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.js CHANGED
@@ -8917,102 +8917,119 @@ class ClickMenu {
8917
8917
  ic.bRunRefnumAgain = false;
8918
8918
  }
8919
8919
 
8920
+ setClashedResidues() { let me = this.icn3dui, ic = me.icn3d;
8921
+ // check contacts between all chains
8922
+ let chainidArray = Object.keys(ic.chains);
8923
+ let radius = 4, bSphereCalc = false, bInteraction = true;
8924
+ for(let i = 0, il = chainidArray.length; i < il; ++i) {
8925
+ let chainid1 = chainidArray[i];
8926
+ for(let j = i + 1, jl = chainidArray.length; j < jl; ++j) {
8927
+ let chainid2 = chainidArray[j];
8928
+ ic.showInterCls.pickCustomSphere_base(radius, ic.chains[chainid1], ic.chains[chainid2], bSphereCalc, bInteraction);
8929
+ }
8930
+ }
8931
+
8932
+ // use domains to determine which one to hide
8933
+ let bNotShowDomain = true;
8934
+ ic.annoDomainCls.showDomainAll(bNotShowDomain);
8935
+ }
8936
+
8920
8937
  clickMenu1() { let me = this.icn3dui; me.icn3d;
8921
8938
  if(me.bNode) return;
8922
8939
 
8923
8940
  let thisClass = this;
8924
8941
  //mn 1
8925
8942
  // clkMn1_mmtfid: function() {
8926
- me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; e.preventDefault();
8943
+ me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; //e.preventDefault();
8927
8944
  me.htmlCls.dialogCls.openDlg('dl_vastplus', 'Please input PDB ID for VAST+');
8928
8945
  });
8929
8946
 
8930
- me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; e.preventDefault();
8947
+ me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; //e.preventDefault();
8931
8948
  me.htmlCls.dialogCls.openDlg('dl_vast', 'Please input chain or PDB file for VAST');
8932
8949
  });
8933
8950
 
8934
- me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; e.preventDefault();
8951
+ me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; //e.preventDefault();
8935
8952
  me.htmlCls.dialogCls.openDlg('dl_foldseek', 'Submit your selection to Foldseek');
8936
8953
  });
8937
8954
 
8938
- me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; e.preventDefault();
8955
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; //e.preventDefault();
8939
8956
  me.htmlCls.dialogCls.openDlg('dl_mmtfid', 'Please input BCIF/MMTF ID');
8940
8957
  });
8941
8958
 
8942
8959
  // clkMn1_pdbid: function() {
8943
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; e.preventDefault();
8960
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; //e.preventDefault();
8944
8961
  me.htmlCls.dialogCls.openDlg('dl_pdbid', 'Please input PDB ID');
8945
8962
  });
8946
8963
 
8947
- me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; e.preventDefault();
8964
+ me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; //e.preventDefault();
8948
8965
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
8949
8966
  });
8950
8967
 
8951
- me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
8968
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; //e.preventDefault();
8952
8969
  me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI Protein Accession');
8953
8970
  });
8954
8971
 
8955
- me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
8972
+ me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; //e.preventDefault();
8956
8973
  me.htmlCls.dialogCls.openDlg('dl_opmid', 'Please input OPM PDB ID');
8957
8974
  });
8958
8975
 
8959
- me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; e.preventDefault();
8976
+ me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; //e.preventDefault();
8960
8977
  me.htmlCls.dialogCls.openDlg('dl_align', 'Align two PDB structures');
8961
8978
  });
8962
8979
 
8963
- me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; e.preventDefault();
8980
+ me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; //e.preventDefault();
8964
8981
  me.htmlCls.dialogCls.openDlg('dl_alignaf', 'Align two AlphaFold structures');
8965
8982
  });
8966
8983
 
8967
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; e.preventDefault();
8984
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; //e.preventDefault();
8968
8985
  me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
8969
8986
  });
8970
8987
 
8971
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; e.preventDefault();
8988
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; //e.preventDefault();
8972
8989
  me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
8973
8990
  });
8974
8991
 
8975
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; e.preventDefault();
8992
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; //e.preventDefault();
8976
8993
  me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
8977
8994
  });
8978
8995
 
8979
- me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; e.preventDefault();
8996
+ me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; //e.preventDefault();
8980
8997
  me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
8981
8998
  });
8982
8999
 
8983
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; e.preventDefault();
9000
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; //e.preventDefault();
8984
9001
  //me = me.setIcn3dui($(this).attr('id'));
8985
9002
  me.htmlCls.dialogCls.openDlg('dl_pdbfile', 'Please input PDB File');
8986
9003
  });
8987
- me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; e.preventDefault();
9004
+ me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; //e.preventDefault();
8988
9005
  //me = me.setIcn3dui($(this).attr('id'));
8989
9006
  me.htmlCls.dialogCls.openDlg('dl_pdbfile_app', 'Please append PDB Files');
8990
9007
  });
8991
9008
 
8992
- me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; e.preventDefault();
9009
+ me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; //e.preventDefault();
8993
9010
  me.htmlCls.dialogCls.openDlg('dl_mol2file', 'Please input Mol2 File');
8994
9011
  });
8995
9012
 
8996
- me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; e.preventDefault();
9013
+ me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; //e.preventDefault();
8997
9014
  me.htmlCls.dialogCls.openDlg('dl_sdffile', 'Please input SDF File');
8998
9015
  });
8999
9016
 
9000
- me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; e.preventDefault();
9017
+ me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; //e.preventDefault();
9001
9018
  me.htmlCls.dialogCls.openDlg('dl_xyzfile', 'Please input XYZ File');
9002
9019
  });
9003
9020
 
9004
- me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; e.preventDefault();
9021
+ me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; //e.preventDefault();
9005
9022
  me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold PAE File');
9006
9023
  });
9007
9024
 
9008
- me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; e.preventDefault();
9025
+ me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; //e.preventDefault();
9009
9026
  me.htmlCls.dialogCls.openDlg('dl_urlfile', 'Load data by URL');
9010
9027
  });
9011
9028
 
9012
- me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
9029
+ me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; //e.preventDefault();
9013
9030
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
9014
9031
  });
9015
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9032
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9016
9033
  let url = $("#" + me.pre + "sharelinkurl").val();
9017
9034
  thisClass.setLogCmd("open " + url, false);
9018
9035
  localStorage.setItem('fixedversion', '1');
@@ -9020,73 +9037,73 @@ class ClickMenu {
9020
9037
  window.open(url, urlTarget);
9021
9038
  });
9022
9039
 
9023
- me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; e.preventDefault();
9040
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; //e.preventDefault();
9024
9041
  me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please append mmCIF File');
9025
9042
  });
9026
9043
 
9027
- me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; e.preventDefault();
9044
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
9028
9045
  me.htmlCls.dialogCls.openDlg('dl_mmcifid', 'Please input mmCIF ID');
9029
9046
  });
9030
9047
 
9031
- me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; e.preventDefault();
9048
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; //e.preventDefault();
9032
9049
  me.htmlCls.dialogCls.openDlg('dl_mmdbid', 'Please input MMDB or PDB ID');
9033
9050
  });
9034
9051
 
9035
- me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; e.preventDefault();
9052
+ me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; //e.preventDefault();
9036
9053
  me.htmlCls.dialogCls.openDlg('dl_mmdbafid', 'Please input PDB/MMDB/AlphaFold UniProt IDs');
9037
9054
  });
9038
9055
 
9039
- me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; e.preventDefault();
9056
+ me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; //e.preventDefault();
9040
9057
  me.htmlCls.dialogCls.openDlg('dl_blast_rep_id', 'Align sequence to structure');
9041
9058
  });
9042
9059
 
9043
- me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; e.preventDefault();
9060
+ me.myEventCls.onIds("#" + me.pre + "mn1_esmfold", "click", function(e) { me.icn3d; //e.preventDefault();
9044
9061
  me.htmlCls.dialogCls.openDlg('dl_esmfold', 'Sequence to structure prediction with ESMFold');
9045
9062
  });
9046
9063
 
9047
- me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; e.preventDefault();
9064
+ me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; //e.preventDefault();
9048
9065
  me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein or gene name');
9049
9066
  });
9050
9067
 
9051
- me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
9068
+ me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; //e.preventDefault();
9052
9069
  me.htmlCls.dialogCls.openDlg('dl_cid', 'Please input PubChem Compound');
9053
9070
  });
9054
9071
 
9055
- me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; e.preventDefault();
9072
+ me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; //e.preventDefault();
9056
9073
  me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please append PNG images');
9057
9074
  });
9058
9075
 
9059
- me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; e.preventDefault();
9076
+ me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; //e.preventDefault();
9060
9077
  me.htmlCls.dialogCls.openDlg('dl_state', 'Please input the state file');
9061
9078
  });
9062
9079
 
9063
- me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; e.preventDefault();
9080
+ me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; //e.preventDefault();
9064
9081
  me.htmlCls.dialogCls.openDlg('dl_selection', 'Please input the selection file');
9065
9082
  });
9066
9083
 
9067
- me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; e.preventDefault();
9084
+ me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; //e.preventDefault();
9068
9085
  me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
9069
9086
  });
9070
9087
 
9071
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; e.preventDefault();
9088
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
9072
9089
  me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
9073
9090
  });
9074
9091
 
9075
9092
 
9076
- me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9093
+ me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9077
9094
  ic.loadPhiFrom = 'delphi';
9078
9095
  $("#" + me.pre + "dl_delphi_tabs").tabs();
9079
9096
  me.htmlCls.dialogCls.openDlg('dl_delphi', 'Please set parameters to display DelPhi potential map');
9080
9097
  });
9081
9098
 
9082
- me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9099
+ me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9083
9100
  ic.loadPhiFrom = 'phi';
9084
9101
  $("#" + me.pre + "dl_phi_tabs").tabs();
9085
9102
  $("#" + me.pre + "phitab1_tabs").tabs();
9086
9103
  $("#" + me.pre + "phitab2_tabs").tabs();
9087
9104
  me.htmlCls.dialogCls.openDlg('dl_phi', 'Please input local phi or cube file to display DelPhi potential map');
9088
9105
  });
9089
- me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9106
+ me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9090
9107
  ic.loadPhiFrom = 'phiurl';
9091
9108
  $("#" + me.pre + "dl_phiurl_tabs").tabs();
9092
9109
  $("#" + me.pre + "phiurltab1_tabs").tabs();
@@ -9095,11 +9112,11 @@ class ClickMenu {
9095
9112
  });
9096
9113
 
9097
9114
 
9098
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; e.preventDefault();
9115
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
9099
9116
  me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the map file to display electron density map');
9100
9117
  });
9101
9118
 
9102
- me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9119
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9103
9120
  thisClass.setLogCmd("export state file", false);
9104
9121
  let file_pref = Object.keys(ic.structures).join(',');
9105
9122
 
@@ -9107,19 +9124,19 @@ class ClickMenu {
9107
9124
  });
9108
9125
 
9109
9126
 
9110
- me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; e.preventDefault();
9127
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; //e.preventDefault();
9111
9128
  me.htmlCls.setHtmlCls.exportPdb();
9112
9129
 
9113
9130
  thisClass.setLogCmd("export pdb", true);
9114
9131
  });
9115
9132
 
9116
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; e.preventDefault();
9133
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; //e.preventDefault();
9117
9134
  me.htmlCls.setHtmlCls.exportSecondary();
9118
9135
 
9119
9136
  thisClass.setLogCmd("export secondary structure", true);
9120
9137
  });
9121
9138
 
9122
- me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9139
+ me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9123
9140
  let pdbStr = ic.saveFileCls.getSelectedResiduePDB();
9124
9141
 
9125
9142
  thisClass.setLogCmd("export PDB of selected residues", false);
@@ -9128,57 +9145,57 @@ class ClickMenu {
9128
9145
  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pdb', 'text', [pdbStr]);
9129
9146
  });
9130
9147
 
9131
- me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; e.preventDefault();
9148
+ me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
9132
9149
  await me.htmlCls.setHtmlCls.exportPqr();
9133
9150
  thisClass.setLogCmd("export pqr", true);
9134
9151
  });
9135
9152
 
9136
- // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9153
+ // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9137
9154
  // let bPdb = true;
9138
9155
  // await me.htmlCls.setHtmlCls.exportPqr(bPdb);
9139
9156
  // thisClass.setLogCmd("export pdbh", false);
9140
9157
  // });
9141
9158
 
9142
- me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9159
+ me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9143
9160
  let bHydrogen = false;
9144
9161
  await ic.scapCls.exportPdbProfix(bHydrogen);
9145
9162
  thisClass.setLogCmd("export pdb missing atoms", true);
9146
9163
  });
9147
9164
 
