbase lines2', true);
10724
10758
  });
10725
10759
 
10726
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10760
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10727
10761
  ic.setOptionCls.setStyle('ntbase', 'stick2');
10728
10762
  thisClass.setLogCmd('style ntbase stick2', true);
10729
10763
  });
10730
10764
 
10731
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10765
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10732
10766
  ic.setOptionCls.setStyle('ntbase', 'ball and stick2');
10733
10767
  thisClass.setLogCmd('style ntbase ball and stick2', true);
10734
10768
  });
10735
10769
 
10736
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10770
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10737
10771
  ic.setOptionCls.setStyle('ntbase', 'sphere2');
10738
10772
  thisClass.setLogCmd('style ntbase sphere2', true);
10739
10773
  });
10740
10774
 
10741
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10775
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10742
10776
  ic.setOptionCls.setStyle('ntbase', 'nothing');
10743
10777
  thisClass.setLogCmd('style ntbase nothing', true);
10744
10778
  });
10745
10779
 
10746
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10780
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10747
10781
  ic.setOptionCls.setStyle('nucleotides', 'nucleotide cartoon');
10748
10782
  thisClass.setLogCmd('style nucleotides nucleotide cartoon', true);
10749
10783
  });
10750
10784
 
10751
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10785
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10752
10786
  ic.setOptionCls.setStyle('nucleotides', 'backbone');
10753
10787
  thisClass.setLogCmd('style nucleotides backbone', true);
10754
10788
  });
10755
10789
 
10756
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10790
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10757
10791
  ic.setOptionCls.setStyle('nucleotides', 'schematic');
10758
10792
  thisClass.setLogCmd('style nucleotides schematic', true);
10759
10793
  });
10760
10794
 
10761
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10795
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10762
10796
  ic.setOptionCls.setStyle('nucleotides', 'o3 trace');
10763
10797
  thisClass.setLogCmd('style nucleotides o3 trace', true);
10764
10798
  });
10765
10799
 
10766
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10800
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10767
10801
  ic.setOptionCls.setStyle('nucleotides', 'lines');
10768
10802
  thisClass.setLogCmd('style nucleotides lines', true);
10769
10803
  });
10770
10804
 
10771
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10805
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10772
10806
  ic.setOptionCls.setStyle('nucleotides', 'stick');
10773
10807
  thisClass.setLogCmd('style nucleotides stick', true);
10774
10808
  });
10775
10809
 
10776
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10810
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10777
10811
  ic.setOptionCls.setStyle('nucleotides', 'ball and stick');
10778
10812
  thisClass.setLogCmd('style nucleotides ball and stick', true);
10779
10813
  });
10780
10814
 
10781
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10815
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10782
10816
  ic.setOptionCls.setStyle('nucleotides', 'sphere');
10783
10817
  thisClass.setLogCmd('style nucleotides sphere', true);
10784
10818
  });
10785
10819
 
10786
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10820
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10787
10821
  ic.setOptionCls.setStyle('nucleotides', 'nothing');
10788
10822
  thisClass.setLogCmd('style nucleotides nothing', true);
10789
10823
  });
10790
10824
 
10791
- me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10825
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10792
10826
  ic.setOptionCls.setStyle('chemicals', 'lines');
10793
10827
  thisClass.setLogCmd('style chemicals lines', true);
10794
10828
  });
10795
10829
 
10796
- me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10830
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10797
10831
  ic.setOptionCls.setStyle('chemicals', 'stick');
10798
10832
  thisClass.setLogCmd('style chemicals stick', true);
10799
10833
  });
10800
10834
 
10801
- me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10835
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10802
10836
  ic.setOptionCls.setStyle('chemicals', 'ball and stick');
10803
10837
  thisClass.setLogCmd('style chemicals ball and stick', true);
10804
10838
  });
10805
10839
 
10806
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10840
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10807
10841
  ic.setOptionCls.setStyle('chemicals', 'schematic');
10808
10842
  thisClass.setLogCmd('style chemicals schematic', true);
10809
10843
  });
10810
10844
 
10811
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10845
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10812
10846
  ic.setOptionCls.setStyle('chemicals', 'sphere');
10813
10847
  thisClass.setLogCmd('style chemicals sphere', true);
10814
10848
  });
10815
10849
 
10816
- me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10850
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10817
10851
  ic.setOptionCls.setStyle('chemicals', 'nothing');
10818
10852
  thisClass.setLogCmd('style chemicals nothing', true);
10819
10853
  });
10820
10854
 
10821
10855
 
10822
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10856
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10823
10857
  ic.bGlycansCartoon = true;
10824
10858
  ic.drawCls.draw();
10825
10859
  thisClass.setLogCmd('glycans cartoon yes', true);
10826
10860
  });
10827
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10861
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10828
10862
  ic.bGlycansCartoon = false;
10829
10863
  ic.drawCls.draw();
10830
10864
  thisClass.setLogCmd('glycans cartoon no', true);
10831
10865
  });
10832
10866
 
10833
10867
 
10834
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10868
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10835
10869
  ic.showInterCls.showHydrogens();
10836
10870
  ic.drawCls.draw();
10837
10871
  thisClass.setLogCmd('hydrogens', true);
10838
10872
  });
10839
10873
 
10840
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10874
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10841
10875
  ic.showInterCls.hideHydrogens();
10842
10876
  ic.drawCls.draw();
10843
10877
  thisClass.setLogCmd('set hydrogens off', true);
10844
10878
  });
10845
10879
 
10846
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10880
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10847
10881
  ic.setOptionCls.setStyle('ions', 'sphere');
10848
10882
  thisClass.setLogCmd('style ions sphere', true);
10849
10883
  });
10850
10884
 
10851
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10885
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10852
10886
  ic.setOptionCls.setStyle('ions', 'dot');
10853
10887
  thisClass.setLogCmd('style ions dot', true);
10854
10888
  });
10855
10889
 
10856
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10890
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10857
10891
  ic.setOptionCls.setStyle('ions', 'nothing');
10858
10892
  thisClass.setLogCmd('style ions nothing', true);
10859
10893
  });
10860
10894
 
10861
- me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10895
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10862
10896
  ic.setOptionCls.setStyle('water', 'sphere');
10863
10897
  thisClass.setLogCmd('style water sphere', true);
10864
10898
  });
10865
10899
 
10866
- me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10900
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10867
10901
  ic.setOptionCls.setStyle('water', 'dot');
10868
10902
  thisClass.setLogCmd('style water dot', true);
10869
10903
  });
10870
10904
 
10871
- me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10905
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10872
10906
  ic.setOptionCls.setStyle('water', 'nothing');
10873
10907
  thisClass.setLogCmd('style water nothing', true);
10874
10908
  });
@@ -10880,16 +10914,16 @@ class ClickMenu {
10880
10914
 
10881
10915
  let thisClass = this;
10882
10916
  // mn 4
10883
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10917
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10884
10918
  ic.setOptionCls.setOption('color', 'spectrum');
10885
10919
  thisClass.setLogCmd('color spectrum', true);
10886
10920
  });
10887
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10921
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10888
10922
  ic.setOptionCls.setOption('color', 'spectrum for chains');
10889
10923
  thisClass.setLogCmd('color spectrum for chains', true);
10890
10924
  });
10891
10925
 
10892
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10926
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10893
10927
  thisClass.SetChainsAdvancedMenu();
10894
10928
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10895
10929
  if($("#" + me.pre + "atomsCustomColorSpectrumAcross").length) {
@@ -10900,7 +10934,7 @@ class ClickMenu {
10900
10934
  $("#" + me.pre + "atomsCustomColorSpectrumAcross").resizable();
10901
10935
  });
10902
10936
 
10903
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10937
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10904
10938
  thisClass.SetChainsAdvancedMenu();
10905
10939
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10906
10940
  if($("#" + me.pre + "atomsCustomColorSpectrum").length) {
@@ -10911,7 +10945,7 @@ class ClickMenu {
10911
10945
  $("#" + me.pre + "atomsCustomColorSpectrum").resizable();
10912
10946
  });
10913
10947
 
10914
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10948
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10915
10949
  thisClass.SetChainsAdvancedMenu();
10916
10950
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10917
10951
  if($("#" + me.pre + "atomsCustomColorRainbowAcross").length) {
@@ -10922,7 +10956,7 @@ class ClickMenu {
10922
10956
  $("#" + me.pre + "atomsCustomColorRainbowAcross").resizable();
10923
10957
  });
10924
10958
 
