icn3d 3.24.0 → 3.24.2

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 +453 -368
  2. package/icn3d.min.js +7 -3
  3. package/icn3d.module.js +453 -368
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -4368,10 +4368,10 @@ class ParasCls {
4368
4368
  ];
4369
4369
 
4370
4370
  this.backgroundColors = {
4371
- black: this.thr(0x000000),
4372
- grey: this.thr(0xCCCCCC),
4373
- white: this.thr(0xFFFFFF),
4374
- transparent: this.thr(0xFFFFFF) //this.thr(0x000000)
4371
+ 'black': this.thr(0x000000),
4372
+ 'grey': this.thr(0xCCCCCC),
4373
+ 'white': this.thr(0xFFFFFF),
4374
+ 'transparent': this.thr(0xFFFFFF) //this.thr(0x000000)
4375
4375
  };
4376
4376
 
4377
4377
  this.residueColors = {
@@ -5785,96 +5785,96 @@ class ClickMenu {
5785
5785
  let thisClass = this;
5786
5786
  //mn 1
5787
5787
  // clkMn1_mmtfid: function() {
5788
- me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; //e.preventDefault();
5788
+ me.myEventCls.onIds("#" + me.pre + "mn1_vastplus", "click", function(e) { me.icn3d; e.preventDefault();
5789
5789
  me.htmlCls.dialogCls.openDlg('dl_vastplus', 'Please input PDB ID for VAST+');
5790
5790
  });
5791
5791
 
5792
- me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; //e.preventDefault();
5792
+ me.myEventCls.onIds("#" + me.pre + "mn1_vast", "click", function(e) { me.icn3d; e.preventDefault();
5793
5793
  me.htmlCls.dialogCls.openDlg('dl_vast', 'Please input chain or PDB file for VAST');
5794
5794
  });
5795
5795
 
5796
- me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; //e.preventDefault();
5796
+ me.myEventCls.onIds("#" + me.pre + "mn1_foldseek", "click", function(e) { me.icn3d; e.preventDefault();
5797
5797
  me.htmlCls.dialogCls.openDlg('dl_foldseek', 'Submit your selection to Foldseek');
5798
5798
  });
5799
5799
 
5800
- me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; //e.preventDefault();
5800
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmtfid", "click", function(e) { me.icn3d; e.preventDefault();
5801
5801
  me.htmlCls.dialogCls.openDlg('dl_mmtfid', 'Please input MMTF ID');
5802
5802
  });
5803
5803
 
5804
5804
  // clkMn1_pdbid: function() {
5805
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; //e.preventDefault();
5805
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbid", "click", function(e) { me.icn3d; e.preventDefault();
5806
5806
  me.htmlCls.dialogCls.openDlg('dl_pdbid', 'Please input PDB ID');
5807
5807
  });
5808
5808
 
5809
- me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; //e.preventDefault();
5809
+ me.myEventCls.onIds("#" + me.pre + "mn1_afid", "click", function(e) { me.icn3d; e.preventDefault();
5810
5810
  me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
5811
5811
  });
5812
5812
 
5813
- me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; //e.preventDefault();
5813
+ me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
5814
5814
  me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI Protein Accession');
5815
5815
  });
5816
5816
 
5817
- me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; //e.preventDefault();
5817
+ me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
5818
5818
  me.htmlCls.dialogCls.openDlg('dl_opmid', 'Please input OPM PDB ID');
5819
5819
  });
5820
5820
 
5821
- me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; //e.preventDefault();
5821
+ me.myEventCls.onIds("#" + me.pre + "mn1_align", "click", function(e) { me.icn3d; e.preventDefault();
5822
5822
  me.htmlCls.dialogCls.openDlg('dl_align', 'Align two PDB structures');
5823
5823
  });
5824
5824
 
5825
- me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; //e.preventDefault();
5825
+ me.myEventCls.onIds("#" + me.pre + "mn1_alignaf", "click", function(e) { me.icn3d; e.preventDefault();
5826
5826
  me.htmlCls.dialogCls.openDlg('dl_alignaf', 'Align two AlphaFold structures');
5827
5827
  });
5828
5828
 
5829
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; //e.preventDefault();
5829
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d; e.preventDefault();
5830
5830
  me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
5831
5831
  });
5832
5832
 
5833
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; //e.preventDefault();
5833
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d; e.preventDefault();
5834
5834
  me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
5835
5835
  });
5836
5836
 
5837
- me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; //e.preventDefault();
5837
+ me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d; e.preventDefault();
5838
5838
  me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
5839
5839
  });
5840
5840
 
5841
- me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; //e.preventDefault();
5841
+ me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d; e.preventDefault();
5842
5842
  me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
5843
5843
  });
5844
5844
 
5845
- me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; //e.preventDefault();
5845
+ me.myEventCls.onIds("#" + me.pre + "mn1_pdbfile", "click", function(e) { me.icn3d; e.preventDefault();
5846
5846
  //me = me.setIcn3dui($(this).attr('id'));
5847
5847
  me.htmlCls.dialogCls.openDlg('dl_pdbfile', 'Please input PDB File');
5848
5848
  });
5849
- me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; //e.preventDefault();
5849
+ me.myEventCls.onIds(["#" + me.pre + "mn1_pdbfile_app", "#" + me.pre + "tool_pdbfile"], "click", function(e) { me.icn3d; e.preventDefault();
5850
5850
  //me = me.setIcn3dui($(this).attr('id'));
5851
5851
  me.htmlCls.dialogCls.openDlg('dl_pdbfile_app', 'Please append PDB Files');
5852
5852
  });
5853
5853
 
5854
- me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; //e.preventDefault();
5854
+ me.myEventCls.onIds("#" + me.pre + "mn1_mol2file", "click", function(e) { me.icn3d; e.preventDefault();
5855
5855
  me.htmlCls.dialogCls.openDlg('dl_mol2file', 'Please input Mol2 File');
5856
5856
  });
5857
5857
 
5858
- me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; //e.preventDefault();
5858
+ me.myEventCls.onIds("#" + me.pre + "mn1_sdffile", "click", function(e) { me.icn3d; e.preventDefault();
5859
5859
  me.htmlCls.dialogCls.openDlg('dl_sdffile', 'Please input SDF File');
5860
5860
  });
5861
5861
 
5862
- me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; //e.preventDefault();
5862
+ me.myEventCls.onIds("#" + me.pre + "mn1_xyzfile", "click", function(e) { me.icn3d; e.preventDefault();
5863
5863
  me.htmlCls.dialogCls.openDlg('dl_xyzfile', 'Please input XYZ File');
5864
5864
  });
5865
5865
 
5866
- me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; //e.preventDefault();
5866
+ me.myEventCls.onIds("#" + me.pre + "mn1_afmapfile", "click", function(e) { me.icn3d; e.preventDefault();
5867
5867
  me.htmlCls.dialogCls.openDlg('dl_afmapfile', 'Please input AlphaFold PAE File');
5868
5868
  });
5869
5869
 
5870
- me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; //e.preventDefault();
5870
+ me.myEventCls.onIds("#" + me.pre + "mn1_urlfile", "click", function(e) { me.icn3d; e.preventDefault();
5871
5871
  me.htmlCls.dialogCls.openDlg('dl_urlfile', 'Load data by URL');
5872
5872
  });
5873
5873
 
5874
- me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; //e.preventDefault();
5874
+ me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
5875
5875
  me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
5876
5876
  });
5877
- me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5877
+ me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
5878
5878
  let url = $("#" + me.pre + "sharelinkurl").val();
5879
5879
  thisClass.setLogCmd("open " + url, false);
5880
5880
  localStorage.setItem('fixedversion', '1');
@@ -5882,65 +5882,65 @@ class ClickMenu {
5882
5882
  window.open(url, urlTarget);
5883
5883
  });
5884
5884
 
5885
- me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; //e.preventDefault();
5885
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; e.preventDefault();
5886
5886
  me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please input mmCIF File');
5887
5887
  });
5888
5888
 
5889
- me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
5889
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; e.preventDefault();
5890
5890
  me.htmlCls.dialogCls.openDlg('dl_mmcifid', 'Please input mmCIF ID');
5891
5891
  });
5892
5892
 
5893
- me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; //e.preventDefault();
5893
+ me.myEventCls.onIds("#" + me.pre + "mn1_mmdbid", "click", function(e) { me.icn3d; e.preventDefault();
5894
5894
  me.htmlCls.dialogCls.openDlg('dl_mmdbid', 'Please input MMDB or PDB ID');
5895
5895
  });
5896
5896
 
5897
- me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; //e.preventDefault();
5897
+ me.myEventCls.onIds(["#" + me.pre + "mn1_mmdbafid", , "#" + me.pre + "tool_mmdbafid"], "click", function(e) { me.icn3d; e.preventDefault();
5898
5898
  me.htmlCls.dialogCls.openDlg('dl_mmdbafid', 'Please input PDB/MMDB/AlphaFold UniProt IDs');
5899
5899
  });
5900
5900
 
5901
- me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; //e.preventDefault();
5901
+ me.myEventCls.onIds("#" + me.pre + "mn1_blast_rep_id", "click", function(e) { me.icn3d; e.preventDefault();
5902
5902
  me.htmlCls.dialogCls.openDlg('dl_blast_rep_id', 'Align sequence to structure');
5903
5903
  });
5904
5904
 
5905
- me.myEventCls.onIds("#" + me.pre + "mn1_gi", "click", function(e) { me.icn3d; //e.preventDefault();
5905
+ me.myEventCls.onIds("#" + me.pre + "mn1_gi", "click", function(e) { me.icn3d; e.preventDefault();
5906
5906
  me.htmlCls.dialogCls.openDlg('dl_gi', 'Please input protein gi');
5907
5907
  });
5908
5908
 
5909
- me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; //e.preventDefault();
5909
+ me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
5910
5910
  me.htmlCls.dialogCls.openDlg('dl_cid', 'Please input PubChem CID');
5911
5911
  });
5912
5912
 
5913
- me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; //e.preventDefault();
5913
+ me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; e.preventDefault();
5914
5914
  me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please input the PNG image');
5915
5915
  });
5916
5916
 
5917
- me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; //e.preventDefault();
5917
+ me.myEventCls.onIds("#" + me.pre + "mn1_state", "click", function(e) { me.icn3d; e.preventDefault();
5918
5918
  me.htmlCls.dialogCls.openDlg('dl_state', 'Please input the state file');
5919
5919
  });
5920
5920
 
5921
- me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; //e.preventDefault();
5921
+ me.myEventCls.onIds("#" + me.pre + "mn1_selection", "click", function(e) { me.icn3d; e.preventDefault();
5922
5922
  me.htmlCls.dialogCls.openDlg('dl_selection', 'Please input the selection file');
5923
5923
  });
5924
5924
 
5925
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
5925
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; e.preventDefault();
5926
5926
  me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the DSN6 file to display electron density map');
5927
5927
  });
5928
5928
 
5929
5929
 
5930
- me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5930
+ me.myEventCls.onIds(["#" + me.pre + "mn1_delphi", "#" + me.pre + "mn1_delphi2", "#" + me.pre + "tool_delphi"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
5931
5931
  ic.loadPhiFrom = 'delphi';
5932
5932
  $("#" + me.pre + "dl_delphi_tabs").tabs();
5933
5933
  me.htmlCls.dialogCls.openDlg('dl_delphi', 'Please set parameters to display DelPhi potential map');
5934
5934
  });
5935
5935
 
5936
- me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5936
+ me.myEventCls.onIds("#" + me.pre + "mn1_phi", "click", function(e) { let ic = me.icn3d; e.preventDefault();
5937
5937
  ic.loadPhiFrom = 'phi';
5938
5938
  $("#" + me.pre + "dl_phi_tabs").tabs();
5939
5939
  $("#" + me.pre + "phitab1_tabs").tabs();
5940
5940
  $("#" + me.pre + "phitab2_tabs").tabs();
5941
5941
  me.htmlCls.dialogCls.openDlg('dl_phi', 'Please input local phi or cube file to display DelPhi potential map');
5942
5942
  });
5943
- me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5943
+ me.myEventCls.onIds("#" + me.pre + "mn1_phiurl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
5944
5944
  ic.loadPhiFrom = 'phiurl';
5945
5945
  $("#" + me.pre + "dl_phiurl_tabs").tabs();
5946
5946
  $("#" + me.pre + "phiurltab1_tabs").tabs();
@@ -5949,11 +5949,11 @@ class ClickMenu {
5949
5949
  });
5950
5950
 
5951
5951
 
5952
- me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
5952
+ me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; e.preventDefault();
5953
5953
  me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the DSN6 file to display electron density map');
5954
5954
  });
5955
5955
 
5956
- me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5956
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; e.preventDefault();
5957
5957
  thisClass.setLogCmd("export state file", false);
5958
5958
  let file_pref =(ic.inputid) ? ic.inputid : "custom";
5959
5959
 
@@ -5961,19 +5961,19 @@ class ClickMenu {
5961
5961
  });
5962
5962
 
5963
5963
 
5964
- me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; //e.preventDefault();
5964
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; e.preventDefault();
5965
5965
  me.htmlCls.setHtmlCls.exportPdb();
5966
5966
 