9148
- me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9165
+ me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9149
9166
  let bHydrogen = true;
9150
9167
  await ic.scapCls.exportPdbProfix(bHydrogen);
9151
9168
  thisClass.setLogCmd("export pdb hydrogen", true);
9152
9169
  });
9153
9170
 
9154
- me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9171
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9155
9172
  ic.refnumCls.exportRefnum('igstrand');
9156
9173
  thisClass.setLogCmd("export refnum igstrand", true);
9157
9174
  });
9158
9175
 
9159
- me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9176
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9160
9177
  ic.refnumCls.exportRefnum('kabat');
9161
9178
  thisClass.setLogCmd("export refnum kabat", true);
9162
9179
  });
9163
9180
 
9164
- me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9181
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportImgt", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9165
9182
  ic.refnumCls.exportRefnum('imgt');
9166
9183
  thisClass.setLogCmd("export refnum imgt", true);
9167
9184
  });
9168
9185
 
9169
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9186
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9170
9187
  thisClass.setLogCmd("export stl file", false);
9171
9188
  //ic.threeDPrintCls.hideStabilizer();
9172
9189
  ic.export3DCls.exportStlFile('');
9173
9190
  });
9174
9191
 
9175
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9192
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9176
9193
  thisClass.setLogCmd("export vrml file", false);
9177
9194
  //ic.threeDPrintCls.hideStabilizer();
9178
9195
  ic.export3DCls.exportVrmlFile('');
9179
9196
  });
9180
9197
 
9181
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9198
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9182
9199
  thisClass.setLogCmd("export stl stabilizer file", false);
9183
9200
  //ic.bRender = false;
9184
9201
  ic.threeDPrintCls.hideStabilizer();
@@ -9187,7 +9204,7 @@ class ClickMenu {
9187
9204
  ic.export3DCls.exportStlFile('_stab');
9188
9205
  });
9189
9206
 
9190
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9207
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9191
9208
  thisClass.setLogCmd("export vrml stabilizer file", false);
9192
9209
  //ic.bRender = false;
9193
9210
  ic.threeDPrintCls.hideStabilizer();
@@ -9196,13 +9213,13 @@ class ClickMenu {
9196
9213
  ic.export3DCls.exportVrmlFile('_stab');
9197
9214
  });
9198
9215
 
9199
- me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9216
+ me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9200
9217
  thisClass.setLogCmd("export interactions", false);
9201
9218
  if(me.cfg.mmdbid !== undefined) await ic.viewInterPairsCls.retrieveInteractionData();
9202
9219
  ic.viewInterPairsCls.exportInteractions();
9203
9220
  });
9204
9221
 
9205
- me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9222
+ me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9206
9223
  // do not record the export command
9207
9224
  //thisClass.setLogCmd("export canvas", true);
9208
9225
  thisClass.setLogCmd("export canvas", false);
@@ -9211,28 +9228,28 @@ class ClickMenu {
9211
9228
  let bPngHtml = true;
9212
9229
  await ic.shareLinkCls.shareLink(bPngHtml);
9213
9230
  });
9214
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9231
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9215
9232
  thisClass.setLogCmd("export canvas 1", true);
9216
9233
  ic.scaleFactor = 1;
9217
9234
  await ic.shareLinkCls.shareLink(true, true);
9218
9235
  });
9219
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9236
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9220
9237
  thisClass.setLogCmd("export canvas 2", true);
9221
9238
  ic.scaleFactor = 2;
9222
9239
  await ic.shareLinkCls.shareLink(true, true);
9223
9240
  });
9224
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9241
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9225
9242
  thisClass.setLogCmd("export canvas 4", true);
9226
9243
  ic.scaleFactor = 4;
9227
9244
  await ic.shareLinkCls.shareLink(true, true);
9228
9245
  });
9229
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9246
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9230
9247
  thisClass.setLogCmd("export canvas 8", true);
9231
9248
  ic.scaleFactor = 8;
9232
9249
  await ic.shareLinkCls.shareLink(true, true);
9233
9250
  });
9234
9251
 
9235
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9252
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9236
9253
  thisClass.setLogCmd("export counts", false);
9237
9254
  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>';
9238
9255
  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>';
@@ -9259,7 +9276,7 @@ class ClickMenu {
9259
9276
  ic.saveFileCls.saveFile(file_pref + '_counts.html', 'html', text);
9260
9277
  });
9261
9278
 
9262
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9279
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9263
9280
  thisClass.setLogCmd("export all selections", false);
9264
9281
 
9265
9282
  thisClass.SetChainsAdvancedMenu();
@@ -9269,7 +9286,7 @@ class ClickMenu {
9269
9286
  ic.saveFileCls.saveFile(file_pref + '_selections.txt', 'text', [text]);
9270
9287
  });
9271
9288
 
9272
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9289
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9273
9290
  thisClass.setLogCmd("export all selections with details", false);
9274
9291
 
9275
9292
  thisClass.SetChainsAdvancedMenu();
@@ -9280,32 +9297,32 @@ class ClickMenu {
9280
9297
  ic.saveFileCls.saveFile(file_pref + '_sel_details.txt', 'text', [text]);
9281
9298
  });
9282
9299
 
9283
- me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9300
+ me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9284
9301
  await ic.shareLinkCls.shareLink();
9285
9302
  });
9286
9303
 
9287
- me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9304
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9288
9305
  await ic.resizeCanvasCls.replayon();
9289
9306
  thisClass.setLogCmd("replay on", true);
9290
9307
  });
9291
- me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9308
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9292
9309
  await ic.resizeCanvasCls.replayoff();
9293
9310
  thisClass.setLogCmd("replay off", true);
9294
9311
  });
9295
9312
 
9296
- me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; e.preventDefault();
9313
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; //e.preventDefault();
9297
9314
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
9298
9315
 
9299
9316
  thisClass.applyShownMenus();
9300
9317
  });
9301
9318
 
9302
- me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; e.preventDefault();
9319
+ me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; //e.preventDefault();
9303
9320
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
9304
9321
 
9305
9322
  thisClass.applyShownMenus();
9306
9323
  });
9307
9324
 
9308
- me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; e.preventDefault();
9325
+ me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; //e.preventDefault();
9309
9326
  me.htmlCls.dialogCls.openDlg('dl_menupref', 'Select Menus');
9310
9327
 
9311
9328
  thisClass.getHiddenMenusFromCache();
@@ -9313,7 +9330,7 @@ class ClickMenu {
9313
9330
  thisClass.displayShownMenus();
9314
9331
  });
9315
9332
 
9316
- me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
9333
+ me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
9317
9334
  var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
9318
9335
  me.htmlCls.shownMenus = {};
9319
9336
  for (var checkbox of checkboxes) {
@@ -9323,21 +9340,21 @@ class ClickMenu {
9323
9340
  thisClass.applyShownMenus();
9324
9341
  });
9325
9342
 
9326
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
9343
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
9327
9344
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
9328
9345
 
9329
9346
  thisClass.applyShownMenus();
9330
9347
  thisClass.displayShownMenus();
9331
9348
  });
9332
9349
 
9333
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; e.preventDefault();
9350
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; //e.preventDefault();
9334
9351
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
9335
9352
 
9336
9353
  thisClass.applyShownMenus();
9337
9354
  thisClass.displayShownMenus();
9338
9355
  });
9339
9356
 
9340
- me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9357
+ me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9341
9358
  let menuStr = '[';
9342
9359
 
9343
9360
  //var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
@@ -9386,30 +9403,30 @@ class ClickMenu {
9386
9403
  }
9387
9404
  });
9388
9405
 
9389
- me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; e.preventDefault();
9406
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; //e.preventDefault();
9390
9407
  me.htmlCls.dialogCls.openDlg('dl_menuloadpref', 'Please input the menu preference file');
9391
9408
  });
9392
9409
 
9393
9410
 
9394
- me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9411
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9395
9412
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
9396
9413
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
9397
9414
  window.open(url, urlTarget);
9398
9415
  });
9399
9416
 
9400
- me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; e.preventDefault();
9417
+ me.myEventCls.onIds("#" + me.pre + "mn1_alphafold", "click", function(e) { me.icn3d; //e.preventDefault();
9401
9418
  let url = 'https://github.com/sokrypton/ColabFold';
9402
9419
  window.open(url, '_blank');
9403
9420
  });
9404
9421
 
9405
- me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9422
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9406
9423
  let url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
9407
9424
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
9408
9425
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
9409
9426
  window.open(url, urlTarget);
9410
9427
  });
9411
9428
 
9412
- me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9429
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9413
9430
  let url;
9414
9431
  if(ic.inputid === undefined) {
9415
9432
  url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
@@ -9438,7 +9455,7 @@ class ClickMenu {
9438
9455
  window.open(url, urlTarget);
9439
9456
  });
9440
9457
 
9441
- me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9458
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9442
9459
  let url;
9443
9460
  if(ic.inputid === undefined) {
9444
9461
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
@@ -9482,7 +9499,7 @@ class ClickMenu {
9482
9499
  }
9483
9500
  });
9484
9501
 
9485
- me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9502
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9486
9503
  //ic.saveFileCls.setEntrezLinks('protein');
9487
9504
  let structArray = Object.keys(ic.structures);
9488
9505
  let chainArray = Object.keys(ic.chains);
@@ -9507,19 +9524,19 @@ class ClickMenu {
9507
9524
 
9508
9525
  let thisClass = this;
9509
9526
 
9510
- me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
9527
+ me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
9511
9528
  await ic.showAnnoCls.showAnnotations();
9512
9529
  thisClass.setLogCmd("view annotations", true);
9513
9530
  //thisClass.setLogCmd("window annotations", true);
9514
9531
  });
9515
9532
 
9516
- me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9533
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9517
9534
  thisClass.setLogCmd("select all", true);
9518
9535
  ic.selectionCls.selectAll();
9519
9536
  ic.hlUpdateCls.removeHlAll();
9520
9537
  ic.drawCls.draw();
9521
9538
  });
9522
- me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9539
+ me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9523
9540
  thisClass.setLogCmd("clear all", true);
9524
9541
  ic.bSelectResidue = false;
9525
9542
  ic.selectionCls.selectAll();
@@ -9527,7 +9544,7 @@ class ClickMenu {
9527
9544
  ic.drawCls.draw();
9528
9545
  });
9529
9546
 
9530
- me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9547
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9531
9548
  thisClass.setLogCmd("select displayed set", true);
9532
9549
  //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
9533
9550
  ic.hAtoms = me.hashUtilsCls.cloneHash(ic.viewSelectionAtoms);
@@ -9535,106 +9552,123 @@ class ClickMenu {
9535
9552
  //ic.drawCls.draw();
9536
9553
  });
9537
9554
 
9538
- me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9555
+ me.myEventCls.onIds("#" + me.pre + "mn2_clashedYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9556
+ ic.bHideClashed = false;
9557
+ ic.annoDomainCls.showHideClashedResidues();
9558
+
9559
+ ic.drawCls.draw();
9560
+ thisClass.setLogCmd('clashed residues show', true);
9561
+ });
9562
+ me.myEventCls.onIds("#" + me.pre + "mn2_clashedNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9563
+ ic.bHideClashed = true;
9564
+
9565
+ thisClass.setClashedResidues();
9566
+ ic.annoDomainCls.showHideClashedResidues();
9567
+
9568
+ ic.drawCls.draw();
9569
+ thisClass.setLogCmd('clashed residues hide', true);
9570
+ });
9571
+
9572
+ me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9539
9573
  thisClass.setLogCmd("show all", true);
9540
9574
  ic.selectionCls.showAll();
9541
9575
  });
9542
9576
 
9543
- me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9577
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9544
9578
  if(Object.keys(ic.hAtoms).length < Object.keys(ic.atoms).length) {
9545
9579
  thisClass.setLogCmd("select complement", true);
9546
9580
  ic.resid2specCls.selectComplement();
9547
9581
  }
9548
9582
  });
9549
9583
 
9550
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9584
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9551
9585
  thisClass.setLogCmd("select main chains", true);
9552
9586
  ic.selectionCls.selectMainChains();
9553
9587
  });
9554
9588
 
9555
- me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9589
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9556
9590
  thisClass.setLogCmd("select side chains", true);
9557
9591
  ic.selectionCls.selectSideChains();
9558
9592
  });
9559
9593
 
9560
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9594
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9561
9595
  thisClass.setLogCmd("select main side chains", true);
9562
9596
  ic.selectionCls.selectMainSideChains();
9563
9597
  });
9564
9598
 