10925
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10959
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10926
10960
  thisClass.SetChainsAdvancedMenu();
10927
10961
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10928
10962
  if($("#" + me.pre + "atomsCustomColorRainbow").length) {
@@ -10933,60 +10967,60 @@ class ClickMenu {
10933
10967
  $("#" + me.pre + "atomsCustomColorRainbow").resizable();
10934
10968
  });
10935
10969
 
10936
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10970
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10937
10971
  ic.setOptionCls.setOption('color', 'rainbow');
10938
10972
 
10939
10973
  thisClass.setLogCmd('color rainbow', true);
10940
10974
  });
10941
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10975
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10942
10976
  ic.setOptionCls.setOption('color', 'rainbow for chains');
10943
10977
  thisClass.setLogCmd('color rainbow for chains', true);
10944
10978
  });
10945
10979
 
10946
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10980
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10947
10981
  ic.setOptionCls.setOption('color', 'chain');
10948
10982
  thisClass.setLogCmd('color chain', true);
10949
10983
  });
10950
- me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10984
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10951
10985
  ic.setOptionCls.setOption('color', 'structure');
10952
10986
  thisClass.setLogCmd('color structure', true);
10953
10987
  });
10954
10988
 
10955
- me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10989
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10956
10990
  ic.setOptionCls.setOption('color', 'domain');
10957
10991
  thisClass.setLogCmd('color domain', true);
10958
10992
  });
10959
10993
 
10960
- me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10994
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10961
10995
  ic.setOptionCls.setOption('color', 'defined sets');
10962
10996
  thisClass.setLogCmd('color defined sets', true);
10963
10997
  });
10964
10998
 
10965
10999
 
10966
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11000
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10967
11001
  ic.sheetcolor = 'green';
10968
11002
  ic.setOptionCls.setOption('color', 'secondary structure green');
10969
11003
  thisClass.setLogCmd('color secondary structure green', true);
10970
11004
  });
10971
11005
 
10972
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11006
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10973
11007
  ic.sheetcolor = 'yellow';
10974
11008
  ic.setOptionCls.setOption('color', 'secondary structure yellow');
10975
11009
  thisClass.setLogCmd('color secondary structure yellow', true);
10976
11010
  });
10977
11011
 
10978
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11012
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10979
11013
  ic.setOptionCls.setOption('color', 'secondary structure spectrum');
10980
11014
  thisClass.setLogCmd('color secondary structure spectrum', true);
10981
11015
  });
10982
11016
 
10983
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11017
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10984
11018
  //ic.legendClick = 2;
10985
11019
  ic.setOptionCls.setOption('color', 'residue');
10986
11020
  thisClass.setLogCmd('color residue', true);
10987
11021
  });
10988
11022
 
10989
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; e.preventDefault();
11023
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; //e.preventDefault();
10990
11024
  //ic.legendClick = 2;
10991
11025
  me.htmlCls.dialogCls.openDlg('dl_rescolorfile', 'Please input the file on residue colors');
10992
11026
  });
@@ -11032,12 +11066,12 @@ class ClickMenu {
11032
11066
  ic.addTrackCls.setCustomFile('color', ic.startColor, ic.midColor, ic.endColor);
11033
11067
  });
11034
11068
 
11035
- me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; e.preventDefault();
11069
+ me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; //e.preventDefault();
11036
11070
 
11037
11071
  me.htmlCls.dialogCls.openDlg('dl_customref', 'Set custom reference numbers');
11038
11072
  });
11039
11073
 
11040
- me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11074
+ me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11041
11075
 
11042
11076
  if(!me.cfg.notebook) dialog.dialog( "close" );
11043
11077
 
@@ -11074,82 +11108,82 @@ class ClickMenu {
11074
11108
  ic.addTrackCls.setCustomFile('tube');
11075
11109
  });
11076
11110
 
11077
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11111
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11078
11112
  //ic.legendClick = 3;
11079
11113
  ic.setOptionCls.setOption('color', 'charge');
11080
11114
  thisClass.setLogCmd('color charge', true);
11081
11115
  });
11082
11116
 
11083
- me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11117
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11084
11118
  //ic.legendClick = 4;
11085
11119
  ic.setOptionCls.setOption('color', 'hydrophobic');
11086
11120
  thisClass.setLogCmd('color hydrophobic', true);
11087
11121
  });
11088
11122
 
11089
- me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11123
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11090
11124
  //ic.legendClick = 4;
11091
11125
  ic.setOptionCls.setOption('color', 'normalized hydrophobic');
11092
11126
  thisClass.setLogCmd('color normalized hydrophobic', true);
11093
11127
  });
11094
11128
 
11095
11129
 
11096
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11130
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11097
11131
  //ic.legendClick = 1;
11098
11132
  ic.setOptionCls.setOption('color', 'atom');
11099
11133
  thisClass.setLogCmd('color atom', true);
11100
11134
  });
11101
11135
 
11102
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11136
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11103
11137
  //ic.legendClick = 5;
11104
11138
  ic.setOptionCls.setOption('color', 'b factor');
11105
11139
  thisClass.setLogCmd('color b factor', true);
11106
11140
  });
11107
11141
 
11108
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11142
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11109
11143
  //ic.legendClick = 6;
11110
11144
  ic.setOptionCls.setOption('color', 'confidence');
11111
11145
  thisClass.setLogCmd('color confidence', true);
11112
11146
  });
11113
11147
 
11114
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11148
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11115
11149
  //ic.legendClick = 6;
11116
11150
  ic.setOptionCls.setOption('color', 'ig strand');
11117
11151
  thisClass.setLogCmd('color ig strand', true);
11118
11152
  });
11119
11153
 
11120
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11154
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11121
11155
  //ic.legendClick = 6;
11122
11156
  ic.setOptionCls.setOption('color', 'ig protodomain');
11123
11157
  thisClass.setLogCmd('color ig protodomain', true);
11124
11158
  });
11125
11159
 
11126
11160
 
11127
- me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; e.preventDefault();
11161
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; //e.preventDefault();
11128
11162
  me.htmlCls.dialogCls.openDlg('dl_colorbyarea', "Color based on residue's solvent accessibility");
11129
11163
  });
11130
- me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11164
+ me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11131
11165
  ic.midpercent = $("#" + me.pre + 'midpercent').val();
11132
11166
  ic.setOptionCls.setOption('color', 'area');
11133
11167
  thisClass.setLogCmd('color area | ' + ic.midpercent, true);
11134
11168
 
11135
11169
  });
11136
11170
 
11137
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11171
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11138
11172
  ic.setOptionCls.setOption('color', 'b factor percentile');
11139
11173
  thisClass.setLogCmd('color b factor percentile', true);
11140
11174
  });
11141
11175
 
11142
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11176
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11143
11177
  ic.setOptionCls.setOption('color', 'identity');
11144
11178
  thisClass.setLogCmd('color identity', true);
11145
11179
  });
11146
11180
 
11147
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11181
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11148
11182
  ic.setOptionCls.setOption('color', 'conservation');
11149
11183
  thisClass.setLogCmd('color conservation', true);
11150
11184
  });
11151
11185
 
11152
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; e.preventDefault();
11186
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; //e.preventDefault();
11153
11187
  me.htmlCls.dialogCls.openDlg('dl_clr', 'Color picker');
11154
11188
  });
11155
11189
 
@@ -11162,22 +11196,22 @@ class ClickMenu {
11162
11196
  thisClass.setLogCmd("color " + color, true);
11163
11197
  });
11164
11198
 
11165
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11199
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11166
11200
  ic.setOptionCls.saveColor();
11167
11201
  thisClass.setLogCmd('save color', true);
11168
11202
  });
11169
11203
 
11170
- me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11204
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11171
11205
  ic.setOptionCls.applySavedColor();
11172
11206
  thisClass.setLogCmd('apply saved color', true);
11173
11207
  });
11174
11208
 
11175
- me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11209
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11176
11210
  ic.setOptionCls.saveStyle();
11177
11211
  thisClass.setLogCmd('save style', true);
11178
11212
  });
11179
11213
 