5967
5967
  thisClass.setLogCmd("export pdb", true);
5968
5968
  });
5969
5969
 
5970
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; //e.preventDefault();
5970
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSecondary", "click", function(e) { me.icn3d; e.preventDefault();
5971
5971
  me.htmlCls.setHtmlCls.exportSecondary();
5972
5972
 
5973
5973
  thisClass.setLogCmd("export secondary structure", true);
5974
5974
  });
5975
5975
 
5976
- me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
5976
+ me.myEventCls.onIds(["#" + me.pre + "delphipdb", "#" + me.pre + "phipdb"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
5977
5977
  let pdbStr = ic.saveFileCls.getSelectedResiduePDB();
5978
5978
 
5979
5979
  thisClass.setLogCmd("export PDB of selected residues", false);
@@ -5981,42 +5981,42 @@ class ClickMenu {
5981
5981
  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pdb', 'text', [pdbStr]);
5982
5982
  });
5983
5983
 
5984
- me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
5984
+ me.myEventCls.onIds(["#" + me.pre + "delphipqr", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; e.preventDefault();
5985
5985
  await me.htmlCls.setHtmlCls.exportPqr();
5986
5986
  thisClass.setLogCmd("export pqr", true);
5987
5987
  });
5988
5988
 
5989
- // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
5989
+ // me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
5990
5990
  // let bPdb = true;
5991
5991
  // await me.htmlCls.setHtmlCls.exportPqr(bPdb);
5992
5992
  // thisClass.setLogCmd("export pdbh", false);
5993
5993
  // });
5994
5994
 
5995
- me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
5995
+ me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
5996
5996
  let bHydrogen = false;
5997
5997
  await ic.scapCls.exportPdbProfix(bHydrogen);
5998
5998
  thisClass.setLogCmd("export pdb missing atoms", true);
5999
5999
  });
6000
6000
 
6001
- me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6001
+ me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6002
6002
  let bHydrogen = true;
6003
6003
  await ic.scapCls.exportPdbProfix(bHydrogen);
6004
6004
  thisClass.setLogCmd("export pdb hydrogen", true);
6005
6005
  });
6006
6006
 
6007
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6007
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6008
6008
  thisClass.setLogCmd("export stl file", false);
6009
6009
  //ic.threeDPrintCls.hideStabilizer();
6010
6010
  ic.export3DCls.exportStlFile('');
6011
6011
  });
6012
6012
 
6013
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6013
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrml", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6014
6014
  thisClass.setLogCmd("export vrml file", false);
6015
6015
  //ic.threeDPrintCls.hideStabilizer();
6016
6016
  ic.export3DCls.exportVrmlFile('');
6017
6017
  });
6018
6018
 
6019
- me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6019
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportStlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6020
6020
  thisClass.setLogCmd("export stl stabilizer file", false);
6021
6021
  //ic.bRender = false;
6022
6022
  ic.threeDPrintCls.hideStabilizer();
@@ -6025,7 +6025,7 @@ class ClickMenu {
6025
6025
  ic.export3DCls.exportStlFile('_stab');
6026
6026
  });
6027
6027
 
6028
- me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6028
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportVrmlStab", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6029
6029
  thisClass.setLogCmd("export vrml stabilizer file", false);
6030
6030
  //ic.bRender = false;
6031
6031
  ic.threeDPrintCls.hideStabilizer();
@@ -6034,13 +6034,13 @@ class ClickMenu {
6034
6034
  ic.export3DCls.exportVrmlFile('_stab');
6035
6035
  });
6036
6036
 
6037
- me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6037
+ me.myEventCls.onIds("#" + me.pre + "mn6_exportInteraction", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6038
6038
  thisClass.setLogCmd("export interactions", false);
6039
6039
  if(me.cfg.mmdbid !== undefined) await ic.viewInterPairsCls.retrieveInteractionData();
6040
6040
  ic.viewInterPairsCls.exportInteractions();
6041
6041
  });
6042
6042
 
6043
- me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6043
+ me.myEventCls.onIds(["#" + me.pre + "mn1_exportCanvas", "#" + me.pre + "saveimage"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6044
6044
  // do not record the export command
6045
6045
  //thisClass.setLogCmd("export canvas", true);
6046
6046
  thisClass.setLogCmd("export canvas", false);
@@ -6049,28 +6049,28 @@ class ClickMenu {
6049
6049
  let bPngHtml = true;
6050
6050
  await ic.shareLinkCls.shareLink(bPngHtml);
6051
6051
  });
6052
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6052
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas1", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6053
6053
  thisClass.setLogCmd("export canvas 1", true);
6054
6054
  ic.scaleFactor = 1;
6055
6055
  await ic.shareLinkCls.shareLink(true, true);
6056
6056
  });
6057
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6057
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas2", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6058
6058
  thisClass.setLogCmd("export canvas 2", true);
6059
6059
  ic.scaleFactor = 2;
6060
6060
  await ic.shareLinkCls.shareLink(true, true);
6061
6061
  });
6062
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6062
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas4", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6063
6063
  thisClass.setLogCmd("export canvas 4", true);
6064
6064
  ic.scaleFactor = 4;
6065
6065
  await ic.shareLinkCls.shareLink(true, true);
6066
6066
  });
6067
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6067
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCanvas8", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6068
6068
  thisClass.setLogCmd("export canvas 8", true);
6069
6069
  ic.scaleFactor = 8;
6070
6070
  await ic.shareLinkCls.shareLink(true, true);
6071
6071
  });
6072
6072
 
6073
- me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6073
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportCounts", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6074
6074
  thisClass.setLogCmd("export counts", false);
6075
6075
  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>';
6076
6076
  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>';
@@ -6097,7 +6097,7 @@ class ClickMenu {
6097
6097
  ic.saveFileCls.saveFile(file_pref + '_counts.html', 'html', text);
6098
6098
  });
6099
6099
 
6100
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6100
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelections", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6101
6101
  thisClass.setLogCmd("export all selections", false);
6102
6102
 
6103
6103
  thisClass.SetChainsAdvancedMenu();
@@ -6107,7 +6107,7 @@ class ClickMenu {
6107
6107
  ic.saveFileCls.saveFile(file_pref + '_selections.txt', 'text', [text]);
6108
6108
  });
6109
6109
 
6110
- me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6110
+ me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6111
6111
  thisClass.setLogCmd("export all selections with details", false);
6112
6112
 
6113
6113
  thisClass.SetChainsAdvancedMenu();
@@ -6118,32 +6118,32 @@ class ClickMenu {
6118
6118
  ic.saveFileCls.saveFile(file_pref + '_sel_details.txt', 'text', [text]);
6119
6119
  });
6120
6120
 
6121
- me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6121
+ me.myEventCls.onIds(["#" + me.pre + "mn1_sharelink", "#" + me.pre + "tool_sharelink"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6122
6122
  await ic.shareLinkCls.shareLink();
6123
6123
  });
6124
6124
 
6125
- me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6125
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayon", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6126
6126
  await ic.resizeCanvasCls.replayon();
6127
6127
  thisClass.setLogCmd("replay on", true);
6128
6128
  });
6129
- me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6129
+ me.myEventCls.onIds("#" + me.pre + "mn1_replayoff", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6130
6130
  await ic.resizeCanvasCls.replayoff();
6131
6131
  thisClass.setLogCmd("replay off", true);
6132
6132
  });
6133
6133
 
6134
- me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; //e.preventDefault();
6134
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuall", "click", function(e) { me.icn3d; e.preventDefault();
6135
6135
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
6136
6136
 
6137
6137
  thisClass.applyShownMenus();
6138
6138
  });
6139
6139
 
6140
- me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; //e.preventDefault();
6140
+ me.myEventCls.onIds("#" + me.pre + "mn1_menusimple", "click", function(e) { me.icn3d; e.preventDefault();
6141
6141
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
6142
6142
 
6143
6143
  thisClass.applyShownMenus();
6144
6144
  });
6145
6145
 
6146
- me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; //e.preventDefault();
6146
+ me.myEventCls.onIds("#" + me.pre + "mn1_menupref", "click", function(e) { me.icn3d; e.preventDefault();
6147
6147
  me.htmlCls.dialogCls.openDlg('dl_menupref', 'Select Menus');
6148
6148
 
6149
6149
  thisClass.getHiddenMenusFromCache();
@@ -6151,7 +6151,7 @@ class ClickMenu {
6151
6151
  thisClass.displayShownMenus();
6152
6152
  });
6153
6153
 
6154
- me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
6154
+ me.myEventCls.onIds(["#" + me.pre + "apply_menupref", "#" + me.pre + "apply_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
6155
6155
  var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
6156
6156
  me.htmlCls.shownMenus = {};
6157
6157
  for (var checkbox of checkboxes) {
@@ -6161,21 +6161,21 @@ class ClickMenu {
6161
6161
  thisClass.applyShownMenus();
6162
6162
  });
6163
6163
 
6164
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; //e.preventDefault();
6164
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref", "#" + me.pre + "reset_menupref2"], "click", function(e) { me.icn3d; e.preventDefault();
6165
6165
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
6166
6166
 
6167
6167
  thisClass.applyShownMenus();
6168
6168
  thisClass.displayShownMenus();
6169
6169
  });
6170
6170
 
6171
- me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; //e.preventDefault();
6171
+ me.myEventCls.onIds(["#" + me.pre + "reset_menupref_all", "#" + me.pre + "reset_menupref_all2"], "click", function(e) { me.icn3d; e.preventDefault();
6172
6172
  me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
6173
6173
 
6174
6174
  thisClass.applyShownMenus();
6175
6175
  thisClass.displayShownMenus();
6176
6176
  });
6177
6177
 
6178
- me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6178
+ me.myEventCls.onIds(["#" + me.pre + "savepref", "#" + me.pre + "savepref2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6179
6179
  let menuStr = '[';
6180
6180
 
6181
6181
  //var checkboxes = document.querySelectorAll('form[name="' + me.pre + 'selmenu"] input:checked');
@@ -6192,7 +6192,7 @@ class ClickMenu {
6192
6192
  ic.saveFileCls.saveFile('icn3d_menus_pref.txt', 'text', [menuStr]);
6193
6193
  });
6194
6194
 
6195
- me.myEventCls.onIds("#" + me.pre + "reload_menupreffile", "click", function(e) { me.icn3d; //e.preventDefault();
6195
+ me.myEventCls.onIds("#" + me.pre + "reload_menupreffile", "click", function(e) { me.icn3d; e.preventDefault();
6196
6196
 
6197
6197
  if(!me.cfg.notebook) dialog.dialog( "close" );
6198
6198
  let file = $("#" + me.pre + "menupreffile")[0].files[0];
@@ -6223,25 +6223,25 @@ class ClickMenu {
6223
6223
  }
6224
6224
  });
6225
6225
 
6226
- me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; //e.preventDefault();
6226
+ me.myEventCls.onIds("#" + me.pre + "mn1_menuloadpref", "click", function(e) { me.icn3d; e.preventDefault();
6227
6227
  me.htmlCls.dialogCls.openDlg('dl_menuloadpref', 'Please input the menu preference file');
6228
6228
  });
6229
6229
 
6230
6230
 
6231
- me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6231
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6232
6232
  let url = ic.saveFileCls.getLinkToStructureSummary(true);
6233
6233
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
6234
6234
  window.open(url, urlTarget);
6235
6235
  });
6236
6236
 
6237
- me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6237
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6238
6238
  url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
6239
6239
  thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
6240
6240
  let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
6241
6241
  window.open(url, urlTarget);
6242
6242
  });
6243
6243
 
6244
- me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6244
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6245
6245
  if(ic.inputid === undefined) {
6246
6246
  url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
6247
6247
  thisClass.setLogCmd("link to compounds " + ic.molTitle + ": " + url, false);
@@ -6270,7 +6270,7 @@ class ClickMenu {
6270
6270
  window.open(url, urlTarget);
6271
6271
  });
6272
6272
 
6273
- me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6273
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6274
6274
  if(ic.inputid === undefined) {
6275
6275
  let url;
6276
6276
  url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
@@ -6316,7 +6316,7 @@ class ClickMenu {
6316
6316
  }
6317
6317
  });
6318
6318
 
6319
- me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6319
+ me.myEventCls.onIds("#" + me.pre + "mn1_link_protein", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6320
6320
  //ic.saveFileCls.setEntrezLinks('protein');
6321
6321
  let structArray = Object.keys(ic.structures);
6322
6322
  let chainArray = Object.keys(ic.chains);
@@ -6341,19 +6341,19 @@ class ClickMenu {
6341
6341
 
6342
6342
  let thisClass = this;
6343
6343
 
6344
- me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
6344
+ me.myEventCls.onIds(["#" + me.pre + "mn6_selectannotations", "#" + me.pre + "tool_selectannotations"], "click", async function(e) { let ic = me.icn3d; e.preventDefault();
6345
6345
  await ic.showAnnoCls.showAnnotations();
6346
6346
  thisClass.setLogCmd("view annotations", true);
6347
6347
  //thisClass.setLogCmd("window annotations", true);
6348
6348
  });
6349
6349
 