9565
- me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9599
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9566
9600
  thisClass.setLogCmd("select prop positive", true);
9567
9601
  ic.resid2specCls.selectProperty('positive');
9568
9602
  });
9569
- me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9603
+ me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9570
9604
  thisClass.setLogCmd("select prop negative", true);
9571
9605
  ic.resid2specCls.selectProperty('negative');
9572
9606
  });
9573
- me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9607
+ me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9574
9608
  thisClass.setLogCmd("select prop hydrophobic", true);
9575
9609
  ic.resid2specCls.selectProperty('hydrophobic');
9576
9610
  });
9577
- me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9611
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9578
9612
  thisClass.setLogCmd("select prop polar", true);
9579
9613
  ic.resid2specCls.selectProperty('polar');
9580
9614
  });
9581
- me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; e.preventDefault();
9615
+ me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; //e.preventDefault();
9582
9616
  me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor/pLDDT');
9583
9617
  });
9584
- me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; e.preventDefault();
9618
+ me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; //e.preventDefault();
9585
9619
  me.htmlCls.dialogCls.openDlg('dl_propbypercentout', 'Select residue based on the percentage of solvent accessilbe surface area');
9586
9620
  });
9587
- me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9621
+ me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9588
9622
  let from = $("#" + me.pre + "minbfactor").val();
9589
9623
  let to = $("#" + me.pre + "maxbfactor").val();
9590
9624
  thisClass.setLogCmd("select prop b factor | " + from + '_' + to, true);
9591
9625
  ic.resid2specCls.selectProperty('b factor', from, to);
9592
9626
  });
9593
- me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9627
+ me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9594
9628
  let from = $("#" + me.pre + "minpercentout").val();
9595
9629
  let to = $("#" + me.pre + "maxpercentout").val();
9596
9630
  thisClass.setLogCmd("select prop percent out | " + from + '_' + to, true);
9597
9631
  ic.resid2specCls.selectProperty('percent out', from, to);
9598
9632
  });
9599
9633
 
9600
- me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; e.preventDefault();
9634
+ me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; //e.preventDefault();
9601
9635
  me.htmlCls.dialogCls.openDlg('dl_alignment', 'Select residues in aligned sequences');
9602
9636
  thisClass.setLogCmd("window aligned sequences", true);
9603
9637
  });
9604
9638
 
9605
- me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; e.preventDefault();
9639
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; //e.preventDefault();
9606
9640
  me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
9607
9641
  thisClass.setLogCmd("window interaction table", true);
9608
9642
  });
9609
- me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; e.preventDefault();
9643
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; //e.preventDefault();
9610
9644
  me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
9611
9645
  thisClass.setLogCmd("window interaction graph", true);
9612
9646
  });
9613
- me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; e.preventDefault();
9647
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; //e.preventDefault();
9614
9648
  me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as map');
9615
9649
  thisClass.setLogCmd("window interaction scatterplot", true);
9616
9650
  });
9617
- me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; e.preventDefault();
9651
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; //e.preventDefault();
9618
9652
  me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
9619
9653
  thisClass.setLogCmd("window force-directed graph", true);
9620
9654
  });
9621
9655
 
9622
- me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; e.preventDefault();
9656
+ me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; //e.preventDefault();
9623
9657
  me.htmlCls.dialogCls.openDlg('dl_yournote', 'Your note about the current display');
9624
9658
  });
9625
9659
 
9626
- me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9660
+ me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9627
9661
  ic.yournote = $("#" + me.pre + "yournote").val();
9628
9662
  if(me.cfg.shownote) document.title = ic.yournote;
9629
9663
  if(!me.cfg.notebook) dialog.dialog( "close" );
9630
9664
  thisClass.setLogCmd('your note | ' + ic.yournote, true);
9631
9665
  });
9632
9666
 
9633
- me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; e.preventDefault();
9667
+ me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; //e.preventDefault();
9634
9668
  me.htmlCls.dialogCls.openDlg('dl_advanced2', 'Select by specification');
9635
9669
  });
9636
9670
 
9637
- 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();
9671
+ 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();
9638
9672
  ic.definedSetsCls.showSets();
9639
9673
  thisClass.setLogCmd('defined sets', true);
9640
9674
  //thisClass.setLogCmd('window defined sets', true);
@@ -9653,7 +9687,7 @@ class ClickMenu {
9653
9687
  });
9654
9688
 
9655
9689
 
9656
- me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9690
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9657
9691
  ic.pk = 0;
9658
9692
  ic.opts['pk'] = 'no';
9659
9693
  thisClass.setLogCmd('set pk off', true);
@@ -9661,50 +9695,50 @@ class ClickMenu {
9661
9695
  ic.hlObjectsCls.removeHlObjects();
9662
9696
  });
9663
9697
 
9664
- me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9698
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9665
9699
  ic.pk = 1;
9666
9700
  ic.opts['pk'] = 'atom';
9667
9701
  thisClass.setLogCmd('set pk atom', true);
9668
9702
  });
9669
9703
 
9670
- me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9704
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9671
9705
  ic.pk = 2;
9672
9706
  ic.opts['pk'] = 'residue';
9673
9707
  thisClass.setLogCmd('set pk residue', true);
9674
9708
  });
9675
9709
 
9676
- me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9710
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9677
9711
  ic.pk = 3;
9678
9712
  ic.opts['pk'] = 'strand';
9679
9713
  thisClass.setLogCmd('set pk strand', true);
9680
9714
  });
9681
9715
 
9682
- me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9716
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9683
9717
  ic.pk = 4;
9684
9718
  ic.opts['pk'] = 'domain';
9685
9719
  thisClass.setLogCmd('set pk domain', true);
9686
9720
  });
9687
9721
 
9688
- me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9722
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9689
9723
  ic.pk = 5;
9690
9724
  ic.opts['pk'] = 'chain';
9691
9725
  thisClass.setLogCmd('set pk chain', true);
9692
9726
  });
9693
9727
 
9694
- me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; e.preventDefault();
9728
+ me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; //e.preventDefault();
9695
9729
  me.htmlCls.dialogCls.openDlg('dl_adjustmem', 'Adjust the Z-axis positions of the membrane');
9696
9730
  });
9697
9731
 
9698
- me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9732
+ me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9699
9733
  ic.selectionCls.toggleMembrane();
9700
9734
  thisClass.setLogCmd('toggle membrane', true);
9701
9735
  });
9702
9736
 
9703
- me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; e.preventDefault();
9737
+ me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; //e.preventDefault();
9704
9738
  me.htmlCls.dialogCls.openDlg('dl_selectplane', 'Select a region between two planes');
9705
9739
  });
9706
9740
 
9707
- me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9741
+ me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9708
9742
  thisClass.SetChainsAdvancedMenu();
9709
9743
 
9710
9744
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -9721,7 +9755,7 @@ class ClickMenu {
9721
9755
  $("#" + me.pre + "atomsCustomSphere2").resizable();
9722
9756
  });
9723
9757
 
9724
- me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; e.preventDefault();
9758
+ me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; //e.preventDefault();
9725
9759
  me.htmlCls.dialogCls.openDlg('dl_select_chain', 'Select Structure/Chain/Custom Selection');
9726
9760
  });
9727
9761
 
@@ -9732,242 +9766,242 @@ class ClickMenu {
9732
9766
 
9733
9767
  let thisClass = this;
9734
9768
  // mn 3
9735
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9769
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9736
9770
  ic.setOptionCls.setStyle('proteins', 'ribbon');
9737
9771
  thisClass.setLogCmd('style proteins ribbon', true);
9738
9772
  });
9739
9773
 
9740
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9774
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9741
9775
  ic.setOptionCls.setStyle('proteins', 'strand');
9742
9776
  thisClass.setLogCmd('style proteins strand', true);
9743
9777
  });
9744
9778
 
9745
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9779
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9746
9780
  ic.setOptionCls.setStyle('proteins', 'cylinder and plate');
9747
9781
  thisClass.setLogCmd('style proteins cylinder and plate', true);
9748
9782
  });
9749
9783
 
9750
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9784
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9751
9785
  ic.setOptionCls.setStyle('proteins', 'schematic');
9752
9786
  thisClass.setLogCmd('style proteins schematic', true);
9753
9787
  });
9754
9788
 
9755
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9789
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9756
9790
  ic.setOptionCls.setStyle('proteins', 'c alpha trace');
9757
9791
  thisClass.setLogCmd('style proteins c alpha trace', true);
9758
9792
  });
9759
9793
 
9760
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9794
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9761
9795
  ic.setOptionCls.setStyle('proteins', 'backbone');
9762
9796
  thisClass.setLogCmd('style proteins backbone', true);
9763
9797
  });
9764
9798
 
9765
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9799
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9766
9800
  ic.setOptionCls.setStyle('proteins', 'b factor tube');
9767
9801
  thisClass.setLogCmd('style proteins b factor tube', true);
9768
9802
  });
9769
9803
 
9770
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9804
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9771
9805
  ic.setOptionCls.setStyle('proteins', 'lines');
9772
9806
  thisClass.setLogCmd('style proteins lines', true);
9773
9807
  });
9774
9808
 
9775
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9809
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9776
9810
  ic.setOptionCls.setStyle('proteins', 'stick');
9777
9811
  thisClass.setLogCmd('style proteins stick', true);
9778
9812
  });
9779
9813
 
9780
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9814
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9781
9815
  ic.setOptionCls.setStyle('proteins', 'ball and stick');
9782
9816
  thisClass.setLogCmd('style proteins ball and stick', true);
9783
9817
  });
9784
9818
 
9785
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
9819
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9786
9820
  ic.setOptionCls.setStyle('proteins', 'sphere');
9787
9821
  thisClass.setLogCmd('style proteins sphere', true);
9788
9822
  });
9789
9823
 
9790
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9824
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9791
9825
  ic.setOptionCls.setStyle('proteins', 'nothing');
9792
9826
  thisClass.setLogCmd('style proteins nothing', true);
9793
9827
  });
9794
9828
 
9795
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9829
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9796
9830
  ic.setOptionCls.setStyle('sidec', 'lines2');
9797
9831
  thisClass.setLogCmd('style sidec lines2', true);
9798
9832
  });
9799
9833
 
9800
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9834
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9801
9835
  ic.setOptionCls.setStyle('sidec', 'stick2');
9802
9836
  thisClass.setLogCmd('style sidec stick2', true);
9803
9837
  });
9804
9838
 
9805
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9839
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9806
9840
  ic.setOptionCls.setStyle('sidec', 'ball and stick2');
9807
9841
  thisClass.setLogCmd('style sidec ball and stick2', true);
9808
9842
  });
9809
9843
 
9810
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9844
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9811
9845
  ic.setOptionCls.setStyle('sidec', 'sphere2');
9812
9846
  thisClass.setLogCmd('style sidec sphere2', true);
9813
9847
  });
9814
9848
 
9815
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9849
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9816
9850
  ic.setOptionCls.setStyle('sidec', 'nothing');
9817
9851
  thisClass.setLogCmd('style sidec nothing', true);
9818
9852
  });
9819
9853
 
9820
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9854
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9821
9855
  ic.setOptionCls.setStyle('ntbase', 'lines2');
9822
9856
  thisClass.setLogCmd('style ntbase lines2', true);
9823
9857
  });
9824
9858
 
9825
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9859
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9826
9860
  ic.setOptionCls.setStyle('ntbase', 'stick2');
9827
9861
  thisClass.setLogCmd('style ntbase stick2', true);
9828
9862
  });
9829
9863
 
9830
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9864
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9831
9865
  ic.setOptionCls.setStyle('ntbase', 'ball and stick2');
9832
9866
  thisClass.setLogCmd('style ntbase ball and stick2', true);
9833
9867
  });
9834
9868
 
9835
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9869
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9836
9870
  ic.setOptionCls.setStyle('ntbase', 'sphere2');
9837
9871
  thisClass.setLogCmd('style ntbase sphere2', true);
9838
9872
  });
9839
9873
 
9840
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9874
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9841
9875
  ic.setOptionCls.setStyle('ntbase', 'nothing');
9842
9876
  thisClass.setLogCmd('style ntbase nothing', true);
9843
9877
  });
9844
9878
 
9845
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9879
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9846
9880
  ic.setOptionCls.setStyle('nucleotides', 'nucleotide cartoon');
9847
9881
  thisClass.setLogCmd('style nucleotides nucleotide cartoon', true);
9848
9882
  });
9849
9883
 
9850
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9884
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9851
9885
  ic.setOptionCls.setStyle('nucleotides', 'backbone');
9852
9886
  thisClass.setLogCmd('style nucleotides backbone', true);
9853
9887
  });
9854
9888
 
9855
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9889
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9856
9890
  ic.setOptionCls.setStyle('nucleotides', 'schematic');
9857
9891
  thisClass.setLogCmd('style nucleotides schematic', true);
9858
9892
  });
9859
9893
 
9860
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9894
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9861
9895
  ic.setOptionCls.setStyle('nucleotides', 'o3 trace');
9862
9896
  thisClass.setLogCmd('style nucleotides o3 trace', true);
9863
9897
  });
9864
9898
 