11180
- me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11214
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11181
11215
  ic.setOptionCls.applySavedStyle();
11182
11216
  thisClass.setLogCmd('apply saved style', true);
11183
11217
  });
@@ -11189,7 +11223,7 @@ class ClickMenu {
11189
11223
 
11190
11224
  let thisClass = this;
11191
11225
  // mn 5
11192
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11226
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11193
11227
  ic.bConsiderNeighbors = true;
11194
11228
  ic.applyMapCls.removeLastSurface();
11195
11229
  ic.applyMapCls.applySurfaceOptions();
@@ -11197,7 +11231,7 @@ class ClickMenu {
11197
11231
  thisClass.setLogCmd('set surface neighbors on', true);
11198
11232
  });
11199
11233
 
11200
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11234
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11201
11235
  ic.bConsiderNeighbors = false;
11202
11236
  ic.applyMapCls.removeLastSurface();
11203
11237
  ic.applyMapCls.applySurfaceOptions();
@@ -11205,48 +11239,48 @@ class ClickMenu {
11205
11239
  thisClass.setLogCmd('set surface neighbors off', true);
11206
11240
  });
11207
11241
 
11208
- me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11242
+ me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11209
11243
  ic.bConsiderNeighbors = false;
11210
11244
  ic.setOptionCls.setOption('surface', 'Van der Waals surface');
11211
11245
  thisClass.setLogCmd('set surface Van der Waals surface', true);
11212
11246
  });
11213
11247
 
11214
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11248
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11215
11249
  ic.bConsiderNeighbors = false;
11216
11250
  ic.setOptionCls.setOption('surface', 'solvent accessible surface');
11217
11251
  thisClass.setLogCmd('set surface solvent accessible surface', true);
11218
11252
  });
11219
11253
 
11220
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11254
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11221
11255
  ic.bConsiderNeighbors = false;
11222
11256
  ic.setOptionCls.setOption('surface', 'molecular surface');
11223
11257
  thisClass.setLogCmd('set surface molecular surface', true);
11224
11258
  });
11225
11259
 
11226
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11260
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11227
11261
  ic.bConsiderNeighbors = true;
11228
11262
  ic.setOptionCls.setOption('surface', 'Van der Waals surface with context');
11229
11263
  thisClass.setLogCmd('set surface Van der Waals surface with context', true);
11230
11264
  });
11231
11265
 
11232
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11266
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11233
11267
  ic.bConsiderNeighbors = true;
11234
11268
  ic.setOptionCls.setOption('surface', 'solvent accessible surface with context');
11235
11269
  thisClass.setLogCmd('set surface solvent accessible surface with context', true);
11236
11270
  });
11237
11271
 
11238
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11272
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11239
11273
  ic.bConsiderNeighbors = true;
11240
11274
  ic.setOptionCls.setOption('surface', 'molecular surface with context');
11241
11275
  thisClass.setLogCmd('set surface molecular surface with context', true);
11242
11276
  });
11243
11277
 
11244
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11278
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11245
11279
  ic.setOptionCls.setOption('surface', 'nothing');
11246
11280
  thisClass.setLogCmd('set surface nothing', true);
11247
11281
  });
11248
11282
 
11249
- $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; e.preventDefault();
11283
+ $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; //e.preventDefault();
11250
11284
  ic.transparentRenderOrder = false;
11251
11285
 
11252
11286
  let value = $(this).attr('v');
@@ -11254,7 +11288,7 @@ class ClickMenu {
11254
11288
  thisClass.setLogCmd('set surface opacity ' + value, true);
11255
11289
  });
11256
11290
 
11257
- $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; e.preventDefault();
11291
+ $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; //e.preventDefault();
11258
11292
  ic.transparentRenderOrder = true;
11259
11293
 
11260
11294
  let value = $(this).attr('v');
@@ -11262,35 +11296,35 @@ class ClickMenu {
11262
11296
  thisClass.setLogCmd('set surface2 opacity ' + value, true);
11263
11297
  });
11264
11298
 
11265
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11299
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11266
11300
  ic.setOptionCls.setOption('wireframe', 'yes');
11267
11301
  thisClass.setLogCmd('set surface wireframe on', true);
11268
11302
  });
11269
11303
 
11270
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11304
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11271
11305
  ic.setOptionCls.setOption('wireframe', 'no');
11272
11306
  thisClass.setLogCmd('set surface wireframe off', true);
11273
11307
  });
11274
11308
 
11275
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; e.preventDefault();
11309
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; //e.preventDefault();
11276
11310
  me.htmlCls.dialogCls.openDlg('dl_elecmap2fofc', '2Fo-Fc Electron Density Map');
11277
11311
  });
11278
11312
 
11279
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; e.preventDefault();
11313
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; //e.preventDefault();
11280
11314
  me.htmlCls.dialogCls.openDlg('dl_elecmapfofc', 'Fo-Fc Electron Density Map');
11281
11315
  });
11282
11316
 
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();
11317
+ 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();
11284
11318
  ic.setOptionCls.setOption('map', 'nothing');
11285
11319
  thisClass.setLogCmd('setoption map nothing', true);
11286
11320
  });
11287
11321
 
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();
11322
+ 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();
11289
11323
  ic.setOptionCls.setOption('phimap', 'nothing');
11290
11324
  thisClass.setLogCmd('setoption phimap nothing', true);
11291
11325
  });
11292
11326
 
11293
- me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11327
+ me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11294
11328
  //ic.setOptionCls.setOption('surface', 'nothing');
11295
11329
  //thisClass.setLogCmd('set surface nothing', true);
11296
11330
  ic.setOptionCls.setOption('phisurface', 'nothing');
@@ -11322,22 +11356,22 @@ class ClickMenu {
11322
11356
  thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
11323
11357
  });
11324
11358
 
11325
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11359
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11326
11360
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
11327
11361
  ic.setOptionCls.setOption('mapwireframe', 'yes');
11328
11362
  thisClass.setLogCmd('set map wireframe on', true);
11329
11363
  });
11330
11364
 
11331
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11365
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11332
11366
  ic.setOptionCls.setOption('mapwireframe', 'no');
11333
11367
  thisClass.setLogCmd('set map wireframe off', true);
11334
11368
  });
11335
11369
 
11336
- me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; e.preventDefault();
11370
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; //e.preventDefault();
11337
11371
  me.htmlCls.dialogCls.openDlg('dl_emmap', 'EM Density Map');
11338
11372
  });
11339
11373
 
11340
- me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11374
+ me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11341
11375
  ic.setOptionCls.setOption('emmap', 'nothing');
11342
11376
  thisClass.setLogCmd('setoption emmap nothing', true);
11343
11377
  });
@@ -11354,13 +11388,13 @@ class ClickMenu {
11354
11388
  thisClass.setLogCmd('set emmap percentage ' + empercentage, true);
11355
11389
  });
11356
11390
 
11357
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11391
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11358
11392
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
11359
11393
  ic.setOptionCls.setOption('emmapwireframe', 'yes');
11360
11394
  thisClass.setLogCmd('set emmap wireframe on', true);
11361
11395
  });
11362
11396
 
11363
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11397
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11364
11398
  ic.setOptionCls.setOption('emmapwireframe', 'no');
11365
11399
  thisClass.setLogCmd('set emmap wireframe off', true);
11366
11400
  });
@@ -11372,19 +11406,19 @@ class ClickMenu {
11372
11406
 
11373
11407
  let thisClass = this;
11374
11408
  // mn 6
11375
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11409
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11376
11410
  ic.bAssembly = true;
11377
11411
  thisClass.setLogCmd('set assembly on', true);
11378
11412
  ic.drawCls.draw();
11379
11413
  });
11380
11414
 
11381
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11415
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11382
11416
  ic.bAssembly = false;
11383
11417
  thisClass.setLogCmd('set assembly off', true);
11384
11418
  ic.drawCls.draw();
11385
11419
  });
11386
11420
 
11387
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11421
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11388
11422
  ic.bRunRefnumAgain = true;
11389
11423
 
11390
11424
  thisClass.setLogCmd('ig refnum on', true);
@@ -11407,11 +11441,11 @@ class ClickMenu {
11407
11441
  ic.bRunRefnumAgain = false;
11408
11442
  });
11409
11443
 
11410
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
11444
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
11411
11445
  me.htmlCls.dialogCls.openDlg('dl_igrefTpl', 'Choose an Ig template');
11412
11446
  });
11413
11447
 