6350
- me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6350
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6351
6351
  thisClass.setLogCmd("select all", true);
6352
6352
  ic.selectionCls.selectAll();
6353
6353
  ic.hlUpdateCls.removeHlAll();
6354
6354
  ic.drawCls.draw();
6355
6355
  });
6356
- me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6356
+ me.myEventCls.onIds("#" + me.pre + "clearall", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6357
6357
  thisClass.setLogCmd("clear all", true);
6358
6358
  ic.bSelectResidue = false;
6359
6359
  ic.selectionCls.selectAll();
@@ -6361,7 +6361,7 @@ class ClickMenu {
6361
6361
  ic.drawCls.draw();
6362
6362
  });
6363
6363
 
6364
- me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6364
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectdisplayed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6365
6365
  thisClass.setLogCmd("select displayed set", true);
6366
6366
  //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
6367
6367
  ic.hAtoms = me.hashUtilsCls.cloneHash(ic.viewSelectionAtoms);
@@ -6369,106 +6369,106 @@ class ClickMenu {
6369
6369
  //ic.drawCls.draw();
6370
6370
  });
6371
6371
 
6372
- me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6372
+ me.myEventCls.onIds("#" + me.pre + "mn2_fullstru", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6373
6373
  thisClass.setLogCmd("show all", true);
6374
6374
  ic.selectionCls.showAll();
6375
6375
  });
6376
6376
 
6377
- me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6377
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectcomplement", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6378
6378
  if(Object.keys(ic.hAtoms).length < Object.keys(ic.atoms).length) {
6379
6379
  thisClass.setLogCmd("select complement", true);
6380
6380
  ic.resid2specCls.selectComplement();
6381
6381
  }
6382
6382
  });
6383
6383
 
6384
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6384
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainchains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6385
6385
  thisClass.setLogCmd("select main chains", true);
6386
6386
  ic.selectionCls.selectMainChains();
6387
6387
  });
6388
6388
 
6389
- me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6389
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6390
6390
  thisClass.setLogCmd("select side chains", true);
6391
6391
  ic.selectionCls.selectSideChains();
6392
6392
  });
6393
6393
 
6394
- me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6394
+ me.myEventCls.onIds("#" + me.pre + "mn2_selectmainsidechains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6395
6395
  thisClass.setLogCmd("select main side chains", true);
6396
6396
  ic.selectionCls.selectMainSideChains();
6397
6397
  });
6398
6398
 
6399
- me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6399
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6400
6400
  thisClass.setLogCmd("select prop positive", true);
6401
6401
  ic.resid2specCls.selectProperty('positive');
6402
6402
  });
6403
- me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6403
+ me.myEventCls.onIds("#" + me.pre + "mn2_propNeg", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6404
6404
  thisClass.setLogCmd("select prop negative", true);
6405
6405
  ic.resid2specCls.selectProperty('negative');
6406
6406
  });
6407
- me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6407
+ me.myEventCls.onIds("#" + me.pre + "mn2_propHydro", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6408
6408
  thisClass.setLogCmd("select prop hydrophobic", true);
6409
6409
  ic.resid2specCls.selectProperty('hydrophobic');
6410
6410
  });
6411
- me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6411
+ me.myEventCls.onIds("#" + me.pre + "mn2_propPolar", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6412
6412
  thisClass.setLogCmd("select prop polar", true);
6413
6413
  ic.resid2specCls.selectProperty('polar');
6414
6414
  });
6415
- me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; //e.preventDefault();
6415
+ me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; e.preventDefault();
6416
6416
  me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor');
6417
6417
  });
6418
- me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; //e.preventDefault();
6418
+ me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; e.preventDefault();
6419
6419
  me.htmlCls.dialogCls.openDlg('dl_propbypercentout', 'Select residue based on the percentage of solvent accessilbe surface area');
6420
6420
  });
6421
- me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6421
+ me.myEventCls.onIds("#" + me.pre + "applypropbybfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6422
6422
  let from = $("#" + me.pre + "minbfactor").val();
6423
6423
  let to = $("#" + me.pre + "maxbfactor").val();
6424
6424
  thisClass.setLogCmd("select prop b factor | " + from + '_' + to, true);
6425
6425
  ic.resid2specCls.selectProperty('b factor', from, to);
6426
6426
  });
6427
- me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6427
+ me.myEventCls.onIds("#" + me.pre + "applypropbypercentout", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6428
6428
  let from = $("#" + me.pre + "minpercentout").val();
6429
6429
  let to = $("#" + me.pre + "maxpercentout").val();
6430
6430
  thisClass.setLogCmd("select prop percent out | " + from + '_' + to, true);
6431
6431
  ic.resid2specCls.selectProperty('percent out', from, to);
6432
6432
  });
6433
6433
 
6434
- me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; //e.preventDefault();
6434
+ me.myEventCls.onIds("#" + me.pre + "mn2_alignment", "click", function(e) { me.icn3d; e.preventDefault();
6435
6435
  me.htmlCls.dialogCls.openDlg('dl_alignment', 'Select residues in aligned sequences');
6436
6436
  thisClass.setLogCmd("window aligned sequences", true);
6437
6437
  });
6438
6438
 
6439
- me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; //e.preventDefault();
6439
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_table", "click", function(e) { me.icn3d; e.preventDefault();
6440
6440
  me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
6441
6441
  thisClass.setLogCmd("window interaction table", true);
6442
6442
  });
6443
- me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; //e.preventDefault();
6443
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_linegraph", "click", function(e) { me.icn3d; e.preventDefault();
6444
6444
  me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
6445
6445
  thisClass.setLogCmd("window interaction graph", true);
6446
6446
  });
6447
- me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; //e.preventDefault();
6447
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_scatterplot", "click", function(e) { me.icn3d; e.preventDefault();
6448
6448
  me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as map');
6449
6449
  thisClass.setLogCmd("window interaction scatterplot", true);
6450
6450
  });
6451
- me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; //e.preventDefault();
6451
+ me.myEventCls.onIds("#" + me.pre + "mn1_window_graph", "click", function(e) { me.icn3d; e.preventDefault();
6452
6452
  me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
6453
6453
  thisClass.setLogCmd("window force-directed graph", true);
6454
6454
  });
6455
6455
 
6456
- me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; //e.preventDefault();
6456
+ me.myEventCls.onIds("#" + me.pre + "mn6_yournote", "click", function(e) { me.icn3d; e.preventDefault();
6457
6457
  me.htmlCls.dialogCls.openDlg('dl_yournote', 'Your note about the current display');
6458
6458
  });
6459
6459
 
6460
- me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6460
+ me.myEventCls.onIds("#" + me.pre + "applyyournote", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6461
6461
  ic.yournote = $("#" + me.pre + "yournote").val();
6462
6462
  if(me.cfg.shownote) document.title = ic.yournote;
6463
6463
  if(!me.cfg.notebook) dialog.dialog( "close" );
6464
6464
  thisClass.setLogCmd('your note | ' + ic.yournote, true);
6465
6465
  });
6466
6466
 
6467
- me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; //e.preventDefault();
6467
+ me.myEventCls.onIds("#" + me.pre + "mn2_command", "click", function(e) { me.icn3d; e.preventDefault();
6468
6468
  me.htmlCls.dialogCls.openDlg('dl_advanced2', 'Select by specification');
6469
6469
  });
6470
6470
 
6471
- 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();
6471
+ 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();
6472
6472
  ic.definedSetsCls.showSets();
6473
6473
  thisClass.setLogCmd('defined sets', true);
6474
6474
  //thisClass.setLogCmd('window defined sets', true);
@@ -6487,7 +6487,7 @@ class ClickMenu {
6487
6487
  });
6488
6488
 
6489
6489
 
6490
- me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6490
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6491
6491
  ic.pk = 0;
6492
6492
  ic.opts['pk'] = 'no';
6493
6493
  thisClass.setLogCmd('set pk off', true);
@@ -6495,50 +6495,50 @@ class ClickMenu {
6495
6495
  ic.hlObjectsCls.removeHlObjects();
6496
6496
  });
6497
6497
 
6498
- me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6498
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6499
6499
  ic.pk = 1;
6500
6500
  ic.opts['pk'] = 'atom';
6501
6501
  thisClass.setLogCmd('set pk atom', true);
6502
6502
  });
6503
6503
 
6504
- me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6504
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6505
6505
  ic.pk = 2;
6506
6506
  ic.opts['pk'] = 'residue';
6507
6507
  thisClass.setLogCmd('set pk residue', true);
6508
6508
  });
6509
6509
 
6510
- me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6510
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6511
6511
  ic.pk = 3;
6512
6512
  ic.opts['pk'] = 'strand';
6513
6513
  thisClass.setLogCmd('set pk strand', true);
6514
6514
  });
6515
6515
 
6516
- me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6516
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkDomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6517
6517
  ic.pk = 4;
6518
6518
  ic.opts['pk'] = 'domain';
6519
6519
  thisClass.setLogCmd('set pk domain', true);
6520
6520
  });
6521
6521
 
6522
- me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6522
+ me.myEventCls.onIds("#" + me.pre + "mn2_pkChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6523
6523
  ic.pk = 5;
6524
6524
  ic.opts['pk'] = 'chain';
6525
6525
  thisClass.setLogCmd('set pk chain', true);
6526
6526
  });
6527
6527
 
6528
- me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; //e.preventDefault();
6528
+ me.myEventCls.onIds("#" + me.pre + "adjustmem", "click", function(e) { me.icn3d; e.preventDefault();
6529
6529
  me.htmlCls.dialogCls.openDlg('dl_adjustmem', 'Adjust the Z-axis positions of the membrane');
6530
6530
  });
6531
6531
 
6532
- me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6532
+ me.myEventCls.onIds("#" + me.pre + "togglemem", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6533
6533
  ic.selectionCls.toggleMembrane();
6534
6534
  thisClass.setLogCmd('toggle membrane', true);
6535
6535
  });
6536
6536
 
6537
- me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; //e.preventDefault();
6537
+ me.myEventCls.onIds("#" + me.pre + "selectplane", "click", function(e) { me.icn3d; e.preventDefault();
6538
6538
  me.htmlCls.dialogCls.openDlg('dl_selectplane', 'Select a region between two planes');
6539
6539
  });
6540
6540
 
6541
- me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6541
+ me.myEventCls.onIds(["#" + me.pre + "mn2_aroundsphere", "#" + me.pre + "tool_aroundsphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6542
6542
  thisClass.SetChainsAdvancedMenu();
6543
6543
 
6544
6544
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -6555,7 +6555,7 @@ class ClickMenu {
6555
6555
  $("#" + me.pre + "atomsCustomSphere2").resizable();
6556
6556
  });
6557
6557
 
6558
- me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; //e.preventDefault();
6558
+ me.myEventCls.onIds(["#" + me.pre + "mn2_select_chain", "#" + me.pre + "definedSets"], "click", function(e) { me.icn3d; e.preventDefault();
6559
6559
  me.htmlCls.dialogCls.openDlg('dl_select_chain', 'Select Structure/Chain/Custom Selection');
6560
6560
  });
6561
6561
 
@@ -6566,242 +6566,242 @@ class ClickMenu {
6566
6566
 
6567
6567
  let thisClass = this;
6568
6568
  // mn 3
6569
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6569
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsRibbon","#" + me.pre + "tool_proteinsRibbon"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6570
6570
  ic.setOptionCls.setStyle('proteins', 'ribbon');
6571
6571
  thisClass.setLogCmd('style proteins ribbon', true);
6572
6572
  });
6573
6573
 
6574
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6574
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6575
6575
  ic.setOptionCls.setStyle('proteins', 'strand');
6576
6576
  thisClass.setLogCmd('style proteins strand', true);
6577
6577
  });
6578
6578
 
6579
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6579
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCylinder", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6580
6580
  ic.setOptionCls.setStyle('proteins', 'cylinder and plate');
6581
6581
  thisClass.setLogCmd('style proteins cylinder and plate', true);
6582
6582
  });
6583
6583
 
6584
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6584
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6585
6585
  ic.setOptionCls.setStyle('proteins', 'schematic');
6586
6586
  thisClass.setLogCmd('style proteins schematic', true);
6587
6587
  });
6588
6588
 
6589
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6589
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsCalpha", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6590
6590
  ic.setOptionCls.setStyle('proteins', 'c alpha trace');
6591
6591
  thisClass.setLogCmd('style proteins c alpha trace', true);
6592
6592
  });
6593
6593
 
6594
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6594
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6595
6595
  ic.setOptionCls.setStyle('proteins', 'backbone');
6596
6596
  thisClass.setLogCmd('style proteins backbone', true);
6597
6597
  });
6598
6598
 
6599
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6599
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6600
6600
  ic.setOptionCls.setStyle('proteins', 'b factor tube');
6601
6601
  thisClass.setLogCmd('style proteins b factor tube', true);
6602
6602
  });
6603
6603
 
6604
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6604
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6605
6605
  ic.setOptionCls.setStyle('proteins', 'lines');
6606
6606
  thisClass.setLogCmd('style proteins lines', true);
6607
6607
  });
6608
6608
 
6609
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6609
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6610
6610
  ic.setOptionCls.setStyle('proteins', 'stick');
6611
6611
  thisClass.setLogCmd('style proteins stick', true);
6612
6612
  });
6613
6613
 
6614
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6614
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsBallstick", "#" + me.pre + "tool_proteinsBallstick"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6615
6615
  ic.setOptionCls.setStyle('proteins', 'ball and stick');
6616
6616
  thisClass.setLogCmd('style proteins ball and stick', true);
6617
6617
  });
6618
6618
 