9865
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9899
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9866
9900
  ic.setOptionCls.setStyle('nucleotides', 'lines');
9867
9901
  thisClass.setLogCmd('style nucleotides lines', true);
9868
9902
  });
9869
9903
 
9870
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9904
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9871
9905
  ic.setOptionCls.setStyle('nucleotides', 'stick');
9872
9906
  thisClass.setLogCmd('style nucleotides stick', true);
9873
9907
  });
9874
9908
 
9875
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9909
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9876
9910
  ic.setOptionCls.setStyle('nucleotides', 'ball and stick');
9877
9911
  thisClass.setLogCmd('style nucleotides ball and stick', true);
9878
9912
  });
9879
9913
 
9880
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9914
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9881
9915
  ic.setOptionCls.setStyle('nucleotides', 'sphere');
9882
9916
  thisClass.setLogCmd('style nucleotides sphere', true);
9883
9917
  });
9884
9918
 
9885
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9919
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9886
9920
  ic.setOptionCls.setStyle('nucleotides', 'nothing');
9887
9921
  thisClass.setLogCmd('style nucleotides nothing', true);
9888
9922
  });
9889
9923
 
9890
- me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9924
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9891
9925
  ic.setOptionCls.setStyle('chemicals', 'lines');
9892
9926
  thisClass.setLogCmd('style chemicals lines', true);
9893
9927
  });
9894
9928
 
9895
- me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9929
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9896
9930
  ic.setOptionCls.setStyle('chemicals', 'stick');
9897
9931
  thisClass.setLogCmd('style chemicals stick', true);
9898
9932
  });
9899
9933
 
9900
- me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9934
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9901
9935
  ic.setOptionCls.setStyle('chemicals', 'ball and stick');
9902
9936
  thisClass.setLogCmd('style chemicals ball and stick', true);
9903
9937
  });
9904
9938
 
9905
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9939
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9906
9940
  ic.setOptionCls.setStyle('chemicals', 'schematic');
9907
9941
  thisClass.setLogCmd('style chemicals schematic', true);
9908
9942
  });
9909
9943
 
9910
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9944
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9911
9945
  ic.setOptionCls.setStyle('chemicals', 'sphere');
9912
9946
  thisClass.setLogCmd('style chemicals sphere', true);
9913
9947
  });
9914
9948
 
9915
- me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9949
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9916
9950
  ic.setOptionCls.setStyle('chemicals', 'nothing');
9917
9951
  thisClass.setLogCmd('style chemicals nothing', true);
9918
9952
  });
9919
9953
 
9920
9954
 
9921
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9955
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9922
9956
  ic.bGlycansCartoon = true;
9923
9957
  ic.drawCls.draw();
9924
9958
  thisClass.setLogCmd('glycans cartoon yes', true);
9925
9959
  });
9926
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9960
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9927
9961
  ic.bGlycansCartoon = false;
9928
9962
  ic.drawCls.draw();
9929
9963
  thisClass.setLogCmd('glycans cartoon no', true);
9930
9964
  });
9931
9965
 
9932
9966
 
9933
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9967
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9934
9968
  ic.showInterCls.showHydrogens();
9935
9969
  ic.drawCls.draw();
9936
9970
  thisClass.setLogCmd('hydrogens', true);
9937
9971
  });
9938
9972
 
9939
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9973
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9940
9974
  ic.showInterCls.hideHydrogens();
9941
9975
  ic.drawCls.draw();
9942
9976
  thisClass.setLogCmd('set hydrogens off', true);
9943
9977
  });
9944
9978
 
9945
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9979
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9946
9980
  ic.setOptionCls.setStyle('ions', 'sphere');
9947
9981
  thisClass.setLogCmd('style ions sphere', true);
9948
9982
  });
9949
9983
 
9950
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9984
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9951
9985
  ic.setOptionCls.setStyle('ions', 'dot');
9952
9986
  thisClass.setLogCmd('style ions dot', true);
9953
9987
  });
9954
9988
 
9955
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9989
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9956
9990
  ic.setOptionCls.setStyle('ions', 'nothing');
9957
9991
  thisClass.setLogCmd('style ions nothing', true);
9958
9992
  });
9959
9993
 
9960
- me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9994
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9961
9995
  ic.setOptionCls.setStyle('water', 'sphere');
9962
9996
  thisClass.setLogCmd('style water sphere', true);
9963
9997
  });
9964
9998
 
9965
- me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
9999
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9966
10000
  ic.setOptionCls.setStyle('water', 'dot');
9967
10001
  thisClass.setLogCmd('style water dot', true);
9968
10002
  });
9969
10003
 
9970
- me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10004
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9971
10005
  ic.setOptionCls.setStyle('water', 'nothing');
9972
10006
  thisClass.setLogCmd('style water nothing', true);
9973
10007
  });
@@ -9979,16 +10013,16 @@ class ClickMenu {
9979
10013
 
9980
10014
  let thisClass = this;
9981
10015
  // mn 4
9982
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10016
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9983
10017
  ic.setOptionCls.setOption('color', 'spectrum');
9984
10018
  thisClass.setLogCmd('color spectrum', true);
9985
10019
  });
9986
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10020
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9987
10021
  ic.setOptionCls.setOption('color', 'spectrum for chains');
9988
10022
  thisClass.setLogCmd('color spectrum for chains', true);
9989
10023
  });
9990
10024
 
9991
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10025
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
9992
10026
  thisClass.SetChainsAdvancedMenu();
9993
10027
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
9994
10028
  if($("#" + me.pre + "atomsCustomColorSpectrumAcross").length) {
@@ -9999,7 +10033,7 @@ class ClickMenu {
9999
10033
  $("#" + me.pre + "atomsCustomColorSpectrumAcross").resizable();
10000
10034
  });
10001
10035
 
10002
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10036
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10003
10037
  thisClass.SetChainsAdvancedMenu();
10004
10038
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10005
10039
  if($("#" + me.pre + "atomsCustomColorSpectrum").length) {
@@ -10010,7 +10044,7 @@ class ClickMenu {
10010
10044
  $("#" + me.pre + "atomsCustomColorSpectrum").resizable();
10011
10045
  });
10012
10046
 
10013
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10047
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10014
10048
  thisClass.SetChainsAdvancedMenu();
10015
10049
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10016
10050
  if($("#" + me.pre + "atomsCustomColorRainbowAcross").length) {
@@ -10021,7 +10055,7 @@ class ClickMenu {
10021
10055
  $("#" + me.pre + "atomsCustomColorRainbowAcross").resizable();
10022
10056
  });
10023
10057
 
10024
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10058
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10025
10059
  thisClass.SetChainsAdvancedMenu();
10026
10060
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
10027
10061
  if($("#" + me.pre + "atomsCustomColorRainbow").length) {
@@ -10032,60 +10066,60 @@ class ClickMenu {
10032
10066
  $("#" + me.pre + "atomsCustomColorRainbow").resizable();
10033
10067
  });
10034
10068
 
10035
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10069
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10036
10070
  ic.setOptionCls.setOption('color', 'rainbow');
10037
10071
 
10038
10072
  thisClass.setLogCmd('color rainbow', true);
10039
10073
  });
10040
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10074
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10041
10075
  ic.setOptionCls.setOption('color', 'rainbow for chains');
10042
10076
  thisClass.setLogCmd('color rainbow for chains', true);
10043
10077
  });
10044
10078
 
10045
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10079
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10046
10080
  ic.setOptionCls.setOption('color', 'chain');
10047
10081
  thisClass.setLogCmd('color chain', true);
10048
10082
  });
10049
- me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10083
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10050
10084
  ic.setOptionCls.setOption('color', 'structure');
10051
10085
  thisClass.setLogCmd('color structure', true);
10052
10086
  });
10053
10087
 
10054
- me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10088
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10055
10089
  ic.setOptionCls.setOption('color', 'domain');
10056
10090
  thisClass.setLogCmd('color domain', true);
10057
10091
  });
10058
10092
 
10059
- me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10093
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10060
10094
  ic.setOptionCls.setOption('color', 'defined sets');
10061
10095
  thisClass.setLogCmd('color defined sets', true);
10062
10096
  });
10063
10097
 
10064
10098
 
10065
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10099
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10066
10100
  ic.sheetcolor = 'green';
10067
10101
  ic.setOptionCls.setOption('color', 'secondary structure green');
10068
10102
  thisClass.setLogCmd('color secondary structure green', true);
10069
10103
  });
10070
10104
 
10071
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10105
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10072
10106
  ic.sheetcolor = 'yellow';
10073
10107
  ic.setOptionCls.setOption('color', 'secondary structure yellow');
10074
10108
  thisClass.setLogCmd('color secondary structure yellow', true);
10075
10109
  });
10076
10110
 
10077
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10111
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10078
10112
  ic.setOptionCls.setOption('color', 'secondary structure spectrum');
10079
10113
  thisClass.setLogCmd('color secondary structure spectrum', true);
10080
10114
  });
10081
10115
 
10082
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10116
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10083
10117
  //ic.legendClick = 2;
10084
10118
  ic.setOptionCls.setOption('color', 'residue');
10085
10119
  thisClass.setLogCmd('color residue', true);
10086
10120
  });
10087
10121
 
10088
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; e.preventDefault();
10122
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; //e.preventDefault();
10089
10123
  //ic.legendClick = 2;
10090
10124
  me.htmlCls.dialogCls.openDlg('dl_rescolorfile', 'Please input the file on residue colors');
10091
10125
  });
@@ -10131,12 +10165,12 @@ class ClickMenu {
10131
10165
  ic.addTrackCls.setCustomFile('color', ic.startColor, ic.midColor, ic.endColor);
10132
10166
  });
10133
10167
 
10134
- me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; e.preventDefault();
10168
+ me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; //e.preventDefault();
10135
10169
 
10136
10170
  me.htmlCls.dialogCls.openDlg('dl_customref', 'Set custom reference numbers');
10137
10171
  });
10138
10172
 
10139
- me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10173
+ me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10140
10174
 
10141
10175
  if(!me.cfg.notebook) dialog.dialog( "close" );
10142
10176
 
@@ -10173,82 +10207,82 @@ class ClickMenu {
10173
10207
  ic.addTrackCls.setCustomFile('tube');
10174
10208
  });
10175
10209
 
10176
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10210
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10177
10211
  //ic.legendClick = 3;
10178
10212
  ic.setOptionCls.setOption('color', 'charge');
10179
10213
  thisClass.setLogCmd('color charge', true);
10180
10214
  });
10181
10215
 
10182
- me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10216
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10183
10217
  //ic.legendClick = 4;
10184
10218
  ic.setOptionCls.setOption('color', 'hydrophobic');
10185
10219
  thisClass.setLogCmd('color hydrophobic', true);
10186
10220
  });
10187
10221
 
10188
- me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10222
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10189
10223
  //ic.legendClick = 4;
10190
10224
  ic.setOptionCls.setOption('color', 'normalized hydrophobic');
10191
10225
  thisClass.setLogCmd('color normalized hydrophobic', true);
10192
10226
  });
10193
10227
 
10194
10228
 
10195
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10229
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10196
10230
  //ic.legendClick = 1;
10197
10231
  ic.setOptionCls.setOption('color', 'atom');
10198
10232
  thisClass.setLogCmd('color atom', true);
10199
10233
  });
10200
10234
 
10201
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10235
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10202
10236
  //ic.legendClick = 5;
10203
10237
  ic.setOptionCls.setOption('color', 'b factor');
10204
10238
  thisClass.setLogCmd('color b factor', true);
10205
10239
  });
10206
10240
 
10207
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10241
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10208
10242
  //ic.legendClick = 6;
10209
10243
  ic.setOptionCls.setOption('color', 'confidence');
10210
10244
  thisClass.setLogCmd('color confidence', true);
10211
10245
  });
10212
10246
 
10213
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10247
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10214
10248
  //ic.legendClick = 6;
10215
10249
  ic.setOptionCls.setOption('color', 'ig strand');
10216
10250
  thisClass.setLogCmd('color ig strand', true);
10217
10251
  });
10218
10252
 
10219
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10253
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10220
10254
  //ic.legendClick = 6;
10221
10255
  ic.setOptionCls.setOption('color', 'ig protodomain');
10222
10256
  thisClass.setLogCmd('color ig protodomain', true);
10223
10257
  });
10224
10258
 
10225
10259
 
10226
- me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; e.preventDefault();
10260
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; //e.preventDefault();
10227
10261
  me.htmlCls.dialogCls.openDlg('dl_colorbyarea', "Color based on residue's solvent accessibility");
10228
10262
  });
10229
- me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10263
+ me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10230
10264
  ic.midpercent = $("#" + me.pre + 'midpercent').val();
10231
10265
  ic.setOptionCls.setOption('color', 'area');
10232
10266
  thisClass.setLogCmd('color area | ' + ic.midpercent, true);
10233
10267
 