11414
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; e.preventDefault();
11448
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; //e.preventDefault();
11415
11449
  if(!me.cfg.notebook) dialog.dialog( "close" );
11416
11450
 
11417
11451
  let template = $("#" + me.pre + "refTpl").val();
@@ -11421,11 +11455,11 @@ class ClickMenu {
11421
11455
  thisClass.setLogCmd('ig template ' + template, true);
11422
11456
  });
11423
11457
 
11424
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
11458
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
11425
11459
  me.htmlCls.dialogCls.openDlg('dl_alignrefTpl', 'Align with an Ig template');
11426
11460
  });
11427
11461
 
11428
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11462
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11429
11463
  if(!me.cfg.notebook) dialog.dialog( "close" );
11430
11464
 
11431
11465
  let template = $("#" + me.pre + "refTpl2").val();
@@ -11449,7 +11483,7 @@ class ClickMenu {
11449
11483
  thisClass.setLogCmd('realign on tmalign', true);
11450
11484
  });
11451
11485
 
11452
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11486
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11453
11487
  thisClass.setLogCmd('ig refnum off', true);
11454
11488
  await ic.refnumCls.hideIgRefNum();
11455
11489
 
@@ -11459,14 +11493,14 @@ class ClickMenu {
11459
11493
  // ic.drawCls.draw();
11460
11494
  });
11461
11495
 
11462
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11496
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11463
11497
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
11464
11498
  ic.selectionCls.saveSelectionIfSelected();
11465
11499
  thisClass.setLogCmd('add atom labels', true);
11466
11500
  ic.drawCls.draw();
11467
11501
  });
11468
11502
 
11469
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11503
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11470
11504
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms, true);
11471
11505
  ic.selectionCls.saveSelectionIfSelected();
11472
11506
  thisClass.setLogCmd('add element labels', true);
@@ -11474,49 +11508,49 @@ class ClickMenu {
11474
11508
  });
11475
11509
 
11476
11510
 
11477
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11511
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11478
11512
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms);
11479
11513
  ic.selectionCls.saveSelectionIfSelected();
11480
11514
  thisClass.setLogCmd('add residue labels', true);
11481
11515
  ic.drawCls.draw();
11482
11516
  });
11483
11517
 
11484
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11518
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11485
11519
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, true);
11486
11520
  ic.selectionCls.saveSelectionIfSelected();
11487
11521
  thisClass.setLogCmd('add residue number labels', true);
11488
11522
  ic.drawCls.draw();
11489
11523
  });
11490
11524
 
11491
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11525
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11492
11526
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
11493
11527
  ic.selectionCls.saveSelectionIfSelected();
11494
11528
  thisClass.setLogCmd('add reference number labels', true);
11495
11529
  ic.drawCls.draw();
11496
11530
  });
11497
11531
 
11498
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11532
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11499
11533
  ic.residueLabelsCls.addIgLabels(ic.hAtoms);
11500
11534
  ic.selectionCls.saveSelectionIfSelected();
11501
11535
  thisClass.setLogCmd('add ig labels', true);
11502
11536
  ic.drawCls.draw();
11503
11537
  });
11504
11538
 
11505
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11539
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11506
11540
  ic.analysisCls.addChainLabels(ic.hAtoms);
11507
11541
  ic.selectionCls.saveSelectionIfSelected();
11508
11542
  thisClass.setLogCmd('add chain labels', true);
11509
11543
  ic.drawCls.draw();
11510
11544
  });
11511
11545
 
11512
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11546
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11513
11547
  ic.analysisCls.addTerminiLabels(ic.hAtoms);
11514
11548
  ic.selectionCls.saveSelectionIfSelected();
11515
11549
  thisClass.setLogCmd('add terminal labels', true);
11516
11550
  ic.drawCls.draw();
11517
11551
  });
11518
11552
 
11519
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11553
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11520
11554
  me.htmlCls.dialogCls.openDlg('dl_addlabel', 'Add custom labels by selection');
11521
11555
  ic.pk = 1;
11522
11556
  ic.opts['pk'] = 'atom';
@@ -11524,19 +11558,19 @@ class ClickMenu {
11524
11558
  ic.pAtomNum = 0;
11525
11559
  });
11526
11560
 
11527
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; e.preventDefault();
11561
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; //e.preventDefault();
11528
11562
  me.htmlCls.dialogCls.openDlg('dl_addlabelselection', 'Add custom labels by the selected');
11529
11563
  });
11530
11564
 
11531
- me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; e.preventDefault();
11565
+ me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; //e.preventDefault();
11532
11566
  me.htmlCls.dialogCls.openDlg('dl_labelColor', 'Change color for all labels');
11533
11567
  });
11534
11568
 
11535
- me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; e.preventDefault();
11569
+ me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; //e.preventDefault();
11536
11570
  me.htmlCls.dialogCls.openDlg('dl_saveselection', 'Save the selected');
11537
11571
  });
11538
11572
 
11539
- me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11573
+ me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11540
11574
  ic.labelcolor = undefined;
11541
11575
  ic.pickpair = false;
11542
11576
  //ic.labels['residue'] = [];
@@ -11551,14 +11585,14 @@ class ClickMenu {
11551
11585
  ic.drawCls.draw();
11552
11586
  });
11553
11587
 
11554
- $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; e.preventDefault();
11588
+ $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; //e.preventDefault();
11555
11589
  let value = $(this).attr('v');
11556
11590
  ic.labelScale = value;
11557
11591
  ic.drawCls.draw();
11558
11592
  thisClass.setLogCmd('set label scale ' + value, true);
11559
11593
  });
11560
11594
 
11561
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11595
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11562
11596
  me.htmlCls.dialogCls.openDlg('dl_distance', 'Measure the distance of atoms');
11563
11597
  ic.pk = 1;
11564
11598
  ic.opts['pk'] = 'atom';
@@ -11568,7 +11602,7 @@ class ClickMenu {
11568
11602
  });
11569
11603
 
11570
11604
 
11571
- me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11605
+ me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11572
11606
  me.htmlCls.dialogCls.openDlg('dl_disttwosets', 'Measure the distance between two sets');
11573
11607
 
11574
11608
  thisClass.setSetsMenus('atomsCustomDist');
@@ -11576,7 +11610,7 @@ class ClickMenu {
11576
11610
  ic.bMeasureDistance = true;
11577
11611
  });
11578
11612
 
11579
- me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11613
+ me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11580
11614
  me.htmlCls.dialogCls.openDlg('dl_distmanysets', 'Measure the pairwise distances among many sets');
11581
11615
 
11582
11616
  thisClass.setSetsMenus('atomsCustomDistTable');
@@ -11584,7 +11618,7 @@ class ClickMenu {
11584
11618
  ic.bMeasureDistance = true;
11585
11619
  });
11586
11620
 
11587
- me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11621
+ me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11588
11622
  me.htmlCls.dialogCls.openDlg('dl_anglemanysets', 'Measure the pairwise angles among many sets');
11589
11623
 
11590
11624
  thisClass.setSetsMenus('atomsCustomAngleTable');
@@ -11592,7 +11626,7 @@ class ClickMenu {
11592
11626
  ic.bMeasureAngle = true;
11593
11627
  });
11594
11628
 
11595
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11629
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11596
11630
  ic.pickpair = false;
11597
11631
  let select = "set lines off";
11598
11632
  thisClass.setLogCmd(select, true);
@@ -11603,7 +11637,7 @@ class ClickMenu {
11603
11637
  ic.drawCls.draw();
11604
11638
  });
11605
11639
 
11606
- me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11640
+ me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11607
11641
  me.htmlCls.dialogCls.openDlg('dl_cartoonshape', 'Draw cartoon for a set');
11608
11642
 
11609
11643
  let bOneset = true;
@@ -11612,7 +11646,7 @@ class ClickMenu {
11612
11646
  ic.bCartoonshape = true;
11613
11647
  });
11614
11648
 
11615
- me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11649
+ me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11616
11650
  me.htmlCls.dialogCls.openDlg('dl_linebtwsets', 'Draw a line between two sets');
11617
11651
 
11618
11652
  thisClass.setSetsMenus('linebtwsets');
@@ -11621,21 +11655,21 @@ class ClickMenu {
11621
11655
  });
11622
11656
 