6619
- me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6619
+ me.myEventCls.onIds(["#" + me.pre + "mn3_proteinsSphere", "#" + me.pre + "tool_proteinsSphere"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6620
6620
  ic.setOptionCls.setStyle('proteins', 'sphere');
6621
6621
  thisClass.setLogCmd('style proteins sphere', true);
6622
6622
  });
6623
6623
 
6624
- me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6624
+ me.myEventCls.onIds("#" + me.pre + "mn3_proteinsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6625
6625
  ic.setOptionCls.setStyle('proteins', 'nothing');
6626
6626
  thisClass.setLogCmd('style proteins nothing', true);
6627
6627
  });
6628
6628
 
6629
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6629
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6630
6630
  ic.setOptionCls.setStyle('sidec', 'lines2');
6631
6631
  thisClass.setLogCmd('style sidec lines2', true);
6632
6632
  });
6633
6633
 
6634
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6634
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6635
6635
  ic.setOptionCls.setStyle('sidec', 'stick2');
6636
6636
  thisClass.setLogCmd('style sidec stick2', true);
6637
6637
  });
6638
6638
 
6639
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6639
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6640
6640
  ic.setOptionCls.setStyle('sidec', 'ball and stick2');
6641
6641
  thisClass.setLogCmd('style sidec ball and stick2', true);
6642
6642
  });
6643
6643
 
6644
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6644
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6645
6645
  ic.setOptionCls.setStyle('sidec', 'sphere2');
6646
6646
  thisClass.setLogCmd('style sidec sphere2', true);
6647
6647
  });
6648
6648
 
6649
- me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6649
+ me.myEventCls.onIds("#" + me.pre + "mn3_sidecNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6650
6650
  ic.setOptionCls.setStyle('sidec', 'nothing');
6651
6651
  thisClass.setLogCmd('style sidec nothing', true);
6652
6652
  });
6653
6653
 
6654
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6654
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6655
6655
  ic.setOptionCls.setStyle('ntbase', 'lines2');
6656
6656
  thisClass.setLogCmd('style ntbase lines2', true);
6657
6657
  });
6658
6658
 
6659
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6659
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6660
6660
  ic.setOptionCls.setStyle('ntbase', 'stick2');
6661
6661
  thisClass.setLogCmd('style ntbase stick2', true);
6662
6662
  });
6663
6663
 
6664
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6664
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6665
6665
  ic.setOptionCls.setStyle('ntbase', 'ball and stick2');
6666
6666
  thisClass.setLogCmd('style ntbase ball and stick2', true);
6667
6667
  });
6668
6668
 
6669
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6669
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6670
6670
  ic.setOptionCls.setStyle('ntbase', 'sphere2');
6671
6671
  thisClass.setLogCmd('style ntbase sphere2', true);
6672
6672
  });
6673
6673
 
6674
- me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6674
+ me.myEventCls.onIds("#" + me.pre + "mn3_ntbaseNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6675
6675
  ic.setOptionCls.setStyle('ntbase', 'nothing');
6676
6676
  thisClass.setLogCmd('style ntbase nothing', true);
6677
6677
  });
6678
6678
 
6679
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6679
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclCartoon", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6680
6680
  ic.setOptionCls.setStyle('nucleotides', 'nucleotide cartoon');
6681
6681
  thisClass.setLogCmd('style nucleotides nucleotide cartoon', true);
6682
6682
  });
6683
6683
 
6684
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6684
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBackbone", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6685
6685
  ic.setOptionCls.setStyle('nucleotides', 'backbone');
6686
6686
  thisClass.setLogCmd('style nucleotides backbone', true);
6687
6687
  });
6688
6688
 
6689
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6689
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6690
6690
  ic.setOptionCls.setStyle('nucleotides', 'schematic');
6691
6691
  thisClass.setLogCmd('style nucleotides schematic', true);
6692
6692
  });
6693
6693
 
6694
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6694
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclPhos", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6695
6695
  ic.setOptionCls.setStyle('nucleotides', 'o3 trace');
6696
6696
  thisClass.setLogCmd('style nucleotides o3 trace', true);
6697
6697
  });
6698
6698
 
6699
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6699
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6700
6700
  ic.setOptionCls.setStyle('nucleotides', 'lines');
6701
6701
  thisClass.setLogCmd('style nucleotides lines', true);
6702
6702
  });
6703
6703
 
6704
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6704
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6705
6705
  ic.setOptionCls.setStyle('nucleotides', 'stick');
6706
6706
  thisClass.setLogCmd('style nucleotides stick', true);
6707
6707
  });
6708
6708
 
6709
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6709
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6710
6710
  ic.setOptionCls.setStyle('nucleotides', 'ball and stick');
6711
6711
  thisClass.setLogCmd('style nucleotides ball and stick', true);
6712
6712
  });
6713
6713
 
6714
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6714
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6715
6715
  ic.setOptionCls.setStyle('nucleotides', 'sphere');
6716
6716
  thisClass.setLogCmd('style nucleotides sphere', true);
6717
6717
  });
6718
6718
 
6719
- me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6719
+ me.myEventCls.onIds("#" + me.pre + "mn3_nuclNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6720
6720
  ic.setOptionCls.setStyle('nucleotides', 'nothing');
6721
6721
  thisClass.setLogCmd('style nucleotides nothing', true);
6722
6722
  });
6723
6723
 
6724
- me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6724
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligLines", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6725
6725
  ic.setOptionCls.setStyle('chemicals', 'lines');
6726
6726
  thisClass.setLogCmd('style chemicals lines', true);
6727
6727
  });
6728
6728
 
6729
- me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6729
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligStick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6730
6730
  ic.setOptionCls.setStyle('chemicals', 'stick');
6731
6731
  thisClass.setLogCmd('style chemicals stick', true);
6732
6732
  });
6733
6733
 
6734
- me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6734
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligBallstick", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6735
6735
  ic.setOptionCls.setStyle('chemicals', 'ball and stick');
6736
6736
  thisClass.setLogCmd('style chemicals ball and stick', true);
6737
6737
  });
6738
6738
 
6739
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6739
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSchematic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6740
6740
  ic.setOptionCls.setStyle('chemicals', 'schematic');
6741
6741
  thisClass.setLogCmd('style chemicals schematic', true);
6742
6742
  });
6743
6743
 
6744
- me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6744
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6745
6745
  ic.setOptionCls.setStyle('chemicals', 'sphere');
6746
6746
  thisClass.setLogCmd('style chemicals sphere', true);
6747
6747
  });
6748
6748
 
6749
- me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6749
+ me.myEventCls.onIds("#" + me.pre + "mn3_ligNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6750
6750
  ic.setOptionCls.setStyle('chemicals', 'nothing');
6751
6751
  thisClass.setLogCmd('style chemicals nothing', true);
6752
6752
  });
6753
6753
 
6754
6754
 
6755
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6755
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6756
6756
  ic.bGlycansCartoon = true;
6757
6757
  ic.drawCls.draw();
6758
6758
  thisClass.setLogCmd('glycans cartoon yes', true);
6759
6759
  });
6760
- me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6760
+ me.myEventCls.onIds("#" + me.pre + "mn3_glycansCartNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6761
6761
  ic.bGlycansCartoon = false;
6762
6762
  ic.drawCls.draw();
6763
6763
  thisClass.setLogCmd('glycans cartoon no', true);
6764
6764
  });
6765
6765
 
6766
6766
 
6767
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6767
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6768
6768
  ic.showInterCls.showHydrogens();
6769
6769
  ic.drawCls.draw();
6770
6770
  thisClass.setLogCmd('hydrogens', true);
6771
6771
  });
6772
6772
 
6773
- me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6773
+ me.myEventCls.onIds("#" + me.pre + "mn3_hydrogensNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6774
6774
  ic.showInterCls.hideHydrogens();
6775
6775
  ic.drawCls.draw();
6776
6776
  thisClass.setLogCmd('set hydrogens off', true);
6777
6777
  });
6778
6778
 
6779
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6779
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6780
6780
  ic.setOptionCls.setStyle('ions', 'sphere');
6781
6781
  thisClass.setLogCmd('style ions sphere', true);
6782
6782
  });
6783
6783
 
6784
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6784
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6785
6785
  ic.setOptionCls.setStyle('ions', 'dot');
6786
6786
  thisClass.setLogCmd('style ions dot', true);
6787
6787
  });
6788
6788
 
6789
- me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6789
+ me.myEventCls.onIds("#" + me.pre + "mn3_ionsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6790
6790
  ic.setOptionCls.setStyle('ions', 'nothing');
6791
6791
  thisClass.setLogCmd('style ions nothing', true);
6792
6792
  });
6793
6793
 
6794
- me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6794
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterSphere", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6795
6795
  ic.setOptionCls.setStyle('water', 'sphere');
6796
6796
  thisClass.setLogCmd('style water sphere', true);
6797
6797
  });
6798
6798
 
6799
- me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6799
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterDot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6800
6800
  ic.setOptionCls.setStyle('water', 'dot');
6801
6801
  thisClass.setLogCmd('style water dot', true);
6802
6802
  });
6803
6803
 
6804
- me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6804
+ me.myEventCls.onIds("#" + me.pre + "mn3_waterNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6805
6805
  ic.setOptionCls.setStyle('water', 'nothing');
6806
6806
  thisClass.setLogCmd('style water nothing', true);
6807
6807
  });
@@ -6813,16 +6813,16 @@ class ClickMenu {
6813
6813
 
6814
6814
  let thisClass = this;
6815
6815
  // mn 4
6816
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6816
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6817
6817
  ic.setOptionCls.setOption('color', 'spectrum');
6818
6818
  thisClass.setLogCmd('color spectrum', true);
6819
6819
  });
6820
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6820
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumChain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6821
6821
  ic.setOptionCls.setOption('color', 'spectrum for chains');
6822
6822
  thisClass.setLogCmd('color spectrum for chains', true);
6823
6823
  });
6824
6824
 
6825
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6825
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6826
6826
  thisClass.SetChainsAdvancedMenu();
6827
6827
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
6828
6828
  if($("#" + me.pre + "atomsCustomColorSpectrumAcross").length) {
@@ -6833,7 +6833,7 @@ class ClickMenu {
6833
6833
  $("#" + me.pre + "atomsCustomColorSpectrumAcross").resizable();
6834
6834
  });
6835
6835
 
6836
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6836
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSpectrumSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6837
6837
  thisClass.SetChainsAdvancedMenu();
6838
6838
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
6839
6839
  if($("#" + me.pre + "atomsCustomColorSpectrum").length) {
@@ -6844,7 +6844,7 @@ class ClickMenu {
6844
6844
  $("#" + me.pre + "atomsCustomColorSpectrum").resizable();
6845
6845
  });
6846
6846
 
6847
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6847
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowAcrossSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6848
6848
  thisClass.SetChainsAdvancedMenu();
6849
6849
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
6850
6850
  if($("#" + me.pre + "atomsCustomColorRainbowAcross").length) {
@@ -6855,7 +6855,7 @@ class ClickMenu {
6855
6855
  $("#" + me.pre + "atomsCustomColorRainbowAcross").resizable();
6856
6856
  });
6857
6857
 
6858
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6858
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbowSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6859
6859
  thisClass.SetChainsAdvancedMenu();
6860
6860
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
6861
6861
  if($("#" + me.pre + "atomsCustomColorRainbow").length) {
@@ -6866,64 +6866,64 @@ class ClickMenu {
6866
6866
  $("#" + me.pre + "atomsCustomColorRainbow").resizable();
6867
6867
  });
6868
6868
 
6869
- me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6869
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrRainbow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6870
6870
  ic.setOptionCls.setOption('color', 'rainbow');
6871
6871
  thisClass.setLogCmd('color rainbow', true);
6872
6872
  });
6873
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6873
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrRainbowChain", "#" + me.pre + "tool_clrRainbowChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6874
6874
  ic.setOptionCls.setOption('color', 'rainbow for chains');
6875
6875
  thisClass.setLogCmd('color rainbow for chains', true);
6876
6876
  });
6877
6877
 
6878
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6878
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrChain", "#" + me.pre + "tool_clrChain"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6879
6879
  ic.setOptionCls.setOption('color', 'chain');
6880
6880
  thisClass.setLogCmd('color chain', true);
6881
6881
  });
6882
- me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6882
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrStructure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6883
6883
  ic.setOptionCls.setOption('color', 'structure');
6884
6884
  thisClass.setLogCmd('color structure', true);
6885
6885
  });
6886
6886
 
6887
- me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6887
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrdomain", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6888
6888
  ic.setOptionCls.setOption('color', 'domain');
6889
6889
  thisClass.setLogCmd('color domain', true);
6890
6890
  });
6891
6891
 
6892
- me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6892
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6893
6893
  ic.setOptionCls.setOption('color', 'defined sets');
6894
6894
  thisClass.setLogCmd('color defined sets', true);
6895
6895
  });
6896
6896
 
6897
6897
 
6898
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6898
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrSSGreen", "#" + me.pre + "tool_clrSSGreen"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
6899
6899
  ic.sheetcolor = 'green';
6900
6900
  ic.setOptionCls.setOption('color', 'secondary structure green');
6901
6901
  thisClass.setLogCmd('color secondary structure green', true);
6902
6902
  });
6903
6903
 