10234
10268
  });
10235
10269
 
10236
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10270
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10237
10271
  ic.setOptionCls.setOption('color', 'b factor percentile');
10238
10272
  thisClass.setLogCmd('color b factor percentile', true);
10239
10273
  });
10240
10274
 
10241
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10275
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10242
10276
  ic.setOptionCls.setOption('color', 'identity');
10243
10277
  thisClass.setLogCmd('color identity', true);
10244
10278
  });
10245
10279
 
10246
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10280
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10247
10281
  ic.setOptionCls.setOption('color', 'conservation');
10248
10282
  thisClass.setLogCmd('color conservation', true);
10249
10283
  });
10250
10284
 
10251
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; e.preventDefault();
10285
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; //e.preventDefault();
10252
10286
  me.htmlCls.dialogCls.openDlg('dl_clr', 'Color picker');
10253
10287
  });
10254
10288
 
@@ -10261,22 +10295,22 @@ class ClickMenu {
10261
10295
  thisClass.setLogCmd("color " + color, true);
10262
10296
  });
10263
10297
 
10264
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10298
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10265
10299
  ic.setOptionCls.saveColor();
10266
10300
  thisClass.setLogCmd('save color', true);
10267
10301
  });
10268
10302
 
10269
- me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10303
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10270
10304
  ic.setOptionCls.applySavedColor();
10271
10305
  thisClass.setLogCmd('apply saved color', true);
10272
10306
  });
10273
10307
 
10274
- me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10308
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10275
10309
  ic.setOptionCls.saveStyle();
10276
10310
  thisClass.setLogCmd('save style', true);
10277
10311
  });
10278
10312
 
10279
- me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10313
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10280
10314
  ic.setOptionCls.applySavedStyle();
10281
10315
  thisClass.setLogCmd('apply saved style', true);
10282
10316
  });
@@ -10288,7 +10322,7 @@ class ClickMenu {
10288
10322
 
10289
10323
  let thisClass = this;
10290
10324
  // mn 5
10291
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10325
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10292
10326
  ic.bConsiderNeighbors = true;
10293
10327
  ic.applyMapCls.removeLastSurface();
10294
10328
  ic.applyMapCls.applySurfaceOptions();
@@ -10296,7 +10330,7 @@ class ClickMenu {
10296
10330
  thisClass.setLogCmd('set surface neighbors on', true);
10297
10331
  });
10298
10332
 
10299
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10333
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10300
10334
  ic.bConsiderNeighbors = false;
10301
10335
  ic.applyMapCls.removeLastSurface();
10302
10336
  ic.applyMapCls.applySurfaceOptions();
@@ -10304,48 +10338,48 @@ class ClickMenu {
10304
10338
  thisClass.setLogCmd('set surface neighbors off', true);
10305
10339
  });
10306
10340
 
10307
- me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10341
+ me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10308
10342
  ic.bConsiderNeighbors = false;
10309
10343
  ic.setOptionCls.setOption('surface', 'Van der Waals surface');
10310
10344
  thisClass.setLogCmd('set surface Van der Waals surface', true);
10311
10345
  });
10312
10346
 
10313
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10347
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10314
10348
  ic.bConsiderNeighbors = false;
10315
10349
  ic.setOptionCls.setOption('surface', 'solvent accessible surface');
10316
10350
  thisClass.setLogCmd('set surface solvent accessible surface', true);
10317
10351
  });
10318
10352
 
10319
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10353
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10320
10354
  ic.bConsiderNeighbors = false;
10321
10355
  ic.setOptionCls.setOption('surface', 'molecular surface');
10322
10356
  thisClass.setLogCmd('set surface molecular surface', true);
10323
10357
  });
10324
10358
 
10325
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10359
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10326
10360
  ic.bConsiderNeighbors = true;
10327
10361
  ic.setOptionCls.setOption('surface', 'Van der Waals surface with context');
10328
10362
  thisClass.setLogCmd('set surface Van der Waals surface with context', true);
10329
10363
  });
10330
10364
 
10331
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10365
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10332
10366
  ic.bConsiderNeighbors = true;
10333
10367
  ic.setOptionCls.setOption('surface', 'solvent accessible surface with context');
10334
10368
  thisClass.setLogCmd('set surface solvent accessible surface with context', true);
10335
10369
  });
10336
10370
 
10337
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10371
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10338
10372
  ic.bConsiderNeighbors = true;
10339
10373
  ic.setOptionCls.setOption('surface', 'molecular surface with context');
10340
10374
  thisClass.setLogCmd('set surface molecular surface with context', true);
10341
10375
  });
10342
10376
 
10343
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10377
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10344
10378
  ic.setOptionCls.setOption('surface', 'nothing');
10345
10379
  thisClass.setLogCmd('set surface nothing', true);
10346
10380
  });
10347
10381
 
10348
- $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; e.preventDefault();
10382
+ $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; //e.preventDefault();
10349
10383
  ic.transparentRenderOrder = false;
10350
10384
 
10351
10385
  let value = $(this).attr('v');
@@ -10353,7 +10387,7 @@ class ClickMenu {
10353
10387
  thisClass.setLogCmd('set surface opacity ' + value, true);
10354
10388
  });
10355
10389
 
10356
- $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; e.preventDefault();
10390
+ $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; //e.preventDefault();
10357
10391
  ic.transparentRenderOrder = true;
10358
10392
 
10359
10393
  let value = $(this).attr('v');
@@ -10361,35 +10395,35 @@ class ClickMenu {
10361
10395
  thisClass.setLogCmd('set surface2 opacity ' + value, true);
10362
10396
  });
10363
10397
 
10364
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10398
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10365
10399
  ic.setOptionCls.setOption('wireframe', 'yes');
10366
10400
  thisClass.setLogCmd('set surface wireframe on', true);
10367
10401
  });
10368
10402
 
10369
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10403
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10370
10404
  ic.setOptionCls.setOption('wireframe', 'no');
10371
10405
  thisClass.setLogCmd('set surface wireframe off', true);
10372
10406
  });
10373
10407
 
10374
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; e.preventDefault();
10408
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; //e.preventDefault();
10375
10409
  me.htmlCls.dialogCls.openDlg('dl_elecmap2fofc', '2Fo-Fc Electron Density Map');
10376
10410
  });
10377
10411
 
10378
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; e.preventDefault();
10412
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; //e.preventDefault();
10379
10413
  me.htmlCls.dialogCls.openDlg('dl_elecmapfofc', 'Fo-Fc Electron Density Map');
10380
10414
  });
10381
10415
 
10382
- 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();
10416
+ 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();
10383
10417
  ic.setOptionCls.setOption('map', 'nothing');
10384
10418
  thisClass.setLogCmd('setoption map nothing', true);
10385
10419
  });
10386
10420
 
10387
- 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();
10421
+ 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();
10388
10422
  ic.setOptionCls.setOption('phimap', 'nothing');
10389
10423
  thisClass.setLogCmd('setoption phimap nothing', true);
10390
10424
  });
10391
10425
 
10392
- me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10426
+ me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10393
10427
  //ic.setOptionCls.setOption('surface', 'nothing');
10394
10428
  //thisClass.setLogCmd('set surface nothing', true);
10395
10429
  ic.setOptionCls.setOption('phisurface', 'nothing');
@@ -10421,22 +10455,22 @@ class ClickMenu {
10421
10455
  thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
10422
10456
  });
10423
10457
 
10424
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10458
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10425
10459
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
10426
10460
  ic.setOptionCls.setOption('mapwireframe', 'yes');
10427
10461
  thisClass.setLogCmd('set map wireframe on', true);
10428
10462
  });
10429
10463
 
10430
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10464
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10431
10465
  ic.setOptionCls.setOption('mapwireframe', 'no');
10432
10466
  thisClass.setLogCmd('set map wireframe off', true);
10433
10467
  });
10434
10468
 
10435
- me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; e.preventDefault();
10469
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; //e.preventDefault();
10436
10470
  me.htmlCls.dialogCls.openDlg('dl_emmap', 'EM Density Map');
10437
10471
  });
10438
10472
 
10439
- me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10473
+ me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10440
10474
  ic.setOptionCls.setOption('emmap', 'nothing');
10441
10475
  thisClass.setLogCmd('setoption emmap nothing', true);
10442
10476
  });
@@ -10453,13 +10487,13 @@ class ClickMenu {
10453
10487
  thisClass.setLogCmd('set emmap percentage ' + empercentage, true);
10454
10488
  });
10455
10489
 
10456
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10490
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10457
10491
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
10458
10492
  ic.setOptionCls.setOption('emmapwireframe', 'yes');
10459
10493
  thisClass.setLogCmd('set emmap wireframe on', true);
10460
10494
  });
10461
10495
 
10462
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10496
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10463
10497
  ic.setOptionCls.setOption('emmapwireframe', 'no');
10464
10498
  thisClass.setLogCmd('set emmap wireframe off', true);
10465
10499
  });
@@ -10471,19 +10505,19 @@ class ClickMenu {
10471
10505
 
10472
10506
  let thisClass = this;
10473
10507
  // mn 6
10474
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10508
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10475
10509
  ic.bAssembly = true;
10476
10510
  thisClass.setLogCmd('set assembly on', true);
10477
10511
  ic.drawCls.draw();
10478
10512
  });
10479
10513
 
10480
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10514
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10481
10515
  ic.bAssembly = false;
10482
10516
  thisClass.setLogCmd('set assembly off', true);
10483
10517
  ic.drawCls.draw();
10484
10518
  });
10485
10519
 
10486
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10520
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10487
10521
  ic.bRunRefnumAgain = true;
10488
10522
 
10489
10523
  thisClass.setLogCmd('ig refnum on', true);
@@ -10506,11 +10540,11 @@ class ClickMenu {
10506
10540
  ic.bRunRefnumAgain = false;
10507
10541
  });
10508
10542
 
10509
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
10543
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
10510
10544
  me.htmlCls.dialogCls.openDlg('dl_igrefTpl', 'Choose an Ig template');
10511
10545
  });
10512
10546
 
10513
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; e.preventDefault();
10547
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; //e.preventDefault();
10514
10548
  if(!me.cfg.notebook) dialog.dialog( "close" );
10515
10549
 
10516
10550
  let template = $("#" + me.pre + "refTpl").val();
@@ -10520,11 +10554,11 @@ class ClickMenu {
10520
10554
  thisClass.setLogCmd('ig template ' + template, true);
10521
10555
  });
10522
10556
 
10523
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; e.preventDefault();
10557
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
10524
10558
  me.htmlCls.dialogCls.openDlg('dl_alignrefTpl', 'Align with an Ig template');
10525
10559
  });
10526
10560
 
10527
- me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10561
+ me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10528
10562
  if(!me.cfg.notebook) dialog.dialog( "close" );
10529
10563
 
10530
10564
  let template = $("#" + me.pre + "refTpl2").val();
@@ -10548,7 +10582,7 @@ class ClickMenu {
10548
10582
  thisClass.setLogCmd('realign on tmalign', true);
10549
10583
  });
10550
10584
 
10551
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10585
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10552
10586
  thisClass.setLogCmd('ig refnum off', true);
10553
10587
  await ic.refnumCls.hideIgRefNum();
10554
10588
 
@@ -10558,14 +10592,14 @@ class ClickMenu {
10558
10592
  // ic.drawCls.draw();
10559
10593
  });
10560
10594
 
10561
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10595
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10562
10596
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
10563
10597
  ic.selectionCls.saveSelectionIfSelected();
10564
10598
  thisClass.setLogCmd('add atom labels', true);
10565
10599
  ic.drawCls.draw();
10566
10600
  });
10567
10601
 
10568
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10602
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10569
10603
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms, true);
10570
10604
  ic.selectionCls.saveSelectionIfSelected();
10571
10605
  thisClass.setLogCmd('add element labels', true);
@@ -10573,49 +10607,49 @@ class ClickMenu {
10573
10607
  });
10574
10608
 
10575
10609
 
10576
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10610
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10577
10611
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms);
10578
10612
  ic.selectionCls.saveSelectionIfSelected();
10579
10613
  thisClass.setLogCmd('add residue labels', true);
10580
10614
  ic.drawCls.draw();
10581
10615
  });
10582
10616
 
10583
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10617
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10584
10618
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, true);
10585
10619
  ic.selectionCls.saveSelectionIfSelected();
10586
10620
  thisClass.setLogCmd('add residue number labels', true);
10587
10621
  ic.drawCls.draw();
10588
10622
  });
10589
10623
 
10590
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10624
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10591
10625
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
10592
10626
  ic.selectionCls.saveSelectionIfSelected();
10593
10627
  thisClass.setLogCmd('add reference number labels', true);
10594
10628
  ic.drawCls.draw();
10595
10629
  });
10596
10630
 