11623
11657
 
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();
11658
+ me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11625
11659
  //thisClass.setLogCmd('zoom selection', true);
11626
11660
  ic.transformCls.zoominSelection();
11627
11661
  ic.drawCls.draw();
11628
11662
  thisClass.setLogCmd('zoom selection', true);
11629
11663
  });
11630
11664
 
11631
- me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11665
+ me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11632
11666
  //thisClass.setLogCmd('center selection', true);
11633
11667
  ic.applyCenterCls.centerSelection();
11634
11668
  ic.drawCls.draw();
11635
11669
  thisClass.setLogCmd('center selection', true);
11636
11670
  });
11637
11671
 
11638
- me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11672
+ me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11639
11673
  //thisClass.setLogCmd('reset orientation', true);
11640
11674
  ic.transformCls.resetOrientation();
11641
11675
  //ic.setColorCls.applyOriginalColor();
@@ -11643,17 +11677,17 @@ class ClickMenu {
11643
11677
  thisClass.setLogCmd('reset orientation', true);
11644
11678
  });
11645
11679
 
11646
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11680
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11647
11681
  ic.setOptionCls.setOption('chemicalbinding', 'show');
11648
11682
  thisClass.setLogCmd('set chemicalbinding show', true);
11649
11683
  });
11650
11684
 
11651
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11685
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11652
11686
  ic.setOptionCls.setOption('chemicalbinding', 'hide');
11653
11687
  thisClass.setLogCmd('set chemicalbinding hide', true);
11654
11688
  });
11655
11689
 
11656
- me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11690
+ me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11657
11691
  if(ic.bInputfile) {
11658
11692
  alert("Side-by-Side does NOT work when the input is from a local file.");
11659
11693
  return;
@@ -11672,19 +11706,19 @@ class ClickMenu {
11672
11706
  //}
11673
11707
  });
11674
11708
 
11675
- $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; e.preventDefault();
11709
+ $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; //e.preventDefault();
11676
11710
  me.htmlCls.dialogCls.openDlg('dl_translate', 'Translate the X,Y,Z coordinates of the structure');
11677
11711
  });
11678
11712
 
11679
- $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; e.preventDefault();
11713
+ $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; //e.preventDefault();
11680
11714
  me.htmlCls.dialogCls.openDlg('dl_angle', 'Measure the angle between two vectors');
11681
11715
  });
11682
11716
 
11683
- $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; e.preventDefault();
11717
+ $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; //e.preventDefault();
11684
11718
  me.htmlCls.dialogCls.openDlg('dl_matrix', 'Apply matrix to the X,Y,Z coordinates of the structure');
11685
11719
  });
11686
11720
 
11687
- $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; e.preventDefault();
11721
+ $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; //e.preventDefault();
11688
11722
  let value = $(this).attr('v').toLowerCase();
11689
11723
  let direction = value.split(' ')[1];
11690
11724
 
@@ -11696,7 +11730,7 @@ class ClickMenu {
11696
11730
  ic.resizeCanvasCls.rotStruc(direction);
11697
11731
  });
11698
11732
 
11699
- $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; e.preventDefault();
11733
+ $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; //e.preventDefault();
11700
11734
  let value = $(this).attr('v').toLowerCase();
11701
11735
  let direction = value.split(' ')[1];
11702
11736
 
@@ -11715,21 +11749,21 @@ class ClickMenu {
11715
11749
  ic.transformCls.setRotation(axis, angle);
11716
11750
  });
11717
11751
 
11718
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11752
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11719
11753
  ic.setOptionCls.setOption('camera', 'perspective');
11720
11754
  thisClass.setLogCmd('set camera perspective', true);
11721
11755
  });
11722
11756
 
11723
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11757
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11724
11758
  ic.setOptionCls.setOption('camera', 'orthographic');
11725
11759
  thisClass.setLogCmd('set camera orthographic', true);
11726
11760
  });
11727
11761
 
11728
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11762
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11729
11763
  ic.setStyleCls.setBackground('black');
11730
11764
  });
11731
11765
 
11732
- me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11766
+ me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11733
11767
  if(ic.opts['background'] == 'black') {
11734
11768
  ic.setStyleCls.setBackground('white');
11735
11769
  }
@@ -11738,19 +11772,19 @@ class ClickMenu {
11738
11772
  }
11739
11773
  });
11740
11774
 
11741
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11775
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11742
11776
  ic.setStyleCls.setBackground('grey');
11743
11777
  });
11744
11778
 
11745
- me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11779
+ me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11746
11780
  ic.setStyleCls.setBackground('white');
11747
11781
  });
11748
11782
 
11749
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11783
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11750
11784
  ic.setStyleCls.setBackground('transparent');
11751
11785
  });
11752
11786
 
11753
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11787
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11754
11788
  //ic.setOptionCls.setOption('fog', 'yes');
11755
11789
  ic.opts['fog'] = 'yes';
11756
11790
  ic.fogCls.setFog(true);
@@ -11758,7 +11792,7 @@ class ClickMenu {
11758
11792
  thisClass.setLogCmd('set fog on', true);
11759
11793
  });
11760
11794
 
11761
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11795
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11762
11796
  //ic.setOptionCls.setOption('fog', 'no');
11763
11797
  ic.opts['fog'] = 'no';
11764
11798
  ic.fogCls.setFog(true);
@@ -11766,22 +11800,22 @@ class ClickMenu {
11766
11800
  thisClass.setLogCmd('set fog off', true);
11767
11801
  });
11768
11802
 
11769
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11803
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11770
11804
  ic.setOptionCls.setOption('slab', 'yes');
11771
11805
  thisClass.setLogCmd('set slab on', true);
11772
11806
  });
11773
11807
 
11774
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11808
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11775
11809
  ic.setOptionCls.setOption('slab', 'no');
11776
11810
  thisClass.setLogCmd('set slab off', true);
11777
11811
  });
11778
11812
 
11779
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11813
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11780
11814
  ic.setOptionCls.setOption('axis', 'yes');
11781
11815
  thisClass.setLogCmd('set axis on', true);
11782
11816
  });
11783
11817
 
11784
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11818
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11785
11819
  ic.pc1 = true;
11786
11820
 
11787
11821
  ic.axesCls.setPc1Axes();
@@ -11789,7 +11823,7 @@ class ClickMenu {
11789
11823
  });
11790
11824
 
11791
11825
 
11792
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11826
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11793
11827
  ic.pc1 = false;
11794
11828
  ic.axes = [];
11795
11829
 
@@ -11798,37 +11832,37 @@ class ClickMenu {
11798
11832
  thisClass.setLogCmd('set axis off', true);
11799
11833
  });
11800
11834
 
11801
- me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11835
+ me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11802
11836
  ic.bAxisOnly = false;
11803
11837
  await ic.symdCls.retrieveSymmetry(Object.keys(ic.structures)[0]);
11804
11838
  //me.htmlCls.dialogCls.openDlg('dl_symmetry', 'Symmetry');
11805
11839
  });
11806
11840
 
11807
- me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11841
+ me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11808
11842
  ic.bAxisOnly = false;
11809
11843
  await ic.symdCls.retrieveSymd();
11810
11844
  ic.bSymd = true;
11811
11845
 
11812
11846
  thisClass.setLogCmd('symd symmetry', true);
11813
11847
  });
11814
- me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11848
+ me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11815
11849
  ic.symdArray = [];
11816
11850
  ic.drawCls.draw();
11817
11851
  thisClass.setLogCmd('clear symd symmetry', true);
11818
11852
  });
11819
- me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11853
+ me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11820
11854
  ic.bAxisOnly = true;
11821
11855
  ic.drawCls.draw();
11822
11856
  thisClass.setLogCmd('show axis', true);
11823
11857
  });
11824
11858
 
11825
11859
 
11826
- me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11860
+ me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11827
11861
  ic.analysisCls.calculateArea();
11828
11862
  thisClass.setLogCmd('area', true);
11829
11863
  });
11830
11864
 
11831
- me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11865
+ me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11832
11866
  ic.bAxisOnly = false;
11833
11867
 