6904
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6904
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSYellow", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6905
6905
  ic.sheetcolor = 'yellow';
6906
6906
  ic.setOptionCls.setOption('color', 'secondary structure yellow');
6907
6907
  thisClass.setLogCmd('color secondary structure yellow', true);
6908
6908
  });
6909
6909
 
6910
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6910
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSSSpectrum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6911
6911
  ic.setOptionCls.setOption('color', 'secondary structure spectrum');
6912
6912
  thisClass.setLogCmd('color secondary structure spectrum', true);
6913
6913
  });
6914
6914
 
6915
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6915
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidue", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6916
6916
  //ic.legendClick = 2;
6917
6917
  ic.setOptionCls.setOption('color', 'residue');
6918
6918
  thisClass.setLogCmd('color residue', true);
6919
6919
  });
6920
6920
 
6921
- me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; //e.preventDefault();
6921
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrResidueCustom", "click", function(e) { me.icn3d; e.preventDefault();
6922
6922
  //ic.legendClick = 2;
6923
6923
  me.htmlCls.dialogCls.openDlg('dl_rescolorfile', 'Please input the file on residue colors');
6924
6924
  });
6925
6925
 
6926
- me.myEventCls.onIds("#" + me.pre + "reload_rescolorfile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6926
+ me.myEventCls.onIds("#" + me.pre + "reload_rescolorfile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6927
6927
 
6928
6928
  if(!me.cfg.notebook) dialog.dialog( "close" );
6929
6929
  let file = $("#" + me.pre + "rescolorfile")[0].files[0];
@@ -6947,7 +6947,7 @@ class ClickMenu {
6947
6947
  }
6948
6948
  });
6949
6949
 
6950
- me.myEventCls.onIds("#" + me.pre + "reload_customcolorfile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6950
+ me.myEventCls.onIds("#" + me.pre + "reload_customcolorfile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6951
6951
 
6952
6952
  if(!me.cfg.notebook) dialog.dialog( "close" );
6953
6953
  ic.startColor = $("#" + me.pre + "startColor").val();
@@ -6962,12 +6962,12 @@ class ClickMenu {
6962
6962
  ic.addTrackCls.setCustomFile('color', ic.startColor, ic.midColor, ic.endColor);
6963
6963
  });
6964
6964
 
6965
- me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; //e.preventDefault();
6965
+ me.myEventCls.onIds("#" + me.pre + "mn6_customref", "click", function(e) { me.icn3d; e.preventDefault();
6966
6966
 
6967
6967
  me.htmlCls.dialogCls.openDlg('dl_customref', 'Set custom reference numbers');
6968
6968
  });
6969
6969
 
6970
- me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6970
+ me.myEventCls.onIds("#" + me.pre + "reload_customreffile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
6971
6971
 
6972
6972
  if(!me.cfg.notebook) dialog.dialog( "close" );
6973
6973
 
@@ -6990,98 +6990,98 @@ class ClickMenu {
6990
6990
  }
6991
6991
  });
6992
6992
 
6993
- me.myEventCls.onIds("#" + me.pre + "remove_legend", "click", function(e) { me.icn3d; //e.preventDefault();
6993
+ me.myEventCls.onIds("#" + me.pre + "remove_legend", "click", function(e) { me.icn3d; e.preventDefault();
6994
6994
 
6995
6995
  $("#" + me.pre + "legend").hide();
6996
6996
 
6997
6997
  thisClass.setLogCmd('remove legend', true);
6998
6998
  });
6999
- me.myEventCls.onIds("#" + me.pre + "reload_customtubefile", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
6999
+ me.myEventCls.onIds("#" + me.pre + "reload_customtubefile", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7000
7000
 
7001
7001
  if(!me.cfg.notebook) dialog.dialog( "close" );
7002
7002
  ic.addTrackCls.setCustomFile('tube');
7003
7003
  });
7004
7004
 
7005
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7005
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCharge", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7006
7006
  //ic.legendClick = 3;
7007
7007
  ic.setOptionCls.setOption('color', 'charge');
7008
7008
  thisClass.setLogCmd('color charge', true);
7009
7009
  });
7010
7010
 
7011
- me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7011
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrHydrophobic", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7012
7012
  //ic.legendClick = 4;
7013
7013
  ic.setOptionCls.setOption('color', 'hydrophobic');
7014
7014
  thisClass.setLogCmd('color hydrophobic', true);
7015
7015
  });
7016
7016
 
7017
- me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7017
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrNormalizedHP", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7018
7018
  //ic.legendClick = 4;
7019
7019
  ic.setOptionCls.setOption('color', 'normalized hydrophobic');
7020
7020
  thisClass.setLogCmd('color normalized hydrophobic', true);
7021
7021
  });
7022
7022
 
7023
7023
 
7024
- me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7024
+ me.myEventCls.onIds(["#" + me.pre + "mn4_clrAtom", "#" + me.pre + "tool_clrAtom"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7025
7025
  //ic.legendClick = 1;
7026
7026
  ic.setOptionCls.setOption('color', 'atom');
7027
7027
  thisClass.setLogCmd('color atom', true);
7028
7028
  });
7029
7029
 
7030
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7030
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactor", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7031
7031
  //ic.legendClick = 5;
7032
7032
  ic.setOptionCls.setOption('color', 'b factor');
7033
7033
  thisClass.setLogCmd('color b factor', true);
7034
7034
  });
7035
7035
 
7036
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7036
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConfidence", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7037
7037
  //ic.legendClick = 6;
7038
7038
  ic.setOptionCls.setOption('color', 'confidence');
7039
7039
  thisClass.setLogCmd('color confidence', true);
7040
7040
  });
7041
7041
 
7042
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7042
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgstrand", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7043
7043
  //ic.legendClick = 6;
7044
7044
  ic.setOptionCls.setOption('color', 'ig strand');
7045
7045
  thisClass.setLogCmd('color ig strand', true);
7046
7046
  });
7047
7047
 
7048
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7048
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIgproto", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7049
7049
  //ic.legendClick = 6;
7050
7050
  ic.setOptionCls.setOption('color', 'ig protodomain');
7051
7051
  thisClass.setLogCmd('color ig protodomain', true);
7052
7052
  });
7053
7053
 
7054
7054
 
7055
- me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; //e.preventDefault();
7055
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrArea", "click", function(e) { me.icn3d; e.preventDefault();
7056
7056
  me.htmlCls.dialogCls.openDlg('dl_colorbyarea', "Color based on residue's solvent accessibility");
7057
7057
  });
7058
- me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7058
+ me.myEventCls.onIds("#" + me.pre + "applycolorbyarea", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7059
7059
  ic.midpercent = $("#" + me.pre + 'midpercent').val();
7060
7060
  ic.setOptionCls.setOption('color', 'area');
7061
7061
  thisClass.setLogCmd('color area | ' + ic.midpercent, true);
7062
7062
 
7063
7063
  });
7064
7064
 
7065
- me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7065
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrBfactorNorm", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7066
7066
  ic.setOptionCls.setOption('color', 'b factor percentile');
7067
7067
  thisClass.setLogCmd('color b factor percentile', true);
7068
7068
  });
7069
7069
 
7070
- me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7070
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrIdentity", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7071
7071
  ic.setOptionCls.setOption('color', 'identity');
7072
7072
  thisClass.setLogCmd('color identity', true);
7073
7073
  });
7074
7074
 
7075
- me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7075
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrConserved", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7076
7076
  ic.setOptionCls.setOption('color', 'conservation');
7077
7077
  thisClass.setLogCmd('color conservation', true);
7078
7078
  });
7079
7079
 
7080
- me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; //e.preventDefault();
7080
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrCustom", "click", function(e) { me.icn3d; e.preventDefault();
7081
7081
  me.htmlCls.dialogCls.openDlg('dl_clr', 'Color picker');
7082
7082
  });
7083
7083
 
7084
- $(document).on("click", ".icn3d-color-rad-text", function(e) { let ic = me.icn3d; //e.preventDefault();
7084
+ $(document).on("click", ".icn3d-color-rad-text", function(e) { let ic = me.icn3d; e.preventDefault();
7085
7085
  e.stopImmediatePropagation();
7086
7086
  e.preventDefault();
7087
7087
  let color = $(this).attr('color');
@@ -7089,22 +7089,22 @@ class ClickMenu {
7089
7089
  thisClass.setLogCmd("color " + color, true);
7090
7090
  });
7091
7091
 
7092
- me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7092
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7093
7093
  ic.setOptionCls.saveColor();
7094
7094
  thisClass.setLogCmd('save color', true);
7095
7095
  });
7096
7096
 
7097
- me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7097
+ me.myEventCls.onIds("#" + me.pre + "mn4_clrApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7098
7098
  ic.setOptionCls.applySavedColor();
7099
7099
  thisClass.setLogCmd('apply saved color', true);
7100
7100
  });
7101
7101
 
7102
- me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7102
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleSave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7103
7103
  ic.setOptionCls.saveStyle();
7104
7104
  thisClass.setLogCmd('save style', true);
7105
7105
  });
7106
7106
 
7107
- me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7107
+ me.myEventCls.onIds("#" + me.pre + "mn3_styleApplySave", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7108
7108
  ic.setOptionCls.applySavedStyle();
7109
7109
  thisClass.setLogCmd('apply saved style', true);
7110
7110
  });
@@ -7116,7 +7116,7 @@ class ClickMenu {
7116
7116
 
7117
7117
  let thisClass = this;
7118
7118
  // mn 5
7119
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7119
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7120
7120
  ic.bConsiderNeighbors = true;
7121
7121
  ic.applyMapCls.removeLastSurface();
7122
7122
  ic.applyMapCls.applySurfaceOptions();
@@ -7124,7 +7124,7 @@ class ClickMenu {
7124
7124
  thisClass.setLogCmd('set surface neighbors on', true);
7125
7125
  });
7126
7126
 
7127
- me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7127
+ me.myEventCls.onIds("#" + me.pre + "mn5_neighborsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7128
7128
  ic.bConsiderNeighbors = false;
7129
7129
  ic.applyMapCls.removeLastSurface();
7130
7130
  ic.applyMapCls.applySurfaceOptions();
@@ -7132,48 +7132,48 @@ class ClickMenu {
7132
7132
  thisClass.setLogCmd('set surface neighbors off', true);
7133
7133
  });
7134
7134
 
7135
- me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7135
+ me.myEventCls.onIds(["#" + me.pre + "mn5_surfaceVDW", "#" + me.pre + "tool_surfaceVDW"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7136
7136
  ic.bConsiderNeighbors = false;
7137
7137
  ic.setOptionCls.setOption('surface', 'Van der Waals surface');
7138
7138
  thisClass.setLogCmd('set surface Van der Waals surface', true);
7139
7139
  });
7140
7140
 
7141
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7141
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSAS", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7142
7142
  ic.bConsiderNeighbors = false;
7143
7143
  ic.setOptionCls.setOption('surface', 'solvent accessible surface');
7144
7144
  thisClass.setLogCmd('set surface solvent accessible surface', true);
7145
7145
  });
7146
7146
 
7147
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7147
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecular", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7148
7148
  ic.bConsiderNeighbors = false;
7149
7149
  ic.setOptionCls.setOption('surface', 'molecular surface');
7150
7150
  thisClass.setLogCmd('set surface molecular surface', true);
7151
7151
  });
7152
7152
 
7153
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7153
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceVDWContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7154
7154
  ic.bConsiderNeighbors = true;
7155
7155
  ic.setOptionCls.setOption('surface', 'Van der Waals surface with context');
7156
7156
  thisClass.setLogCmd('set surface Van der Waals surface with context', true);
7157
7157
  });
7158
7158
 
7159
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7159
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceSASContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7160
7160
  ic.bConsiderNeighbors = true;
7161
7161
  ic.setOptionCls.setOption('surface', 'solvent accessible surface with context');
7162
7162
  thisClass.setLogCmd('set surface solvent accessible surface with context', true);
7163
7163
  });
7164
7164
 
7165
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7165
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceMolecularContext", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7166
7166
  ic.bConsiderNeighbors = true;
7167
7167
  ic.setOptionCls.setOption('surface', 'molecular surface with context');
7168
7168
  thisClass.setLogCmd('set surface molecular surface with context', true);
7169
7169
  });
7170
7170
 
7171
- me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7171
+ me.myEventCls.onIds("#" + me.pre + "mn5_surfaceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7172
7172
  ic.setOptionCls.setOption('surface', 'nothing');
7173
7173
  thisClass.setLogCmd('set surface nothing', true);
7174
7174
  });
7175
7175
 
7176
- $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; //e.preventDefault();
7176
+ $(document).on("click", "." + me.pre + "mn5_opacity", function(e) { let ic = me.icn3d; e.preventDefault();
7177
7177
  ic.transparentRenderOrder = false;
7178
7178
 
7179
7179
  let value = $(this).attr('v');
@@ -7181,7 +7181,7 @@ class ClickMenu {
7181
7181
  thisClass.setLogCmd('set surface opacity ' + value, true);
7182
7182
  });
7183
7183
 
7184
- $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; //e.preventDefault();
7184
+ $(document).on("click", "." + me.pre + "mn5_opacityslow", function(e) { let ic = me.icn3d; e.preventDefault();
7185
7185
  ic.transparentRenderOrder = true;
7186
7186
 