10597
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10631
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelIg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10598
10632
  ic.residueLabelsCls.addIgLabels(ic.hAtoms);
10599
10633
  ic.selectionCls.saveSelectionIfSelected();
10600
10634
  thisClass.setLogCmd('add ig labels', true);
10601
10635
  ic.drawCls.draw();
10602
10636
  });
10603
10637
 
10604
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10638
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10605
10639
  ic.analysisCls.addChainLabels(ic.hAtoms);
10606
10640
  ic.selectionCls.saveSelectionIfSelected();
10607
10641
  thisClass.setLogCmd('add chain labels', true);
10608
10642
  ic.drawCls.draw();
10609
10643
  });
10610
10644
 
10611
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10645
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10612
10646
  ic.analysisCls.addTerminiLabels(ic.hAtoms);
10613
10647
  ic.selectionCls.saveSelectionIfSelected();
10614
10648
  thisClass.setLogCmd('add terminal labels', true);
10615
10649
  ic.drawCls.draw();
10616
10650
  });
10617
10651
 
10618
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10652
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10619
10653
  me.htmlCls.dialogCls.openDlg('dl_addlabel', 'Add custom labels by selection');
10620
10654
  ic.pk = 1;
10621
10655
  ic.opts['pk'] = 'atom';
@@ -10623,19 +10657,19 @@ class ClickMenu {
10623
10657
  ic.pAtomNum = 0;
10624
10658
  });
10625
10659
 
10626
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; e.preventDefault();
10660
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; //e.preventDefault();
10627
10661
  me.htmlCls.dialogCls.openDlg('dl_addlabelselection', 'Add custom labels by the selected');
10628
10662
  });
10629
10663
 
10630
- me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; e.preventDefault();
10664
+ me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; //e.preventDefault();
10631
10665
  me.htmlCls.dialogCls.openDlg('dl_labelColor', 'Change color for all labels');
10632
10666
  });
10633
10667
 
10634
- me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; e.preventDefault();
10668
+ me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; //e.preventDefault();
10635
10669
  me.htmlCls.dialogCls.openDlg('dl_saveselection', 'Save the selected');
10636
10670
  });
10637
10671
 
10638
- me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10672
+ me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10639
10673
  ic.labelcolor = undefined;
10640
10674
  ic.pickpair = false;
10641
10675
  //ic.labels['residue'] = [];
@@ -10650,14 +10684,14 @@ class ClickMenu {
10650
10684
  ic.drawCls.draw();
10651
10685
  });
10652
10686
 
10653
- $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; e.preventDefault();
10687
+ $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; //e.preventDefault();
10654
10688
  let value = $(this).attr('v');
10655
10689
  ic.labelScale = value;
10656
10690
  ic.drawCls.draw();
10657
10691
  thisClass.setLogCmd('set label scale ' + value, true);
10658
10692
  });
10659
10693
 
10660
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10694
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10661
10695
  me.htmlCls.dialogCls.openDlg('dl_distance', 'Measure the distance of atoms');
10662
10696
  ic.pk = 1;
10663
10697
  ic.opts['pk'] = 'atom';
@@ -10667,7 +10701,7 @@ class ClickMenu {
10667
10701
  });
10668
10702
 
10669
10703
 
10670
- me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10704
+ me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10671
10705
  me.htmlCls.dialogCls.openDlg('dl_disttwosets', 'Measure the distance between two sets');
10672
10706
 
10673
10707
  thisClass.setSetsMenus('atomsCustomDist');
@@ -10675,7 +10709,7 @@ class ClickMenu {
10675
10709
  ic.bMeasureDistance = true;
10676
10710
  });
10677
10711
 
10678
- me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10712
+ me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10679
10713
  me.htmlCls.dialogCls.openDlg('dl_distmanysets', 'Measure the pairwise distances among many sets');
10680
10714
 
10681
10715
  thisClass.setSetsMenus('atomsCustomDistTable');
@@ -10683,7 +10717,7 @@ class ClickMenu {
10683
10717
  ic.bMeasureDistance = true;
10684
10718
  });
10685
10719
 
10686
- me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10720
+ me.myEventCls.onIds("#" + me.pre + "mn6_angleManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10687
10721
  me.htmlCls.dialogCls.openDlg('dl_anglemanysets', 'Measure the pairwise angles among many sets');
10688
10722
 
10689
10723
  thisClass.setSetsMenus('atomsCustomAngleTable');
@@ -10691,7 +10725,7 @@ class ClickMenu {
10691
10725
  ic.bMeasureAngle = true;
10692
10726
  });
10693
10727
 
10694
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10728
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10695
10729
  ic.pickpair = false;
10696
10730
  let select = "set lines off";
10697
10731
  thisClass.setLogCmd(select, true);
@@ -10702,7 +10736,7 @@ class ClickMenu {
10702
10736
  ic.drawCls.draw();
10703
10737
  });
10704
10738
 
10705
- me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10739
+ me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10706
10740
  me.htmlCls.dialogCls.openDlg('dl_cartoonshape', 'Draw cartoon for a set');
10707
10741
 
10708
10742
  let bOneset = true;
@@ -10711,7 +10745,7 @@ class ClickMenu {
10711
10745
  ic.bCartoonshape = true;
10712
10746
  });
10713
10747
 
10714
- me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10748
+ me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10715
10749
  me.htmlCls.dialogCls.openDlg('dl_linebtwsets', 'Draw a line between two sets');
10716
10750
 
10717
10751
  thisClass.setSetsMenus('linebtwsets');
@@ -10720,21 +10754,21 @@ class ClickMenu {
10720
10754
  });
10721
10755
 
10722
10756
 
10723
- me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10757
+ me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10724
10758
  //thisClass.setLogCmd('zoom selection', true);
10725
10759
  ic.transformCls.zoominSelection();
10726
10760
  ic.drawCls.draw();
10727
10761
  thisClass.setLogCmd('zoom selection', true);
10728
10762
  });
10729
10763
 
10730
- me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10764
+ me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10731
10765
  //thisClass.setLogCmd('center selection', true);
10732
10766
  ic.applyCenterCls.centerSelection();
10733
10767
  ic.drawCls.draw();
10734
10768
  thisClass.setLogCmd('center selection', true);
10735
10769
  });
10736
10770
 
10737
- me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10771
+ me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10738
10772
  //thisClass.setLogCmd('reset orientation', true);
10739
10773
  ic.transformCls.resetOrientation();
10740
10774
  //ic.setColorCls.applyOriginalColor();
@@ -10742,17 +10776,17 @@ class ClickMenu {
10742
10776
  thisClass.setLogCmd('reset orientation', true);
10743
10777
  });
10744
10778
 
10745
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10779
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10746
10780
  ic.setOptionCls.setOption('chemicalbinding', 'show');
10747
10781
  thisClass.setLogCmd('set chemicalbinding show', true);
10748
10782
  });
10749
10783
 
10750
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10784
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10751
10785
  ic.setOptionCls.setOption('chemicalbinding', 'hide');
10752
10786
  thisClass.setLogCmd('set chemicalbinding hide', true);
10753
10787
  });
10754
10788
 
10755
- me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10789
+ me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10756
10790
  if(ic.bInputfile) {
10757
10791
  var aaa = 1; //alert("Side-by-Side does NOT work when the input is from a local file.");
10758
10792
  return;
@@ -10771,19 +10805,19 @@ class ClickMenu {
10771
10805
  //}
10772
10806
  });
10773
10807
 
10774
- $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; e.preventDefault();
10808
+ $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; //e.preventDefault();
10775
10809
  me.htmlCls.dialogCls.openDlg('dl_translate', 'Translate the X,Y,Z coordinates of the structure');
10776
10810
  });
10777
10811
 
10778
- $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; e.preventDefault();
10812
+ $(document).on("click", "#" + me.pre + "mn6_angleTwoSets", function(e) { me.icn3d; //e.preventDefault();
10779
10813
  me.htmlCls.dialogCls.openDlg('dl_angle', 'Measure the angle between two vectors');
10780
10814
  });
10781
10815
 
10782
- $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; e.preventDefault();
10816
+ $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; //e.preventDefault();
10783
10817
  me.htmlCls.dialogCls.openDlg('dl_matrix', 'Apply matrix to the X,Y,Z coordinates of the structure');
10784
10818
  });
10785
10819
 
10786
- $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; e.preventDefault();
10820
+ $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; //e.preventDefault();
10787
10821
  let value = $(this).attr('v').toLowerCase();
10788
10822
  let direction = value.split(' ')[1];
10789
10823
 
@@ -10795,7 +10829,7 @@ class ClickMenu {
10795
10829
  ic.resizeCanvasCls.rotStruc(direction);
10796
10830
  });
10797
10831
 
10798
- $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; e.preventDefault();
10832
+ $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; //e.preventDefault();
10799
10833
  let value = $(this).attr('v').toLowerCase();
10800
10834
  let direction = value.split(' ')[1];
10801
10835
 
@@ -10814,21 +10848,21 @@ class ClickMenu {
10814
10848
  ic.transformCls.setRotation(axis, angle);
10815
10849
  });
10816
10850
 
10817
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10851
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10818
10852
  ic.setOptionCls.setOption('camera', 'perspective');
10819
10853
  thisClass.setLogCmd('set camera perspective', true);
10820
10854
  });
10821
10855
 
10822
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10856
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10823
10857
  ic.setOptionCls.setOption('camera', 'orthographic');
10824
10858
  thisClass.setLogCmd('set camera orthographic', true);
10825
10859
  });
10826
10860
 
10827
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10861
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10828
10862
  ic.setStyleCls.setBackground('black');
10829
10863
  });
10830
10864
 
10831
- me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10865
+ me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10832
10866
  if(ic.opts['background'] == 'black') {
10833
10867
  ic.setStyleCls.setBackground('white');
10834
10868
  }
@@ -10837,19 +10871,19 @@ class ClickMenu {
10837
10871
  }
10838
10872
  });
10839
10873
 
10840
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10874
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10841
10875
  ic.setStyleCls.setBackground('grey');
10842
10876
  });
10843
10877
 
10844
- me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10878
+ me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10845
10879
  ic.setStyleCls.setBackground('white');
10846
10880
  });
10847
10881
 
10848
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10882
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10849
10883
  ic.setStyleCls.setBackground('transparent');
10850
10884
  });
10851
10885
 
10852
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10886
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10853
10887
  //ic.setOptionCls.setOption('fog', 'yes');
10854
10888
  ic.opts['fog'] = 'yes';
10855
10889
  ic.fogCls.setFog(true);
@@ -10857,7 +10891,7 @@ class ClickMenu {
10857
10891
  thisClass.setLogCmd('set fog on', true);
10858
10892
  });
10859
10893
 
10860
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10894
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10861
10895
  //ic.setOptionCls.setOption('fog', 'no');
10862
10896
  ic.opts['fog'] = 'no';
10863
10897
  ic.fogCls.setFog(true);
@@ -10865,22 +10899,22 @@ class ClickMenu {
10865
10899
  thisClass.setLogCmd('set fog off', true);
10866
10900
  });
10867
10901
 
10868
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10902
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10869
10903
  ic.setOptionCls.setOption('slab', 'yes');
10870
10904
  thisClass.setLogCmd('set slab on', true);
10871
10905
  });
10872
10906
 
10873
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10907
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10874
10908
  ic.setOptionCls.setOption('slab', 'no');
10875
10909
  thisClass.setLogCmd('set slab off', true);
10876
10910
  });
10877
10911
 
10878
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10912
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10879
10913
  ic.setOptionCls.setOption('axis', 'yes');
10880
10914
  thisClass.setLogCmd('set axis on', true);
10881
10915
  });
10882
10916
 
10883
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10917
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10884
10918
  ic.pc1 = true;
10885
10919
 
10886
10920
  ic.axesCls.setPc1Axes();
@@ -10888,7 +10922,7 @@ class ClickMenu {
10888
10922
  });
10889
10923
 
10890
10924
 
10891
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10925
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10892
10926
  ic.pc1 = false;
10893
10927
  ic.axes = [];
10894
10928
 
@@ -10897,37 +10931,37 @@ class ClickMenu {
10897
10931
  thisClass.setLogCmd('set axis off', true);
10898
10932
  });
10899
10933
 
10900
- me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10934
+ me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10901
10935
  ic.bAxisOnly = false;
10902
10936
  await ic.symdCls.retrieveSymmetry(Object.keys(ic.structures)[0]);
10903
10937
  //me.htmlCls.dialogCls.openDlg('dl_symmetry', 'Symmetry');
10904
10938
  });
10905
10939
 