11834
11868
  let title = $("#" + me.pre + "selectSymmetry" ).val();
@@ -11838,14 +11872,14 @@ class ClickMenu {
11838
11872
  ic.drawCls.draw();
11839
11873
  thisClass.setLogCmd('symmetry ' + title, true);
11840
11874
  });
11841
- me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11875
+ me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11842
11876
  let title = 'none';
11843
11877
  ic.symmetrytitle = undefined;
11844
11878
  ic.drawCls.draw();
11845
11879
  thisClass.setLogCmd('symmetry ' + title, true);
11846
11880
  });
11847
11881
 
11848
- me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
11882
+ me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11849
11883
  thisClass.SetChainsAdvancedMenu();
11850
11884
 
11851
11885
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -11862,11 +11896,11 @@ class ClickMenu {
11862
11896
  $("#" + me.pre + "atomsCustomHbond2").resizable();
11863
11897
  });
11864
11898
 
11865
- me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; e.preventDefault();
11899
+ me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; //e.preventDefault();
11866
11900
  me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
11867
11901
  });
11868
11902
 
11869
- me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11903
+ me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
11870
11904
  thisClass.setLogCmd('set dssp sse', true);
11871
11905
  await ic.pdbParserCls.applyCommandDssp();
11872
11906
  ic.bResetAnno = true;
@@ -11879,12 +11913,12 @@ class ClickMenu {
11879
11913
  });
11880
11914
 
11881
11915
 
11882
- me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11916
+ me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11883
11917
  ic.showInterCls.hideHbondsContacts();
11884
11918
  ic.drawCls.draw();
11885
11919
  });
11886
11920
 
11887
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11921
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11888
11922
  let select = "stabilizer";
11889
11923
  ic.threeDPrintCls.addStabilizer();
11890
11924
  ic.threeDPrintCls.prepareFor3Dprint();
@@ -11892,14 +11926,14 @@ class ClickMenu {
11892
11926
  thisClass.setLogCmd(select, true);
11893
11927
  });
11894
11928
 
11895
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11929
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11896
11930
  let select = "set stabilizer off";
11897
11931
  thisClass.setLogCmd(select, true);
11898
11932
  ic.threeDPrintCls.hideStabilizer();
11899
11933
  ic.drawCls.draw();
11900
11934
  });
11901
11935
 
11902
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11936
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11903
11937
  me.htmlCls.dialogCls.openDlg('dl_stabilizer', 'Add One Stabilizer');
11904
11938
  ic.pk = 1;
11905
11939
  ic.opts['pk'] = 'atom';
@@ -11907,7 +11941,7 @@ class ClickMenu {
11907
11941
  ic.pAtomNum = 0;
11908
11942
  });
11909
11943
 
11910
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11944
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11911
11945
  me.htmlCls.dialogCls.openDlg('dl_stabilizer_rm', 'Remove One Stabilizer');
11912
11946
  ic.pk = 1;
11913
11947
  ic.opts['pk'] = 'atom';
@@ -11915,27 +11949,27 @@ class ClickMenu {
11915
11949
  ic.pAtomNum = 0;
11916
11950
  });
11917
11951
 
11918
- me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; e.preventDefault();
11952
+ me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; //e.preventDefault();
11919
11953
  me.htmlCls.dialogCls.openDlg('dl_thickness', 'Set Thickness for 3D Printing');
11920
11954
  });
11921
11955
 
11922
- me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; e.preventDefault();
11956
+ me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; //e.preventDefault();
11923
11957
  me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Style Preferences');
11924
11958
  });
11925
11959
 
11926
11960
 
11927
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11961
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11928
11962
  let select = "disulfide bonds";
11929
11963
  thisClass.setLogCmd(select, true);
11930
11964
  ic.showInterCls.showSsbonds();
11931
11965
  });
11932
11966
 
11933
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11967
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11934
11968
  ic.viewInterPairsCls.exportSsbondPairs();
11935
11969
  thisClass.setLogCmd("export disulfide bond pairs", false);
11936
11970
  });
11937
11971
 
11938
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11972
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11939
11973
  ic.opts["ssbonds"] = "no";
11940
11974
  let select = "set disulfide bonds off";
11941
11975
  thisClass.setLogCmd(select, true);
@@ -11943,7 +11977,7 @@ class ClickMenu {
11943
11977
  ic.setOptionCls.setStyle('sidec', 'nothing');
11944
11978
  });
11945
11979
 
11946
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11980
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11947
11981
  let select = "cross linkage";
11948
11982
  thisClass.setLogCmd(select, true);
11949
11983
  //ic.bShowCrossResidueBond = true;
@@ -11951,12 +11985,12 @@ class ClickMenu {
11951
11985
  ic.showInterCls.showClbonds();
11952
11986
  });
11953
11987
 
11954
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11988
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11955
11989
  ic.viewInterPairsCls.exportClbondPairs();
11956
11990
  thisClass.setLogCmd("export cross linkage pairs", false);
11957
11991
  });
11958
11992
 
11959
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11993
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11960
11994
  ic.opts["clbonds"] = "no";
11961
11995
  let select = "set cross linkage off";
11962
11996
  thisClass.setLogCmd(select, true);
@@ -12004,7 +12038,7 @@ class ClickMenu {
12004
12038
  });
12005
12039
  });
12006
12040
 
12007
- me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; e.preventDefault();
12041
+ me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; //e.preventDefault();
12008
12042
  let text = $("#" + me.pre + "jn_commands").val();
12009
12043
  navigator.clipboard.writeText(text);
12010
12044
  });
@@ -12925,6 +12959,7 @@ class SetMenu {
12925
12959
  html += this.getLink('mn2_selectedcenter', 'Zoom in Selection', 1, 1);
12926
12960
  //html += this.getLink('mn6_center', 'Center Selection', undefined, 1);
12927
12961
  html += this.getLink('mn6_center', 'Center Selection', 1, 1);
12962
+
12928
12963
  html += this.getLink('mn2_fullstru', 'View Full Structure');
12929
12964
  html += this.getLinkWrapper('mn2_alternate', 'Alternate(Key "a")', 'mn2_alternateWrap', undefined, 1);
12930
12965
 
@@ -13172,6 +13207,15 @@ class SetMenu {
13172
13207
  html += "</ul>";
13173
13208
  html += "</li>";
13174
13209
 
13210
+ if(me.cfg.cid === undefined) {
13211
+ html += this.getMenuText('mn2_clashedwrap', 'Clashed Residues', undefined, undefined, 1);
13212
+ html += "<ul>";
13213
+ html += this.getRadio('mn2_clashed', 'mn2_clashedYes', 'Show', true, undefined, 2);
13214
+ html += this.getRadio('mn2_clashed', 'mn2_clashedNo', 'Hide', undefined, undefined, 2);
13215
+ html += "</ul>";
13216
+ html += "</li>";
13217
+ }
13218
+
13175
13219
  html += this.getLink('mn3_setThickness', 'Preferences', undefined, 1);
13176
13220
 
13177
13221
  html += this.getMenuSep();
@@ -37768,7 +37812,7 @@ class Contact {
37768
37812
  //This function returns atoms within a certain "distance" (in angstrom) from the "targetAtoms".
37769
37813
  //The returned atoms are stored in a hash with atom indices as keys and 1 as values.
37770
37814
  //Only those atoms in "allAtoms" are considered.
37771
- getAtomsWithinAtom(atomlist, atomlistTarget, distance, bGetPairs, bInteraction, bInternal, bIncludeTarget) { let ic = this.icn3d; ic.icn3dui;
37815
+ getAtomsWithinAtom(atomlist, atomlistTarget, distance, bGetPairs, bInteraction, bInternal, bIncludeTarget) { let ic = this.icn3d, me = ic.icn3dui;
37772
37816
  let neighbors = this.getNeighboringAtoms(atomlist, atomlistTarget, distance, bIncludeTarget);
37773
37817
  if(bGetPairs) ic.resid2Residhash = {};
37774
37818
 
@@ -37776,6 +37820,8 @@ class Contact {
37776
37820
  for(let i in atomlistTarget) {
37777
37821
  //var oriAtom = atomlistTarget[i];
37778
37822
  let oriAtom = ic.atoms[i];
37823
+ let r1 = me.parasCls.vdwRadii[oriAtom.elem.toUpperCase()];
37824
+ let chainid1 = oriAtom.structure + '_' + oriAtom.chain;
37779
37825
 