7187
7187
  let value = $(this).attr('v');
@@ -7189,42 +7189,42 @@ class ClickMenu {
7189
7189
  thisClass.setLogCmd('set surface2 opacity ' + value, true);
7190
7190
  });
7191
7191
 
7192
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7192
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7193
7193
  ic.setOptionCls.setOption('wireframe', 'yes');
7194
7194
  thisClass.setLogCmd('set surface wireframe on', true);
7195
7195
  });
7196
7196
 
7197
- me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7197
+ me.myEventCls.onIds("#" + me.pre + "mn5_wireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7198
7198
  ic.setOptionCls.setOption('wireframe', 'no');
7199
7199
  thisClass.setLogCmd('set surface wireframe off', true);
7200
7200
  });
7201
7201
 
7202
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; //e.preventDefault();
7202
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmap2fofc", "click", function(e) { me.icn3d; e.preventDefault();
7203
7203
  me.htmlCls.dialogCls.openDlg('dl_elecmap2fofc', '2Fo-Fc Electron Density Map');
7204
7204
  });
7205
7205
 
7206
- me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; //e.preventDefault();
7206
+ me.myEventCls.onIds("#" + me.pre + "mn5_elecmapfofc", "click", function(e) { me.icn3d; e.preventDefault();
7207
7207
  me.htmlCls.dialogCls.openDlg('dl_elecmapfofc', 'Fo-Fc Electron Density Map');
7208
7208
  });
7209
7209
 
7210
- 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();
7210
+ 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();
7211
7211
  ic.setOptionCls.setOption('map', 'nothing');
7212
7212
  thisClass.setLogCmd('setoption map nothing', true);
7213
7213
  });
7214
7214
 
7215
- 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();
7215
+ 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();
7216
7216
  ic.setOptionCls.setOption('phimap', 'nothing');
7217
7217
  thisClass.setLogCmd('setoption phimap nothing', true);
7218
7218
  });
7219
7219
 
7220
- me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7220
+ me.myEventCls.onIds(["#" + me.pre + "delphimapNo2", "#" + me.pre + "phimapNo2", "#" + me.pre + "phiurlmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7221
7221
  //ic.setOptionCls.setOption('surface', 'nothing');
7222
7222
  //thisClass.setLogCmd('set surface nothing', true);
7223
7223
  ic.setOptionCls.setOption('phisurface', 'nothing');
7224
7224
  thisClass.setLogCmd('setoption phisurface nothing', true);
7225
7225
  });
7226
7226
 
7227
- me.myEventCls.onIds("#" + me.pre + "applymap2fofc", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7227
+ me.myEventCls.onIds("#" + me.pre + "applymap2fofc", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7228
7228
 
7229
7229
  //if(!me.cfg.notebook) dialog.dialog( "close" );
7230
7230
  let sigma2fofc = parseFloat($("#" + me.pre + "sigma2fofc" ).val());
@@ -7234,7 +7234,7 @@ class ClickMenu {
7234
7234
  thisClass.setLogCmd('set map 2fofc sigma ' + sigma2fofc, true);
7235
7235
  });
7236
7236
 
7237
- me.myEventCls.onIds("#" + me.pre + "applymapfofc", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7237
+ me.myEventCls.onIds("#" + me.pre + "applymapfofc", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7238
7238
 
7239
7239
  //if(!me.cfg.notebook) dialog.dialog( "close" );
7240
7240
  let sigmafofc = parseFloat($("#" + me.pre + "sigmafofc" ).val());
@@ -7244,27 +7244,27 @@ class ClickMenu {
7244
7244
  thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
7245
7245
  });
7246
7246
 
7247
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7247
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7248
7248
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
7249
7249
  ic.setOptionCls.setOption('mapwireframe', 'yes');
7250
7250
  thisClass.setLogCmd('set map wireframe on', true);
7251
7251
  });
7252
7252
 
7253
- me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7253
+ me.myEventCls.onIds("#" + me.pre + "mn5_mapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7254
7254
  ic.setOptionCls.setOption('mapwireframe', 'no');
7255
7255
  thisClass.setLogCmd('set map wireframe off', true);
7256
7256
  });
7257
7257
 
7258
- me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; //e.preventDefault();
7258
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmap", "click", function(e) { me.icn3d; e.preventDefault();
7259
7259
  me.htmlCls.dialogCls.openDlg('dl_emmap', 'EM Density Map');
7260
7260
  });
7261
7261
 
7262
- me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7262
+ me.myEventCls.onIds(["#" + me.pre + "mn5_emmapNo", "#" + me.pre + "emmapNo2"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7263
7263
  ic.setOptionCls.setOption('emmap', 'nothing');
7264
7264
  thisClass.setLogCmd('setoption emmap nothing', true);
7265
7265
  });
7266
7266
 
7267
- me.myEventCls.onIds("#" + me.pre + "applyemmap", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7267
+ me.myEventCls.onIds("#" + me.pre + "applyemmap", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7268
7268
 
7269
7269
  //if(!me.cfg.notebook) dialog.dialog( "close" );
7270
7270
  let empercentage = parseFloat($("#" + me.pre + "empercentage" ).val());
@@ -7275,13 +7275,13 @@ class ClickMenu {
7275
7275
  thisClass.setLogCmd('set emmap percentage ' + empercentage, true);
7276
7276
  });
7277
7277
 
7278
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7278
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7279
7279
  //ic.dsn6ParserCls.dsn6Parser(ic.inputid);
7280
7280
  ic.setOptionCls.setOption('emmapwireframe', 'yes');
7281
7281
  thisClass.setLogCmd('set emmap wireframe on', true);
7282
7282
  });
7283
7283
 
7284
- me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7284
+ me.myEventCls.onIds("#" + me.pre + "mn5_emmapwireframeNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7285
7285
  ic.setOptionCls.setOption('emmapwireframe', 'no');
7286
7286
  thisClass.setLogCmd('set emmap wireframe off', true);
7287
7287
  });
@@ -7293,19 +7293,19 @@ class ClickMenu {
7293
7293
 
7294
7294
  let thisClass = this;
7295
7295
  // mn 6
7296
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7296
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7297
7297
  ic.bAssembly = true;
7298
7298
  thisClass.setLogCmd('set assembly on', true);
7299
7299
  ic.drawCls.draw();
7300
7300
  });
7301
7301
 
7302
- me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7302
+ me.myEventCls.onIds("#" + me.pre + "mn6_assemblyNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7303
7303
  ic.bAssembly = false;
7304
7304
  thisClass.setLogCmd('set assembly off', true);
7305
7305
  ic.drawCls.draw();
7306
7306
  });
7307
7307
 
7308
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
7308
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
7309
7309
  thisClass.setLogCmd('ig refnum on', true);
7310
7310
  await ic.refnumCls.showIgRefNum();
7311
7311
 
@@ -7319,7 +7319,7 @@ class ClickMenu {
7319
7319
  }
7320
7320
  });
7321
7321
 
7322
- me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
7322
+ me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
7323
7323
  thisClass.setLogCmd('ig refnum off', true);
7324
7324
  await ic.refnumCls.hideIgRefNum();
7325
7325
 
@@ -7332,14 +7332,14 @@ class ClickMenu {
7332
7332
  });
7333
7333
 
7334
7334
 
7335
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7335
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelAtoms", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7336
7336
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
7337
7337
  ic.selectionCls.saveSelectionIfSelected();
7338
7338
  thisClass.setLogCmd('add atom labels', true);
7339
7339
  ic.drawCls.draw();
7340
7340
  });
7341
7341
 
7342
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7342
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelElements", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7343
7343
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms, true);
7344
7344
  ic.selectionCls.saveSelectionIfSelected();
7345
7345
  thisClass.setLogCmd('add element labels', true);
@@ -7347,35 +7347,42 @@ class ClickMenu {
7347
7347
  });
7348
7348
 
7349
7349
 
7350
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7350
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResidues", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7351
7351
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms);
7352
7352
  ic.selectionCls.saveSelectionIfSelected();
7353
7353
  thisClass.setLogCmd('add residue labels', true);
7354
7354
  ic.drawCls.draw();
7355
7355
  });
7356
7356
 
7357
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7357
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelResnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7358
7358
  ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, true);
7359
7359
  ic.selectionCls.saveSelectionIfSelected();
7360
7360
  thisClass.setLogCmd('add residue number labels', true);
7361
7361
  ic.drawCls.draw();
7362
7362
  });
7363
7363
 
7364
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7364
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7365
+ ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
7366
+ ic.selectionCls.saveSelectionIfSelected();
7367
+ thisClass.setLogCmd('add reference number labels', true);
7368
+ ic.drawCls.draw();
7369
+ });
7370
+
7371
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7365
7372
  ic.analysisCls.addChainLabels(ic.hAtoms);
7366
7373
  ic.selectionCls.saveSelectionIfSelected();
7367
7374
  thisClass.setLogCmd('add chain labels', true);
7368
7375
  ic.drawCls.draw();
7369
7376
  });
7370
7377
 
7371
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7378
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelTermini", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7372
7379
  ic.analysisCls.addTerminiLabels(ic.hAtoms);
7373
7380
  ic.selectionCls.saveSelectionIfSelected();
7374
7381
  thisClass.setLogCmd('add terminal labels', true);
7375
7382
  ic.drawCls.draw();
7376
7383
  });
7377
7384
 
7378
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7385
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7379
7386
  me.htmlCls.dialogCls.openDlg('dl_addlabel', 'Add custom labels by selection');
7380
7387
  ic.pk = 1;
7381
7388
  ic.opts['pk'] = 'atom';
@@ -7383,19 +7390,19 @@ class ClickMenu {
7383
7390
  ic.pAtomNum = 0;
7384
7391
  });
7385
7392
 
7386
- me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; //e.preventDefault();
7393
+ me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d; e.preventDefault();
7387
7394
  me.htmlCls.dialogCls.openDlg('dl_addlabelselection', 'Add custom labels by the selected');
7388
7395
  });
7389
7396
 
7390
- me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; //e.preventDefault();
7397
+ me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d; e.preventDefault();
7391
7398
  me.htmlCls.dialogCls.openDlg('dl_labelColor', 'Change color for all labels');
7392
7399
  });
7393
7400
 
7394
- me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; //e.preventDefault();
7401
+ me.myEventCls.onIds(["#" + me.pre + "mn2_saveselection","#" + me.pre + "tool_saveselection"], "click", function(e) { me.icn3d; e.preventDefault();
7395
7402
  me.htmlCls.dialogCls.openDlg('dl_saveselection', 'Save the selected');
7396
7403
  });
7397
7404
 
7398
- me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7405
+ me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7399
7406
  ic.labelcolor = undefined;
7400
7407
  ic.pickpair = false;
7401
7408
  //ic.labels['residue'] = [];
@@ -7410,14 +7417,14 @@ class ClickMenu {
7410
7417
  ic.drawCls.draw();
7411
7418
  });
7412
7419
 
7413
- $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; //e.preventDefault();
7420
+ $(document).on("click", "." + me.pre + "mn6_labelscale", function(e) { let ic = me.icn3d; e.preventDefault();
7414
7421
  let value = $(this).attr('v');
7415
7422
  ic.labelScale = value;
7416
7423
  ic.drawCls.draw();
7417
7424
  thisClass.setLogCmd('set label scale ' + value, true);
7418
7425
  });
7419
7426
 
7420
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7427
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7421
7428
  me.htmlCls.dialogCls.openDlg('dl_distance', 'Measure the distance of atoms');
7422
7429
  ic.pk = 1;
7423
7430
  ic.opts['pk'] = 'atom';
@@ -7427,7 +7434,7 @@ class ClickMenu {
7427
7434
  });
7428
7435
 
7429
7436
 
7430
- me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7437
+ me.myEventCls.onIds("#" + me.pre + "mn6_distTwoSets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7431
7438
  me.htmlCls.dialogCls.openDlg('dl_disttwosets', 'Measure the distance between two sets');
7432
7439
 
7433
7440
  thisClass.setSetsMenus('atomsCustomDist');
@@ -7435,7 +7442,7 @@ class ClickMenu {
7435
7442
  ic.bMeasureDistance = true;
7436
7443
  });
7437
7444
 
7438
- me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7445
+ me.myEventCls.onIds("#" + me.pre + "mn6_distManySets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7439
7446
  me.htmlCls.dialogCls.openDlg('dl_distmanysets', 'Measure the pairwise distance among many sets');
7440
7447
 
7441
7448
  thisClass.setSetsMenus('atomsCustomDistTable');
@@ -7443,7 +7450,7 @@ class ClickMenu {
7443
7450
  ic.bMeasureDistance = true;
7444
7451
  });
7445
7452
 
7446
- me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7453
+ me.myEventCls.onIds("#" + me.pre + "mn6_distanceNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7447
7454
  ic.pickpair = false;
7448
7455
  let select = "set lines off";
7449
7456
  thisClass.setLogCmd(select, true);
@@ -7454,7 +7461,7 @@ class ClickMenu {
7454
7461
  ic.drawCls.draw();
7455
7462
  });
7456
7463
 
7457
- me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7464
+ me.myEventCls.onIds("#" + me.pre + "mn5_cartoonshape", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7458
7465
  me.htmlCls.dialogCls.openDlg('dl_cartoonshape', 'Draw cartoon for a set');
7459
7466
 