10906
- me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
10940
+ me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10907
10941
  ic.bAxisOnly = false;
10908
10942
  await ic.symdCls.retrieveSymd();
10909
10943
  ic.bSymd = true;
10910
10944
 
10911
10945
  thisClass.setLogCmd('symd symmetry', true);
10912
10946
  });
10913
- me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10947
+ me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10914
10948
  ic.symdArray = [];
10915
10949
  ic.drawCls.draw();
10916
10950
  thisClass.setLogCmd('clear symd symmetry', true);
10917
10951
  });
10918
- me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10952
+ me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10919
10953
  ic.bAxisOnly = true;
10920
10954
  ic.drawCls.draw();
10921
10955
  thisClass.setLogCmd('show axis', true);
10922
10956
  });
10923
10957
 
10924
10958
 
10925
- me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10959
+ me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10926
10960
  ic.analysisCls.calculateArea();
10927
10961
  thisClass.setLogCmd('area', true);
10928
10962
  });
10929
10963
 
10930
- me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10964
+ me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10931
10965
  ic.bAxisOnly = false;
10932
10966
 
10933
10967
  let title = $("#" + me.pre + "selectSymmetry" ).val();
@@ -10937,14 +10971,14 @@ class ClickMenu {
10937
10971
  ic.drawCls.draw();
10938
10972
  thisClass.setLogCmd('symmetry ' + title, true);
10939
10973
  });
10940
- me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
10974
+ me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10941
10975
  let title = 'none';
10942
10976
  ic.symmetrytitle = undefined;
10943
10977
  ic.drawCls.draw();
10944
10978
  thisClass.setLogCmd('symmetry ' + title, true);
10945
10979
  });
10946
10980
 
10947
- me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
10981
+ me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10948
10982
  thisClass.SetChainsAdvancedMenu();
10949
10983
 
10950
10984
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -10961,11 +10995,11 @@ class ClickMenu {
10961
10995
  $("#" + me.pre + "atomsCustomHbond2").resizable();
10962
10996
  });
10963
10997
 
10964
- me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; e.preventDefault();
10998
+ me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; //e.preventDefault();
10965
10999
  me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
10966
11000
  });
10967
11001
 
10968
- me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
11002
+ me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
10969
11003
  thisClass.setLogCmd('set dssp sse', true);
10970
11004
  await ic.pdbParserCls.applyCommandDssp();
10971
11005
  ic.bResetAnno = true;
@@ -10978,12 +11012,12 @@ class ClickMenu {
10978
11012
  });
10979
11013
 
10980
11014
 
10981
- me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11015
+ me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10982
11016
  ic.showInterCls.hideHbondsContacts();
10983
11017
  ic.drawCls.draw();
10984
11018
  });
10985
11019
 
10986
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11020
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10987
11021
  let select = "stabilizer";
10988
11022
  ic.threeDPrintCls.addStabilizer();
10989
11023
  ic.threeDPrintCls.prepareFor3Dprint();
@@ -10991,14 +11025,14 @@ class ClickMenu {
10991
11025
  thisClass.setLogCmd(select, true);
10992
11026
  });
10993
11027
 
10994
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11028
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
10995
11029
  let select = "set stabilizer off";
10996
11030
  thisClass.setLogCmd(select, true);
10997
11031
  ic.threeDPrintCls.hideStabilizer();
10998
11032
  ic.drawCls.draw();
10999
11033
  });
11000
11034
 
11001
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11035
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11002
11036
  me.htmlCls.dialogCls.openDlg('dl_stabilizer', 'Add One Stabilizer');
11003
11037
  ic.pk = 1;
11004
11038
  ic.opts['pk'] = 'atom';
@@ -11006,7 +11040,7 @@ class ClickMenu {
11006
11040
  ic.pAtomNum = 0;
11007
11041
  });
11008
11042
 
11009
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11043
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11010
11044
  me.htmlCls.dialogCls.openDlg('dl_stabilizer_rm', 'Remove One Stabilizer');
11011
11045
  ic.pk = 1;
11012
11046
  ic.opts['pk'] = 'atom';
@@ -11014,27 +11048,27 @@ class ClickMenu {
11014
11048
  ic.pAtomNum = 0;
11015
11049
  });
11016
11050
 
11017
- me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; e.preventDefault();
11051
+ me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; //e.preventDefault();
11018
11052
  me.htmlCls.dialogCls.openDlg('dl_thickness', 'Set Thickness for 3D Printing');
11019
11053
  });
11020
11054
 
11021
- me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; e.preventDefault();
11055
+ me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; //e.preventDefault();
11022
11056
  me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Style Preferences');
11023
11057
  });
11024
11058
 
11025
11059
 
11026
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11060
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11027
11061
  let select = "disulfide bonds";
11028
11062
  thisClass.setLogCmd(select, true);
11029
11063
  ic.showInterCls.showSsbonds();
11030
11064
  });
11031
11065
 
11032
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11066
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11033
11067
  ic.viewInterPairsCls.exportSsbondPairs();
11034
11068
  thisClass.setLogCmd("export disulfide bond pairs", false);
11035
11069
  });
11036
11070
 
11037
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11071
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11038
11072
  ic.opts["ssbonds"] = "no";
11039
11073
  let select = "set disulfide bonds off";
11040
11074
  thisClass.setLogCmd(select, true);
@@ -11042,7 +11076,7 @@ class ClickMenu {
11042
11076
  ic.setOptionCls.setStyle('sidec', 'nothing');
11043
11077
  });
11044
11078
 
11045
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11079
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11046
11080
  let select = "cross linkage";
11047
11081
  thisClass.setLogCmd(select, true);
11048
11082
  //ic.bShowCrossResidueBond = true;
@@ -11050,12 +11084,12 @@ class ClickMenu {
11050
11084
  ic.showInterCls.showClbonds();
11051
11085
  });
11052
11086
 
11053
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11087
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11054
11088
  ic.viewInterPairsCls.exportClbondPairs();
11055
11089
  thisClass.setLogCmd("export cross linkage pairs", false);
11056
11090
  });
11057
11091
 
11058
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
11092
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
11059
11093
  ic.opts["clbonds"] = "no";
11060
11094
  let select = "set cross linkage off";
11061
11095
  thisClass.setLogCmd(select, true);
@@ -11103,7 +11137,7 @@ class ClickMenu {
11103
11137
  });
11104
11138
  });
11105
11139
 
11106
- me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; e.preventDefault();
11140
+ me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; //e.preventDefault();
11107
11141
  let text = $("#" + me.pre + "jn_commands").val();
11108
11142
  navigator.clipboard.writeText(text);
11109
11143
  });
@@ -12024,6 +12058,7 @@ class SetMenu {
12024
12058
  html += this.getLink('mn2_selectedcenter', 'Zoom in Selection', 1, 1);
12025
12059
  //html += this.getLink('mn6_center', 'Center Selection', undefined, 1);
12026
12060
  html += this.getLink('mn6_center', 'Center Selection', 1, 1);
12061
+
12027
12062
  html += this.getLink('mn2_fullstru', 'View Full Structure');
12028
12063
  html += this.getLinkWrapper('mn2_alternate', 'Alternate(Key "a")', 'mn2_alternateWrap', undefined, 1);
12029
12064
 
@@ -12271,6 +12306,15 @@ class SetMenu {
12271
12306
  html += "</ul>";
12272
12307
  html += "</li>";
12273
12308
 
12309
+ if(me.cfg.cid === undefined) {
12310
+ html += this.getMenuText('mn2_clashedwrap', 'Clashed Residues', undefined, undefined, 1);
12311
+ html += "<ul>";
12312
+ html += this.getRadio('mn2_clashed', 'mn2_clashedYes', 'Show', true, undefined, 2);
12313
+ html += this.getRadio('mn2_clashed', 'mn2_clashedNo', 'Hide', undefined, undefined, 2);
12314
+ html += "</ul>";
12315
+ html += "</li>";
12316
+ }
12317
+
12274
12318
  html += this.getLink('mn3_setThickness', 'Preferences', undefined, 1);
12275
12319
 
12276
12320
  html += this.getMenuSep();
@@ -36867,7 +36911,7 @@ class Contact {
36867
36911
  //This function returns atoms within a certain "distance" (in angstrom) from the "targetAtoms".
36868
36912
  //The returned atoms are stored in a hash with atom indices as keys and 1 as values.
36869
36913
  //Only those atoms in "allAtoms" are considered.
36870
- getAtomsWithinAtom(atomlist, atomlistTarget, distance, bGetPairs, bInteraction, bInternal, bIncludeTarget) { let ic = this.icn3d; ic.icn3dui;
36914
+ getAtomsWithinAtom(atomlist, atomlistTarget, distance, bGetPairs, bInteraction, bInternal, bIncludeTarget) { let ic = this.icn3d, me = ic.icn3dui;
36871
36915
  let neighbors = this.getNeighboringAtoms(atomlist, atomlistTarget, distance, bIncludeTarget);
36872
36916
  if(bGetPairs) ic.resid2Residhash = {};
36873
36917
 
@@ -36875,6 +36919,8 @@ class Contact {
36875
36919
  for(let i in atomlistTarget) {
36876
36920
  //var oriAtom = atomlistTarget[i];
36877
36921
  let oriAtom = ic.atoms[i];
36922
+ let r1 = me.parasCls.vdwRadii[oriAtom.elem.toUpperCase()];
36923
+ let chainid1 = oriAtom.structure + '_' + oriAtom.chain;
36878
36924
 
36879
36925
  let oriCalpha = undefined, oriResidName = undefined;
36880
36926
  let oriResid = oriAtom.structure + '_' + oriAtom.chain + '_' + oriAtom.resi;
@@ -36899,6 +36945,8 @@ class Contact {
36899
36945
 
36900
36946
  for (let j in neighbors) {
36901
36947
  let atom = neighbors[j];
36948
+ let r2 = me.parasCls.vdwRadii[atom.elem.toUpperCase()];
36949
+ let chainid2 = atom.structure + '_' + atom.chain;
36902
36950
 
36903
36951
  if(bInteraction && !ic.crossstrucinter && oriAtom.structure != atom.structure) continue;
36904
36952
 
@@ -36909,7 +36957,16 @@ class Contact {
36909
36957
  //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);
36910
36958
  let atomDist = atom.coord.distanceTo(oriAtom.coord);
36911
36959
 
36912
- //if(atomDistSq < maxDistSq) {
36960
+ // consider backbone clashes
36961
+ if(bInteraction && atomDist < r1 + r2
36962
+ && (oriAtom.name === "N" || oriAtom.name === "C" || oriAtom.name === "O" || (oriAtom.name === "CA" && oriAtom.elem === "C") )
36963
+ && (atom.name === "N" || atom.name === "C" || atom.name === "O" || (atom.name === "CA" && atom.elem === "C") ) ) { // clashed atoms are not counted as interactions
36964
+ // store the clashed residues
36965
+ if(!ic.chainid2clashedResidpair) ic.chainid2clashedResidpair = {};
36966
+
36967
+ ic.chainid2clashedResidpair[chainid1 + '_' + oriAtom.resi + '|' + chainid2 + '_' + atom.resi] = '0|0';
36968
+ }
36969
+
36913
36970
  if(atomDist < distance) {
36914
36971
  ret[atom.serial] = atom;
36915
36972
  let calpha = undefined, residName = undefined;
@@ -41850,7 +41907,7 @@ class AnnoDomain {
41850
41907
  this.icn3d = icn3d;
41851
41908
  }
41852
41909
 
41853
- showDomainPerStructure(index) { let ic = this.icn3d; ic.icn3dui;
41910
+ showDomainPerStructure(index, bNotShowDomain) { let ic = this.icn3d; ic.icn3dui;
41854
41911
  let thisClass = this;
41855
41912
  //var chnid = Object.keys(ic.protein_chainid)[0];
41856
41913
  //var pdbid = chnid.substr(0, chnid.indexOf('_'));
@@ -41882,7 +41939,8 @@ class AnnoDomain {
41882
41939
  data.domains = {};
41883
41940
  for(let chainid in ic.chains) {
41884
41941
  let structure = chainid.substr(0, chainid.indexOf('_'));
41885
- if(pdbid == structure && ic.protein_chainid.hasOwnProperty(chainid)) {
41942
+ // if(pdbid == structure && ic.protein_chainid.hasOwnProperty(chainid)) {
41943
+ if(pdbid == structure) {
41886
41944
  data.domains[chainid] = {};
41887
41945
  data.domains[chainid].domains = [];
41888
41946
 