37780
37826
  let oriCalpha = undefined, oriResidName = undefined;
37781
37827
  let oriResid = oriAtom.structure + '_' + oriAtom.chain + '_' + oriAtom.resi;
@@ -37800,6 +37846,8 @@ class Contact {
37800
37846
 
37801
37847
  for (let j in neighbors) {
37802
37848
  let atom = neighbors[j];
37849
+ let r2 = me.parasCls.vdwRadii[atom.elem.toUpperCase()];
37850
+ let chainid2 = atom.structure + '_' + atom.chain;
37803
37851
 
37804
37852
  if(bInteraction && !ic.crossstrucinter && oriAtom.structure != atom.structure) continue;
37805
37853
 
@@ -37810,7 +37858,16 @@ class Contact {
37810
37858
  //var atomDistSq = (atom.coord.x - oriAtom.coord.x) * (atom.coord.x - oriAtom.coord.x) + (atom.coord.y - oriAtom.coord.y) * (atom.coord.y - oriAtom.coord.y) + (atom.coord.z - oriAtom.coord.z) * (atom.coord.z - oriAtom.coord.z);
37811
37859
  let atomDist = atom.coord.distanceTo(oriAtom.coord);
37812
37860
 
37813
- //if(atomDistSq < maxDistSq) {
37861
+ // consider backbone clashes
37862
+ if(bInteraction && atomDist < r1 + r2
37863
+ && (oriAtom.name === "N" || oriAtom.name === "C" || oriAtom.name === "O" || (oriAtom.name === "CA" && oriAtom.elem === "C") )
37864
+ && (atom.name === "N" || atom.name === "C" || atom.name === "O" || (atom.name === "CA" && atom.elem === "C") ) ) { // clashed atoms are not counted as interactions
37865
+ // store the clashed residues
37866
+ if(!ic.chainid2clashedResidpair) ic.chainid2clashedResidpair = {};
37867
+
37868
+ ic.chainid2clashedResidpair[chainid1 + '_' + oriAtom.resi + '|' + chainid2 + '_' + atom.resi] = '0|0';
37869
+ }
37870
+
37814
37871
  if(atomDist < distance) {
37815
37872
  ret[atom.serial] = atom;
37816
37873
  let calpha = undefined, residName = undefined;
@@ -42751,7 +42808,7 @@ class AnnoDomain {
42751
42808
  this.icn3d = icn3d;
42752
42809
  }
42753
42810
 
42754
- showDomainPerStructure(index) { let ic = this.icn3d; ic.icn3dui;
42811
+ showDomainPerStructure(index, bNotShowDomain) { let ic = this.icn3d; ic.icn3dui;
42755
42812
  let thisClass = this;
42756
42813
  //var chnid = Object.keys(ic.protein_chainid)[0];
42757
42814
  //var pdbid = chnid.substr(0, chnid.indexOf('_'));
@@ -42783,7 +42840,8 @@ class AnnoDomain {
42783
42840
  data.domains = {};
42784
42841
  for(let chainid in ic.chains) {
42785
42842
  let structure = chainid.substr(0, chainid.indexOf('_'));
42786
- if(pdbid == structure && ic.protein_chainid.hasOwnProperty(chainid)) {
42843
+ // if(pdbid == structure && ic.protein_chainid.hasOwnProperty(chainid)) {
42844
+ if(pdbid == structure) {
42787
42845
  data.domains[chainid] = {};
42788
42846
  data.domains[chainid].domains = [];
42789
42847
 
@@ -42810,10 +42868,10 @@ class AnnoDomain {
42810
42868
  }
42811
42869
 
42812
42870
  ic.mmdb_dataArray[index] = data;
42813
- let bCalcDirect = true;
42814
- for(let chnid in ic.protein_chainid) {
42871
+ // for(let chnid in ic.protein_chainid) {
42872
+ for(let chnid in ic.chains) {
42815
42873
  if(chnid.indexOf(pdbid) !== -1) {
42816
- thisClass.showDomainWithData(chnid, ic.mmdb_dataArray[index], bCalcDirect);
42874
+ thisClass.showDomainWithData(chnid, ic.mmdb_dataArray[index], bNotShowDomain);
42817
42875
  }
42818
42876
  }
42819
42877
 
@@ -42823,7 +42881,7 @@ class AnnoDomain {
42823
42881
  }
42824
42882
 
42825
42883
  //Show the annotations of 3D domains.
42826
- showDomainAll() { let ic = this.icn3d; ic.icn3dui;
42884
+ showDomainAll(bNotShowDomain) { let ic = this.icn3d; ic.icn3dui;
42827
42885
  //var chnid = Object.keys(ic.protein_chainid)[0];
42828
42886
  //var pdbid = chnid.substr(0, chnid.indexOf('_'));
42829
42887
  let pdbArray = Object.keys(ic.structures);
@@ -42835,7 +42893,7 @@ class AnnoDomain {
42835
42893
  }
42836
42894
 
42837
42895
  for(let i = 0, il = pdbArray.length; i < il; ++i) {
42838
- this.showDomainPerStructure(i);
42896
+ this.showDomainPerStructure(i, bNotShowDomain);
42839
42897
  }
42840
42898
  }
42841
42899
 
@@ -42853,7 +42911,7 @@ class AnnoDomain {
42853
42911
  return resi;
42854
42912
  }
42855
42913
 
42856
- showDomainWithData(chnid, data, bCalcDirect) { let ic = this.icn3d, me = ic.icn3dui;
42914
+ showDomainWithData(chnid, data, bNotShowDomain) { let ic = this.icn3d, me = ic.icn3dui;
42857
42915
  let html = '<div id="' + ic.pre + chnid + '_domainseq_sequence" class="icn3d-dl_sequence">';
42858
42916
  let html2 = html;
42859
42917
  let html3 = html;
@@ -42927,6 +42985,26 @@ class AnnoDomain {
42927
42985
  }
42928
42986
  }
42929
42987
 