7460
7467
  let bOneset = true;
@@ -7463,7 +7470,7 @@ class ClickMenu {
7463
7470
  ic.bCartoonshape = true;
7464
7471
  });
7465
7472
 
7466
- me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7473
+ me.myEventCls.onIds("#" + me.pre + "mn5_linebtwsets", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7467
7474
  me.htmlCls.dialogCls.openDlg('dl_linebtwsets', 'Draw a line between two sets');
7468
7475
 
7469
7476
  thisClass.setSetsMenus('linebtwsets');
@@ -7472,21 +7479,21 @@ class ClickMenu {
7472
7479
  });
7473
7480
 
7474
7481
 
7475
- me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7482
+ me.myEventCls.onIds(["#" + me.pre + "mn2_selectedcenter", "#" + me.pre + "zoomin_selection", "#" + me.pre + "tool_selectedcenter"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7476
7483
  //thisClass.setLogCmd('zoom selection', true);
7477
7484
  ic.transformCls.zoominSelection();
7478
7485
  ic.drawCls.draw();
7479
7486
  thisClass.setLogCmd('zoom selection', true);
7480
7487
  });
7481
7488
 
7482
- me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7489
+ me.myEventCls.onIds("#" + me.pre + "mn6_center", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7483
7490
  //thisClass.setLogCmd('center selection', true);
7484
7491
  ic.applyCenterCls.centerSelection();
7485
7492
  ic.drawCls.draw();
7486
7493
  thisClass.setLogCmd('center selection', true);
7487
7494
  });
7488
7495
 
7489
- me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7496
+ me.myEventCls.onIds(["#" + me.pre + "mn6_resetOrientation", "#" + me.pre + "resetOrientation", "#" + me.pre + "tool_resetOrientation"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7490
7497
  //thisClass.setLogCmd('reset orientation', true);
7491
7498
  ic.transformCls.resetOrientation();
7492
7499
  //ic.setColorCls.applyOriginalColor();
@@ -7494,17 +7501,17 @@ class ClickMenu {
7494
7501
  thisClass.setLogCmd('reset orientation', true);
7495
7502
  });
7496
7503
 
7497
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7504
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindingshow", "#" + me.pre + "chemicalbindingshow"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7498
7505
  ic.setOptionCls.setOption('chemicalbinding', 'show');
7499
7506
  thisClass.setLogCmd('set chemicalbinding show', true);
7500
7507
  });
7501
7508
 
7502
- me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7509
+ me.myEventCls.onIds(["#" + me.pre + "mn6_chemicalbindinghide", "#" + me.pre + "chemicalbindinghide"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7503
7510
  ic.setOptionCls.setOption('chemicalbinding', 'hide');
7504
7511
  thisClass.setLogCmd('set chemicalbinding hide', true);
7505
7512
  });
7506
7513
 
7507
- me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7514
+ me.myEventCls.onIds("#" + me.pre + "mn6_sidebyside", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7508
7515
  if(ic.bInputfile) {
7509
7516
  var aaa = 1; //alert("Side-by-Side does NOT work when the input is from a local file.");
7510
7517
  return;
@@ -7523,7 +7530,7 @@ class ClickMenu {
7523
7530
  });
7524
7531
 
7525
7532
 
7526
- $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; //e.preventDefault();
7533
+ $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; e.preventDefault();
7527
7534
  let value = $(this).attr('v').toLowerCase();
7528
7535
  let direction = value.split(' ')[1];
7529
7536
 
@@ -7535,7 +7542,7 @@ class ClickMenu {
7535
7542
  ic.resizeCanvasCls.rotStruc(direction);
7536
7543
  });
7537
7544
 
7538
- $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; //e.preventDefault();
7545
+ $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; e.preventDefault();
7539
7546
  let value = $(this).attr('v').toLowerCase();
7540
7547
  let direction = value.split('-')[0];
7541
7548
 
@@ -7554,21 +7561,21 @@ class ClickMenu {
7554
7561
  ic.transformCls.setRotation(axis, angle);
7555
7562
  });
7556
7563
 
7557
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7564
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7558
7565
  ic.setOptionCls.setOption('camera', 'perspective');
7559
7566
  thisClass.setLogCmd('set camera perspective', true);
7560
7567
  });
7561
7568
 
7562
- me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7569
+ me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7563
7570
  ic.setOptionCls.setOption('camera', 'orthographic');
7564
7571
  thisClass.setLogCmd('set camera orthographic', true);
7565
7572
  });
7566
7573
 
7567
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7574
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdBlack", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7568
7575
  ic.setStyleCls.setBackground('black');
7569
7576
  });
7570
7577
 
7571
- me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7578
+ me.myEventCls.onIds("#" + me.pre + "tool_bkgd", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7572
7579
  if(ic.opts['background'] == 'black') {
7573
7580
  ic.setStyleCls.setBackground('white');
7574
7581
  }
@@ -7577,19 +7584,19 @@ class ClickMenu {
7577
7584
  }
7578
7585
  });
7579
7586
 
7580
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7587
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdGrey", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7581
7588
  ic.setStyleCls.setBackground('grey');
7582
7589
  });
7583
7590
 
7584
- me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7591
+ me.myEventCls.onIds(["#" + me.pre + "mn6_bkgdWhite", "#" + me.pre + "tool_bkgdWhite"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7585
7592
  ic.setStyleCls.setBackground('white');
7586
7593
  });
7587
7594
 
7588
- me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7595
+ me.myEventCls.onIds("#" + me.pre + "mn6_bkgdTransparent", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7589
7596
  ic.setStyleCls.setBackground('transparent');
7590
7597
  });
7591
7598
 
7592
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7599
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7593
7600
  //ic.setOptionCls.setOption('fog', 'yes');
7594
7601
  ic.opts['fog'] = 'yes';
7595
7602
  ic.fogCls.setFog(true);
@@ -7597,7 +7604,7 @@ class ClickMenu {
7597
7604
  thisClass.setLogCmd('set fog on', true);
7598
7605
  });
7599
7606
 
7600
- me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7607
+ me.myEventCls.onIds("#" + me.pre + "mn6_showfogNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7601
7608
  //ic.setOptionCls.setOption('fog', 'no');
7602
7609
  ic.opts['fog'] = 'no';
7603
7610
  ic.fogCls.setFog(true);
@@ -7605,22 +7612,22 @@ class ClickMenu {
7605
7612
  thisClass.setLogCmd('set fog off', true);
7606
7613
  });
7607
7614
 
7608
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7615
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7609
7616
  ic.setOptionCls.setOption('slab', 'yes');
7610
7617
  thisClass.setLogCmd('set slab on', true);
7611
7618
  });
7612
7619
 
7613
- me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7620
+ me.myEventCls.onIds("#" + me.pre + "mn6_showslabNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7614
7621
  ic.setOptionCls.setOption('slab', 'no');
7615
7622
  thisClass.setLogCmd('set slab off', true);
7616
7623
  });
7617
7624
 
7618
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7625
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7619
7626
  ic.setOptionCls.setOption('axis', 'yes');
7620
7627
  thisClass.setLogCmd('set axis on', true);
7621
7628
  });
7622
7629
 
7623
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7630
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisSel", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7624
7631
  ic.pc1 = true;
7625
7632
 
7626
7633
  ic.axesCls.setPc1Axes();
@@ -7628,7 +7635,7 @@ class ClickMenu {
7628
7635
  });
7629
7636
 
7630
7637
 
7631
- me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7638
+ me.myEventCls.onIds("#" + me.pre + "mn6_showaxisNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7632
7639
  ic.pc1 = false;
7633
7640
  ic.axes = [];
7634
7641
 
@@ -7637,37 +7644,37 @@ class ClickMenu {
7637
7644
  thisClass.setLogCmd('set axis off', true);
7638
7645
  });
7639
7646
 
7640
- me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
7647
+ me.myEventCls.onIds("#" + me.pre + "mn6_symmetry", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
7641
7648
  ic.bAxisOnly = false;
7642
7649
  await ic.symdCls.retrieveSymmetry(Object.keys(ic.structures)[0]);
7643
7650
  //me.htmlCls.dialogCls.openDlg('dl_symmetry', 'Symmetry');
7644
7651
  });
7645
7652
 
7646
- me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
7653
+ me.myEventCls.onIds("#" + me.pre + "mn6_symd", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
7647
7654
  ic.bAxisOnly = false;
7648
7655
  await ic.symdCls.retrieveSymd();
7649
7656
  ic.bSymd = true;
7650
7657
 
7651
7658
  thisClass.setLogCmd('symd symmetry', true);
7652
7659
  });
7653
- me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7660
+ me.myEventCls.onIds("#" + me.pre + "mn6_clear_sym", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7654
7661
  ic.symdArray = [];
7655
7662
  ic.drawCls.draw();
7656
7663
  thisClass.setLogCmd('clear symd symmetry', true);
7657
7664
  });
7658
- me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7665
+ me.myEventCls.onIds("#" + me.pre + "mn6_axes_only", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7659
7666
  ic.bAxisOnly = true;
7660
7667
  ic.drawCls.draw();
7661
7668
  thisClass.setLogCmd('show axis', true);
7662
7669
  });
7663
7670
 
7664
7671
 
7665
- me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7672
+ me.myEventCls.onIds("#" + me.pre + "mn6_area", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7666
7673
  ic.analysisCls.calculateArea();
7667
7674
  thisClass.setLogCmd('area', true);
7668
7675
  });
7669
7676
 
7670
- me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7677
+ me.myEventCls.onIds("#" + me.pre + "applysymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7671
7678
  ic.bAxisOnly = false;
7672
7679
 
7673
7680
  let title = $("#" + me.pre + "selectSymmetry" ).val();
@@ -7677,14 +7684,14 @@ class ClickMenu {
7677
7684
  ic.drawCls.draw();
7678
7685
  thisClass.setLogCmd('symmetry ' + title, true);
7679
7686
  });
7680
- me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7687
+ me.myEventCls.onIds("#" + me.pre + "clearsymmetry", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7681
7688
  let title = 'none';
7682
7689
  ic.symmetrytitle = undefined;
7683
7690
  ic.drawCls.draw();
7684
7691
  thisClass.setLogCmd('symmetry ' + title, true);
7685
7692
  });
7686
7693
 
7687
- me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7694
+ me.myEventCls.onIds(["#" + me.pre + "mn6_hbondsYes", "#" + me.pre + "hbondsYes"], "click", function(e) { let ic = me.icn3d; e.preventDefault();
7688
7695
  thisClass.SetChainsAdvancedMenu();
7689
7696
 
7690
7697
  let definedAtomsHtml = ic.definedSetsCls.setAtomMenu(['protein']);
@@ -7701,17 +7708,17 @@ class ClickMenu {
7701
7708
  $("#" + me.pre + "atomsCustomHbond2").resizable();
7702
7709
  });
7703
7710
 
7704
- me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; //e.preventDefault();
7711
+ me.myEventCls.onIds(["#" + me.pre + "mn6_contactmap"], "click", function(e) { me.icn3d; e.preventDefault();
7705
7712
  me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
7706
7713
  });
7707
7714
 
7708
7715
 
7709
- me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7716
+ me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7710
7717
  ic.showInterCls.hideHbondsContacts();
7711
7718
  ic.drawCls.draw();
7712
7719
  });
7713
7720
 
7714
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7721
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7715
7722
  let select = "stabilizer";
7716
7723
  ic.threeDPrintCls.addStabilizer();
7717
7724
  ic.threeDPrintCls.prepareFor3Dprint();
@@ -7719,14 +7726,14 @@ class ClickMenu {
7719
7726
  thisClass.setLogCmd(select, true);
7720
7727
  });
7721
7728
 
7722
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7729
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7723
7730
  let select = "set stabilizer off";
7724
7731
  thisClass.setLogCmd(select, true);
7725
7732
  ic.threeDPrintCls.hideStabilizer();
7726
7733
  ic.drawCls.draw();
7727
7734
  });
7728
7735
 
7729
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7736
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7730
7737
  me.htmlCls.dialogCls.openDlg('dl_stabilizer', 'Add One Stabilizer');
7731
7738
  ic.pk = 1;
7732
7739
  ic.opts['pk'] = 'atom';
@@ -7734,7 +7741,7 @@ class ClickMenu {
7734
7741
  ic.pAtomNum = 0;
7735
7742
  });
7736
7743
 
7737
- me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7744
+ me.myEventCls.onIds("#" + me.pre + "mn1_stabilizerRmOne", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7738
7745
  me.htmlCls.dialogCls.openDlg('dl_stabilizer_rm', 'Remove One Stabilizer');
7739
7746
  ic.pk = 1;
7740
7747
  ic.opts['pk'] = 'atom';
@@ -7742,27 +7749,27 @@ class ClickMenu {
7742
7749
  ic.pAtomNum = 0;
7743
7750
  });
7744
7751
 
7745
- me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; //e.preventDefault();
7752
+ me.myEventCls.onIds("#" + me.pre + "mn1_thicknessSet", "click", function(e) { me.icn3d; e.preventDefault();
7746
7753
  me.htmlCls.dialogCls.openDlg('dl_thickness', 'Set Thickness for 3D Printing');
7747
7754
  });
7748
7755
 