@@ -41909,10 +41967,10 @@ class AnnoDomain {
41909
41967
  }
41910
41968
 
41911
41969
  ic.mmdb_dataArray[index] = data;
41912
- let bCalcDirect = true;
41913
- for(let chnid in ic.protein_chainid) {
41970
+ // for(let chnid in ic.protein_chainid) {
41971
+ for(let chnid in ic.chains) {
41914
41972
  if(chnid.indexOf(pdbid) !== -1) {
41915
- thisClass.showDomainWithData(chnid, ic.mmdb_dataArray[index], bCalcDirect);
41973
+ thisClass.showDomainWithData(chnid, ic.mmdb_dataArray[index], bNotShowDomain);
41916
41974
  }
41917
41975
  }
41918
41976
 
@@ -41922,7 +41980,7 @@ class AnnoDomain {
41922
41980
  }
41923
41981
 
41924
41982
  //Show the annotations of 3D domains.
41925
- showDomainAll() { let ic = this.icn3d; ic.icn3dui;
41983
+ showDomainAll(bNotShowDomain) { let ic = this.icn3d; ic.icn3dui;
41926
41984
  //var chnid = Object.keys(ic.protein_chainid)[0];
41927
41985
  //var pdbid = chnid.substr(0, chnid.indexOf('_'));
41928
41986
  let pdbArray = Object.keys(ic.structures);
@@ -41934,7 +41992,7 @@ class AnnoDomain {
41934
41992
  }
41935
41993
 
41936
41994
  for(let i = 0, il = pdbArray.length; i < il; ++i) {
41937
- this.showDomainPerStructure(i);
41995
+ this.showDomainPerStructure(i, bNotShowDomain);
41938
41996
  }
41939
41997
  }
41940
41998
 
@@ -41952,7 +42010,7 @@ class AnnoDomain {
41952
42010
  return resi;
41953
42011
  }
41954
42012
 
41955
- showDomainWithData(chnid, data, bCalcDirect) { let ic = this.icn3d, me = ic.icn3dui;
42013
+ showDomainWithData(chnid, data, bNotShowDomain) { let ic = this.icn3d, me = ic.icn3dui;
41956
42014
  let html = '<div id="' + ic.pre + chnid + '_domainseq_sequence" class="icn3d-dl_sequence">';
41957
42015
  let html2 = html;
41958
42016
  let html3 = html;
@@ -42026,6 +42084,26 @@ class AnnoDomain {
42026
42084
  }
42027
42085
  }
42028
42086
 
42087
+ if(ic.chainid2clashedResidpair) { //assign domain size to each residue in the clashed residues
42088
+ for(let residpair in ic.chainid2clashedResidpair) {
42089
+ let residArray = residpair.split('|');
42090
+ let valueArray = ic.chainid2clashedResidpair[residpair].split('|');
42091
+
42092
+ for(let i = 0, il = residArray.length; i < il; ++i) {
42093
+ let chainid = residArray[i][0] + '_' + residArray[i][1];
42094
+
42095
+ if(chainid == chnid) {
42096
+ let resi = residArray[i][3];
42097
+ if(resiHash.hasOwnProperty(resi)) {
42098
+ ic.chainid2clashedResidpair[residpair] = (i == 0) ? resCnt + '|' + valueArray[1] : valueArray[1] + '|' + resCnt;
42099
+ }
42100
+ }
42101
+ }
42102
+ }
42103
+ }
42104
+
42105
+ if(bNotShowDomain) continue;
42106
+
42029
42107
  // save 3D domain info for node.js script
42030
42108
  if(me.bNode) {
42031
42109
  let domainName = '3D domain ' +(index+1).toString();
@@ -42120,12 +42198,103 @@ class AnnoDomain {
42120
42198
  html += htmlTmp;
42121
42199
  html2 += htmlTmp;
42122
42200
  }
42123
- html += '</div>';
42124
- html2 += '</div>';
42125
- html3 += '</div>';
42126
- $("#" + ic.pre + "dt_domain_" + chnid).html(html);
42127
- $("#" + ic.pre + "ov_domain_" + chnid).html(html2);
42128
- $("#" + ic.pre + "tt_domain_" + chnid).html(html3);
42201
+
42202
+ if(!bNotShowDomain) {
42203
+ html += '</div>';
42204
+ html2 += '</div>';
42205
+ html3 += '</div>';
42206
+ $("#" + ic.pre + "dt_domain_" + chnid).html(html);
42207
+ $("#" + ic.pre + "ov_domain_" + chnid).html(html2);
42208
+ $("#" + ic.pre + "tt_domain_" + chnid).html(html3);
42209
+ }
42210
+
42211
+ // hide clashed residues between two chains
42212
+ if(bNotShowDomain && ic.chainid2clashedResidpair) {
42213
+ ic.clashedResidHash = {};
42214
+ for(let residpair in ic.chainid2clashedResidpair) {
42215
+ let residArray = residpair.split('|');
42216
+ let valueArray = ic.chainid2clashedResidpair[residpair].split('|');
42217
+
42218
+ if(parseInt(valueArray[0]) < parseInt(valueArray[1])) {
42219
+ ic.clashedResidHash[residArray[0]] = 1;
42220
+ }
42221
+ else {
42222
+ ic.clashedResidHash[residArray[1]] = 1;
42223
+ }
42224
+ }
42225
+
42226
+ // expand clashed residues to the SSE and the loops connecting the SSE
42227
+ let addResidHash = {}, tmpHash = {};
42228
+ for(let resid in ic.clashedResidHash) {
42229
+ let pos = resid.lastIndexOf('_');
42230
+ let resi = parseInt(resid.substr(pos + 1));
42231
+ let chainid = resid.substr(0, pos);
42232
+ let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
42233
+ if(atom.ss == 'coil') {
42234
+ tmpHash = this.getMoreResidues(resi, chainid, 1, 'not coil');
42235
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
42236
+ tmpHash = this.getMoreResidues(resi, chainid, -1, 'not coil');
42237
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
42238
+ }
42239
+ else {
42240
+ tmpHash = this.getMoreResidues(resi, chainid, 1, 'ssbegin');
42241
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
42242
+ tmpHash = this.getMoreResidues(resi, chainid, -1, 'ssend');
42243
+ addResidHash = me.hashUtilsCls.unionHash(addResidHash, tmpHash);
42244
+ }
42245
+ }
42246
+
42247
+ ic.clashedResidHash = me.hashUtilsCls.unionHash(ic.clashedResidHash, addResidHash);
42248
+ }
42249
+ }
42250
+
42251
+ showHideClashedResidues() { let ic = this.icn3d, me = ic.icn3dui;
42252
+ // show or hide clashed residues
42253
+ if(ic.clashedResidHash && Object.keys(ic.clashedResidHash).length > 0) {
42254
+ let tmpHash = {};
42255
+ for(let resid in ic.clashedResidHash) {
42256
+ tmpHash = me.hashUtilsCls.unionHash(tmpHash, ic.residues[resid]);
42257
+ }
42258
+
42259
+ if(ic.bHideClashed) {
42260
+ ic.hAtoms = me.hashUtilsCls.exclHash(ic.hAtoms, tmpHash);
42261
+ }
42262
+ else {
42263
+ ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, tmpHash);
42264
+ }
42265
+
42266
+ // if(ic.bHideClashed) ic.definedSetsCls.setMode('selection');
42267
+ ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
42268
+ }
42269
+ }
42270
+
42271
+ getMoreResidues(resi, chainid, direction, condition) { let ic = this.icn3d; ic.icn3dui;
42272
+ let addResidHash = {};
42273
+ for(let i = 1; i < 100; ++i) {
42274
+ let resid2 = chainid + '_' + (resi + direction * i).toString();
42275
+ let atom2 = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid2]);
42276
+ if(atom2) {
42277
+ let bBreak = false;
42278
+ if(condition == 'not coil') {
42279
+ bBreak = (atom2.ss != 'coil');
42280
+ }
42281
+ else if(condition == 'ssbegin') {
42282
+ bBreak = atom2.ssbegin;
42283
+ }
42284
+ else if(condition == 'ssend') {
42285
+ bBreak = atom2.ssend;
42286
+ }
42287
+
42288
+ if(bBreak) {
42289
+ break;
42290
+ }
42291
+ else {
42292
+ addResidHash[resid2] = 1;
42293
+ }
42294
+ }
42295
+ }
42296
+
42297
+ return addResidHash;
42129
42298
  }
42130
42299
 
42131
42300
  }
@@ -51058,7 +51227,6 @@ class ShowInter {
51058
51227
  pickCustomSphere_base(radius, atomlistTarget, otherAtoms, bSphereCalc, bInteraction, type, select, bGetPairs, bIncludeTarget) { let ic = this.icn3d, me = ic.icn3dui; // ic.pAtom is set already
51059
51228
  let atoms;
51060
51229
  if(bInteraction) {
51061
- // 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);
51062
51230
  atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.hash2Atoms(otherAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
51063
51231
  ic.resid2ResidhashInteractions = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
51064
51232
  }
@@ -53319,7 +53487,7 @@ class ChainalignParser {
53319
53487
  return hAtomsAll;
53320
53488
  }
53321
53489
 
53322
- downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse) { let ic = this.icn3d, me = ic.icn3dui;
53490
+ async downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse) { let ic = this.icn3d, me = ic.icn3dui;
53323
53491
  // set trans and rotation matrix
53324
53492
  ic.t_trans_add = [];
53325
53493
  ic.q_trans_sub = [];
@@ -53371,9 +53539,22 @@ class ChainalignParser {
53371
53539
  return;
53372
53540
  }
53373
53541
  else {
53374
- /// if(ic.deferredRealignByStruct !== undefined) ic.deferredRealignByStruct.resolve();
53375
- if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned...");
53376
- return;
53542
+ if(me.cfg.aligntool == 'tmalign') {
53543
+ if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned...");
53544
+ return;
53545
+ }
53546
+ else {
53547
+ console.log("These structures can NOT be aligned with VAST. Realign the chains with TM-align.");
53548
+
53549
+ // ic.hAtoms = {};
53550
+ // for(let i = 0, il = chainidPairArray.length; i < il; ++i) {
53551
+ // ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.chains[chainidPairArray[i]]);
53552
+ // }
53553
+
53554
+ me.cfg.aligntool = 'tmalign';
53555
+ await ic.realignParserCls.realignOnStructAlign();
53556
+ return;
53557
+ }
53377
53558
  }
53378
53559
  }
53379
53560
 
@@ -66849,6 +67030,19 @@ class ApplyCommand {
66849
67030
  ic.bGlycansCartoon = false;
66850
67031
  }
66851
67032
  }
67033
+ else if(command.indexOf('clashed residues') == 0) {
67034
+ let value = command.substr(command.lastIndexOf(' ') + 1);
67035
+
67036
+ if(value == 'show') {
67037
+ ic.bHideClashed = false;
67038
+ ic.annoDomainCls.showHideClashedResidues();
67039
+ }
67040
+ else {
67041
+ ic.bHideClashed = true;
67042
+ me.htmlCls.clickMenuCls.setClashedResidues();
67043
+ ic.annoDomainCls.showHideClashedResidues();
67044
+ }
67045
+ }
66852
67046
  else if(command.indexOf('save html') == 0) {
66853
67047
  let id = command.substr(command.lastIndexOf(' ') + 1);
66854
67048
  me.htmlCls.eventsCls.saveHtml(id);
@@ -79110,7 +79304,7 @@ class ShareLink {
79110
79304
  }
79111
79305
 
79112
79306
  shareLinkUrl(bAllCommands, bOutputCmd, bStatefile) { let ic = this.icn3d, me = ic.icn3dui;
79113
- let url = me.htmlCls.baseUrl + "icn3d/?";
79307
+ let url = me.htmlCls.baseUrl + "icn3d/full_" + me.REVISION + ".html?";
79114
79308
  let outputCmd = '';
79115
79309
  if(me.cfg.bSidebyside) url = me.htmlCls.baseUrl + "icn3d/full2.html?";
79116
79310
 
@@ -79265,6 +79459,7 @@ class ShareLink {
79265
79459
  else if(prevCommandStr.indexOf('pickatom') !== -1 && commandStr.indexOf('pickatom') !== -1) ;
79266
79460
  // remove all "show selection" except the last one
79267
79461
  else if(prevCommandStr == 'show selection' && ic.commands.slice(i).toString().indexOf('show selection') != -1) ;
79462
+ else if(prevCommandStr == commandStr) ;
79268
79463
  else if(prevCommandStr.indexOf(toggleStr) !== -1) {
79269
79464
  ++cntToggle;
79270
79465
  }
@@ -82221,7 +82416,7 @@ class iCn3DUI {
82221
82416
  //even when multiple iCn3D viewers are shown together.
82222
82417
  this.pre = this.cfg.divid + "_";
82223
82418
 
82224
- this.REVISION = '3.36.1';
82419
+ this.REVISION = '3.37.0';
82225
82420
 
82226
82421
  // In nodejs, iCn3D defines "window = {navigator: {}}"
82227
82422
  this.bNode = (Object.keys(window).length < 2) ? true : false;