42988
+ if(ic.chainid2clashedResidpair) { //assign domain size to each residue in the clashed residues
42989
+ for(let residpair in ic.chainid2clashedResidpair) {
42990
+ let residArray = residpair.split('|');
42991
+ let valueArray = ic.chainid2clashedResidpair[residpair].split('|');
42992
+
42993
+ for(let i = 0, il = residArray.length; i < il; ++i) {
42994
+ let chainid = residArray[i][0] + '_' + residArray[i][1];
42995
+
42996
+ if(chainid == chnid) {
42997
+ let resi = residArray[i][3];
42998
+ if(resiHash.hasOwnProperty(resi)) {
42999
+ ic.chainid2clashedResidpair[residpair] = (i == 0) ? resCnt + '|' + valueArray[1] : valueArray[1] + '|' + resCnt;
43000
+ }
43001
+ }
43002
+ }
43003
+ }
43004
+ }
43005
+
43006
+ if(bNotShowDomain) continue;
43007
+
42930
43008
  // save 3D domain info for node.js script
42931
43009
  if(me.bNode) {
42932
43010
  let domainName = '3D domain ' +(index+1).toString();
@@ -43021,12 +43099,103 @@ class AnnoDomain {
43021
43099
  html += htmlTmp;
43022
43100
  html2 += htmlTmp;
43023
43101
  }
43024
- html += '</div>';
43025
- html2 += '</div>';
43026
- html3 += '</div>';
43027
- $("#" + ic.pre + "dt_domain_" + chnid).html(html);
43028
- $("#" + ic.pre + "ov_domain_" + chnid).html(html2);
43029
- $("#" + ic.pre + "tt_domain_" + chnid).html(html3);
43102
+
43103
+ if(!bNotShowDomain) {
43104
+ html += '</div>';
43105
+ html2 += '</div>';
43106
+ html3 += '</div>';
43107
+ $("#" + ic.pre + "dt_domain_" + chnid).html(html);
43108
+ $("#" + ic.pre + "ov_domain_" + chnid).html(html2);
43109
+ $("#" + ic.pre + "tt_domain_" + chnid).html(html3);
43110
+ }
43111
+
43112
+ // hide clashed residues between two chains
43113
+ if(bNotShowDomain && ic.chainid2clashedResidpair) {
43114
+ ic.clashedResidHash = {};
43115
+ for(let residpair in ic.chainid2clashedResidpair) {
43116
+ let residArray = residpair.split('|');
43117
+ let valueArray = ic.chainid2clashedResidpair[residpair].split('|');
43118
+
43119
+ if(parseInt(valueArray[0]) < parseInt(valueArray[1])) {
43120
+ ic.clashedResidHash[residArray[0]] = 1;
43121
+ }
43122
+ else {
43123
+ ic.clashedResidHash[residArray[1]] = 1;
43124
+ }
43125
+ }
43126
+
43127
+ // expand clashed residues to the SSE and the loops connecting the SSE
43128
+ let addResidHash = {}, tmpHash = {};
43129
+ for(let resid in ic.clashedResidHash) {
43130
+ let pos = resid.lastIndexOf('_');
43131
+ let resi = parseInt(resid.substr(pos + 1));
43132
+ let chainid = resid.substr(0, pos);
43133
+ let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
43134
+ if(atom.ss == 'coil') {
43135
+ tmpHash = this.getMoreResidues(resi, chainid, 1, 'not coil');
43136
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
43137
+ tmpHash = this.getMoreResidues(resi, chainid, -1, 'not coil');
43138
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
43139
+ }
43140
+ else {
43141
+ tmpHash = this.getMoreResidues(resi, chainid, 1, 'ssbegin');
43142
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
43143
+ tmpHash = this.getMoreResidues(resi, chainid, -1, 'ssend');
43144
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
43145
+ }
43146
+ }
43147
+
43148
+ ic.clashedResidHash = me.hashUtilsCls.unionHash(ic.clashedResidHash, addResidHash);
43149
+ }
43150
+ }
43151
+
43152
+ showHideClashedResidues() { let ic = this.icn3d, me = ic.icn3dui;
43153
+ // show or hide clashed residues
43154
+ if(ic.clashedResidHash && Object.keys(ic.clashedResidHash).length > 0) {
43155
+ let tmpHash = {};
43156
+ for(let resid in ic.clashedResidHash) {
43157
+ tmpHash = me.hashUtilsCls.unionHash(tmpHash, ic.residues[resid]);
43158
+ }
43159
+
43160
+ if(ic.bHideClashed) {
43161
+ ic.hAtoms = me.hashUtilsCls.exclHash(ic.hAtoms, tmpHash);
43162
+ }
43163
+ else {
43164
+ ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, tmpHash);
43165
+ }
43166
+
43167
+ // if(ic.bHideClashed) ic.definedSetsCls.setMode('selection');
43168
+ ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
43169
+ }
43170
+ }
43171
+
43172
+ getMoreResidues(resi, chainid, direction, condition) { let ic = this.icn3d; ic.icn3dui;
43173
+ let addResidHash = {};
43174
+ for(let i = 1; i < 100; ++i) {
43175
+ let resid2 = chainid + '_' + (resi + direction * i).toString();
43176
+ let atom2 = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid2]);
43177
+ if(atom2) {
43178
+ let bBreak = false;
43179
+ if(condition == 'not coil') {
43180
+ bBreak = (atom2.ss != 'coil');
43181
+ }
43182
+ else if(condition == 'ssbegin') {
43183
+ bBreak = atom2.ssbegin;
43184
+ }
43185
+ else if(condition == 'ssend') {
43186
+ bBreak = atom2.ssend;
43187
+ }
43188
+
43189
+ if(bBreak) {
43190
+ break;
43191
+ }
43192
+ else {
43193
+ addResidHash[resid2] = 1;
43194
+ }
43195
+ }
43196
+ }
43197
+
43198
+ return addResidHash;
43030
43199
  }
43031
43200
 
43032
43201
  }
@@ -51959,7 +52128,6 @@ class ShowInter {
51959
52128
  pickCustomSphere_base(radius, atomlistTarget, otherAtoms, bSphereCalc, bInteraction, type, select, bGetPairs, bIncludeTarget) { let ic = this.icn3d, me = ic.icn3dui; // ic.pAtom is set already
51960
52129
  let atoms;
51961
52130
  if(bInteraction) {
51962
- // atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, otherAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
51963
52131
  atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.hash2Atoms(otherAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
51964
52132
  ic.resid2ResidhashInteractions = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
51965
52133
  }
@@ -54220,7 +54388,7 @@ class ChainalignParser {
54220
54388
  return hAtomsAll;
54221
54389
  }
54222
54390
 
54223
- downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse) { let ic = this.icn3d, me = ic.icn3dui;
54391
+ async downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse) { let ic = this.icn3d, me = ic.icn3dui;
54224
54392
  // set trans and rotation matrix
54225
54393
  ic.t_trans_add = [];
54226
54394
  ic.q_trans_sub = [];
@@ -54272,9 +54440,22 @@ class ChainalignParser {
54272
54440
  return;
54273
54441
  }
54274
54442
  else {
54275
- /// if(ic.deferredRealignByStruct !== undefined) ic.deferredRealignByStruct.resolve();
54276
- if(ic.bRender) alert("These structures can NOT be aligned...");
54277
- return;
54443
+ if(me.cfg.aligntool == 'tmalign') {
54444
+ if(ic.bRender) alert("These structures can NOT be aligned...");
54445
+ return;
54446
+ }
54447
+ else {
54448
+ console.log("These structures can NOT be aligned with VAST. Realign the chains with TM-align.");
54449
+
54450
+ // ic.hAtoms = {};
54451
+ // for(let i = 0, il = chainidPairArray.length; i < il; ++i) {
54452
+ // ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[chainidPairArray[i]]);
54453
+ // }
54454
+
54455
+ me.cfg.aligntool = 'tmalign';
54456
+ await ic.realignParserCls.realignOnStructAlign();
54457
+ return;
54458
+ }
54278
54459
  }
54279
54460
  }
54280
54461
 
@@ -67750,6 +67931,19 @@ class ApplyCommand {
67750
67931
  ic.bGlycansCartoon = false;
67751
67932
  }
67752
67933
  }
67934
+ else if(command.indexOf('clashed residues') == 0) {
67935
+ let value = command.substr(command.lastIndexOf(' ') + 1);
67936
+
67937
+ if(value == 'show') {
67938
+ ic.bHideClashed = false;
67939
+ ic.annoDomainCls.showHideClashedResidues();
67940
+ }
67941
+ else {
67942
+ ic.bHideClashed = true;
67943
+ me.htmlCls.clickMenuCls.setClashedResidues();
67944
+ ic.annoDomainCls.showHideClashedResidues();
67945
+ }
67946
+ }
67753
67947
  else if(command.indexOf('save html') == 0) {
67754
67948
  let id = command.substr(command.lastIndexOf(' ') + 1);
67755
67949
  me.htmlCls.eventsCls.saveHtml(id);
@@ -80011,7 +80205,7 @@ class ShareLink {
80011
80205
  }
80012
80206
 
80013
80207
  shareLinkUrl(bAllCommands, bOutputCmd, bStatefile) { let ic = this.icn3d, me = ic.icn3dui;
80014
- let url = me.htmlCls.baseUrl + "icn3d/?";
80208
+ let url = me.htmlCls.baseUrl + "icn3d/full_" + me.REVISION + ".html?";
80015
80209
  let outputCmd = '';
80016
80210
  if(me.cfg.bSidebyside) url = me.htmlCls.baseUrl + "icn3d/full2.html?";
80017
80211
 
@@ -80166,6 +80360,7 @@ class ShareLink {
80166
80360
  else if(prevCommandStr.indexOf('pickatom') !== -1 && commandStr.indexOf('pickatom') !== -1) ;
80167
80361
  // remove all "show selection" except the last one
80168
80362
  else if(prevCommandStr == 'show selection' && ic.commands.slice(i).toString().indexOf('show selection') != -1) ;
80363
+ else if(prevCommandStr == commandStr) ;
80169
80364
  else if(prevCommandStr.indexOf(toggleStr) !== -1) {
80170
80365
  ++cntToggle;
80171
80366
  }
@@ -83122,7 +83317,7 @@ class iCn3DUI {
83122
83317
  //even when multiple iCn3D viewers are shown together.
83123
83318
  this.pre = this.cfg.divid + "_";
83124
83319
 
83125
- this.REVISION = '3.36.1';
83320
+ this.REVISION = '3.37.0';
83126
83321
 
83127
83322
  // In nodejs, iCn3D defines "window = {navigator: {}}"
83128
83323
  this.bNode = (Object.keys(window).length < 2) ? true : false;