7749
- me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; //e.preventDefault();
7756
+ me.myEventCls.onIds("#" + me.pre + "mn3_setThickness", "click", function(e) { me.icn3d; e.preventDefault();
7750
7757
  me.htmlCls.dialogCls.openDlg('dl_thickness2', 'Style Preferences');
7751
7758
  });
7752
7759
 
7753
7760
 
7754
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7761
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7755
7762
  let select = "disulfide bonds";
7756
7763
  thisClass.setLogCmd(select, true);
7757
7764
  ic.showInterCls.showSsbonds();
7758
7765
  });
7759
7766
 
7760
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7767
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7761
7768
  ic.viewInterPairsCls.exportSsbondPairs();
7762
7769
  thisClass.setLogCmd("export disulfide bond pairs", false);
7763
7770
  });
7764
7771
 
7765
- me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7772
+ me.myEventCls.onIds("#" + me.pre + "mn6_ssbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7766
7773
  ic.opts["ssbonds"] = "no";
7767
7774
  let select = "set disulfide bonds off";
7768
7775
  thisClass.setLogCmd(select, true);
@@ -7770,7 +7777,7 @@ class ClickMenu {
7770
7777
  ic.setOptionCls.setStyle('sidec', 'nothing');
7771
7778
  });
7772
7779
 
7773
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7780
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsYes", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7774
7781
  let select = "cross linkage";
7775
7782
  thisClass.setLogCmd(select, true);
7776
7783
  //ic.bShowCrossResidueBond = true;
@@ -7778,12 +7785,12 @@ class ClickMenu {
7778
7785
  ic.showInterCls.showClbonds();
7779
7786
  });
7780
7787
 
7781
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7788
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsExport", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7782
7789
  ic.viewInterPairsCls.exportClbondPairs();
7783
7790
  thisClass.setLogCmd("export cross linkage pairs", false);
7784
7791
  });
7785
7792
 
7786
- me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
7793
+ me.myEventCls.onIds("#" + me.pre + "mn6_clbondsNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
7787
7794
  ic.opts["clbonds"] = "no";
7788
7795
  let select = "set cross linkage off";
7789
7796
  thisClass.setLogCmd(select, true);
@@ -7830,6 +7837,11 @@ class ClickMenu {
7830
7837
  }
7831
7838
  });
7832
7839
  });
7840
+
7841
+ me.myEventCls.onIds("#" + me.pre + "jn_copy", "click", function(e) { me.icn3d; e.preventDefault();
7842
+ let text = $("#" + me.pre + "jn_commands").val();
7843
+ navigator.clipboard.writeText(text);
7844
+ });
7833
7845
  }
7834
7846
 
7835
7847
  //Show the input command in log. If "bSetCommand" is true, the command will be saved in the state file as well.
@@ -9384,8 +9396,8 @@ class SetMenu {
9384
9396
  //}
9385
9397
 
9386
9398
  //!!!
9387
- //!!!html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
9388
- //!!!html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
9399
+ html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
9400
+ html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
9389
9401
  }
9390
9402
  else {
9391
9403
  //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9515,6 +9527,8 @@ class SetMenu {
9515
9527
  if(me.cfg.cid === undefined) {
9516
9528
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
9517
9529
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
9530
+ //!!!
9531
+ html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
9518
9532
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
9519
9533
  html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
9520
9534
  }
@@ -9606,12 +9620,11 @@ class SetMenu {
9606
9620
 
9607
9621
  html += "<ul>";
9608
9622
  //!!!
9609
- /*
9610
9623
  html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
9611
9624
  html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
9612
9625
 
9613
9626
  html += this.getMenuSep();
9614
- */
9627
+
9615
9628
  html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
9616
9629
  html += "</ul>";
9617
9630
  html += "</li>";
@@ -10289,6 +10302,7 @@ class Dialog {
10289
10302
  if(id === me.pre + 'dl_selectannotations' || id === me.pre + 'dl_graph' || id === me.pre + 'dl_linegraph' || id === me.pre + 'dl_scatterplot' || id === me.pre + 'dl_contactmap' || id === me.pre + 'dl_alignerrormap' || id === me.pre + 'dl_interactionsorted' || id === me.pre + 'dl_alignment') {
10290
10303
  $( "#" + id ).show();
10291
10304
  $( "#" + id + "_nb").show();
10305
+ $( "#" + id + "_title").html(title);
10292
10306
 
10293
10307
  height =(me.htmlCls.HEIGHT) * 0.5;
10294
10308
 
@@ -10336,6 +10350,7 @@ class Dialog {
10336
10350
  if(ic.bRender) {
10337
10351
  $( "#" + id ).show();
10338
10352
  $( "#" + id + "_nb").show();
10353
+ $( "#" + id + "_title").html(title);
10339
10354
  }
10340
10355
 
10341
10356
  height = 'auto';
@@ -10389,7 +10404,7 @@ class SetDialog {
10389
10404
  addNotebookTitle(id, title, bAddExtraDiv) { let me = this.icn3dui; me.icn3d;
10390
10405
  //return '<div id="' + me.pre + id + '_nb" style="display:none; background-color:#1c94c4; width:100%"><span style="color:white; font-weight:bold">' + title + '</span>&nbsp;&nbsp;&nbsp;<span onclick="$(\'#' + me.pre + id + '\').hide(); return false;" class="icn3d-nbclose" title="Close">x</span></div>';
10391
10406
 
10392
- let html = '<div id="' + me.pre + id + '_nb" style="display:none; background-color:#5C9CCC; width:100%"><span style="color:white; font-weight:bold">' + title + '</span>&nbsp;&nbsp;&nbsp;<div onclick="$(\'#' + me.pre + id + '\').hide(); return false;" class="icn3d-nbclose ui-icon ui-icon-close" title="Close"></div></div>';
10407
+ let html = '<div id="' + me.pre + id + '_nb" style="display:none; background-color:#5C9CCC; width:100%"><span id="' + me.pre + id + '_title" style="color:white; font-weight:bold">' + title + '</span>&nbsp;&nbsp;&nbsp;<div onclick="$(\'#' + me.pre + id + '\').hide(); return false;" class="icn3d-nbclose ui-icon ui-icon-close" title="Close"></div></div>';
10393
10408
 
10394
10409
  if(bAddExtraDiv) {
10395
10410
  html += '<div id="' + me.pre + id + '_html"></div>';
@@ -11527,10 +11542,23 @@ class SetDialog {
11527
11542
 
11528
11543
  html += me.htmlCls.divStr + "dl_copyurl' style='width:520px;' class='" + dialogClass + "'>";
11529
11544
  html += this.addNotebookTitle('dl_copyurl', 'Share Link');
11545
+ html += "<br>";
11546
+ html += "1. <b>URLs Used in Browsers</b><br><br>";
11547
+
11530
11548
  html += "Please copy one of the URLs below. They show the same result.<br>(To add a title to share link, click \"Windows > Your Note\" and click \"File > Share Link\" again.)<br><br>";
11531
11549
  html += "Original URL with commands: <br><textarea id='" + me.pre + "ori_url' rows='4' style='width:100%'></textarea><br><br>";
11532
- html += "Lifelong Short URL:(To replace this URL, send a pull request to update share.html at <a href='https://github.com/ncbi/icn3d' target='_blank'>iCn3D GitHub</a>)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url' value='' style='width:100%'><br><br>";
11533
- html += "Lifelong Short URL + Window Title:(To update the window title, click \"Analysis > Your Note/Window Title\".)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url_title' value='' style='width:100%'><br><br>";
11550
+ if(!me.cfg.notebook) {
11551
+ html += "Lifelong Short URL:(To replace this URL, send a pull request to update share.html at <a href='https://github.com/ncbi/icn3d' target='_blank'>iCn3D GitHub</a>)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url' value='' style='width:100%'><br><br>";
11552
+ html += "Lifelong Short URL + Window Title:(To update the window title, click \"Analysis > Your Note/Window Title\".)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url_title' value='' style='width:100%'><br><br>";
11553
+ }
11554
+
11555
+ html += "2. <b>Commands Used in Jupyter Noteboook</b><br><br>";
11556
+ html += "Please copy the following commands into a cell in Jupyter Notebook to show the same result.<br><br>";
11557
+
11558
+ html += '<textarea id="' + me.pre + 'jn_commands" rows="4" style="width:100%"></textarea><br>';
11559
+
11560
+ html += buttonStrTmp + me.pre + 'jn_copy">Copy Commands</button><br>';
11561
+
11534
11562
  html += "</div>";
11535
11563
 
11536
11564
  html += me.htmlCls.divStr + "dl_selectannotations' class='" + dialogClass + " icn3d-annotation' style='background-color:white;'>";
@@ -30718,7 +30746,7 @@ class ResidueLabels {
30718
30746
 
30719
30747
  //Add labels for all residues containing the input "atoms". The labels are one-letter residue abbreviations.
30720
30748
  //If "bSchematic" is true, the labels are in circles. Otherwise, they are in round-corner rectangles.
30721
- addResidueLabels(atoms, bSchematic, alpha, bNumber) { let ic = this.icn3d, me = ic.icn3dui;
30749
+ addResidueLabels(atoms, bSchematic, alpha, bNumber, bRefnum) { let ic = this.icn3d, me = ic.icn3dui;
30722
30750
  if(me.bNode) return;
30723
30751
 
30724
30752
  let size = 18;
@@ -30758,6 +30786,15 @@ class ResidueLabels {
30758
30786
  label.text += atom.resi;
30759
30787
  //label.factor = 0.3;
30760
30788
  }
30789
+ else if(bRefnum) {
30790
+ let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
30791
+ let refnum = '';
30792
+ if(ic.resid2refnum[resid]) {
30793
+ refnum = (ic.resid2refnum[resid].substr(0, 1) == ' ') ? '' : ic.resid2refnum[resid];
30794
+ }
30795
+
30796
+ label.text = refnum;
30797
+ }
30761
30798
  label.size = size;
30762
30799
  label.factor = 0.3;
30763
30800
 
@@ -30768,6 +30805,9 @@ class ResidueLabels {
30768
30805
  if(bNumber) {
30769
30806
  label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd;
30770
30807
  }
30808
+ else if(bRefnum) {
30809
+ label.color = '#00FFFF';
30810
+ }
30771
30811
  else {
30772
30812
  label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
30773
30813
  }
@@ -30973,6 +31013,7 @@ class Impostor {
30973
31013
 
30974
31014
  setParametersForShader (opacity) { let ic = this.icn3d, me = ic.icn3dui;
30975
31015
  let background = me.parasCls.backgroundColors[ic.opts.background.toLowerCase()];
31016
+ //if(!background) background = me.parasCls.thr(0x000000);
30976
31017
 
30977
31018
  let near = 2.5*ic.maxD;
30978
31019
  let far = 4*ic.maxD;
@@ -31977,6 +32018,8 @@ class Alternate {
31977
32018
  // change the display atom when alternating
31978
32019
  //Show structures one by one.
31979
32020
  alternateStructures() { let ic = this.icn3d, me = ic.icn3dui;
32021
+ //ic.transformCls.zoominSelection();
32022
+
31980
32023
  // default ic.ALTERNATE_STRUCTURE = -1
31981
32024
  if(ic.ALTERNATE_STRUCTURE == -1) {
31982
32025
  ic.viewSelectionAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
@@ -32159,7 +32202,7 @@ class Alternate {
32159
32202
 
32160
32203
  // show membranes
32161
32204
  if(ic.bOpm) {
32162
- //if(window.dialog) window.dialog.dialog( "close" );
32205
+ //if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
32163
32206
 
32164
32207
  let html = me.utilsCls.getMemDesc();
32165
32208
  $("#" + ic.pre + "dl_rmsd_html").html(html);
@@ -35377,11 +35420,13 @@ class SetOption {
35377
35420
  bClose = true;
35378
35421
  }
35379
35422
 
35380
- $("#" + me.pre + "dl_legend_html").html(html);
35381
- me.htmlCls.dialogCls.openDlg('dl_legend', 'Color Legend');
35423
+ if(html) {
35424
+ $("#" + me.pre + "dl_legend_html").html(html);
35425
+ me.htmlCls.dialogCls.openDlg('dl_legend', 'Color Legend');
35426
+ }
35382
35427
 
35383
35428
  if(bClose) {
35384
- if(window.dialog) window.dialog.dialog( "close" );
35429
+ if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
35385
35430
  }
35386
35431
  }
35387
35432
 
@@ -35568,23 +35613,27 @@ class SetOption {
35568
35613
  let html = '';
35569
35614
 
35570
35615
  const name2color = {
35616
+ "<b>Protodomain 1</b>": "",
35571
35617
  "A Strand": "0000FF",
35572
35618
  "B Strand": "006400",
35573
35619
  "C Strand": "FFFF00", //"F0E68C",
35574
35620
  "C' Strand": "FFA500",
35621
+ "<br><b>Linker</b>": "",
35575
35622
  "C'' Strand": "FF0000",
35623
+ "<br><b>Protodomain 2</b>": "",
35576
35624
  "D Strand": "0000FF",
35577
35625
  "E Strand": "006400",
35578
35626
  "F Strand": "FFFF00", //"F0E68C",
35579
35627
  "G Strand": "FFA500",
35628
+ "": "",
35580
35629
  "Loop": "CCCCCC"
35581
35630
  };
35582
35631
 
35583
- html += "<div>";
35632
+ html += "<div>A protodomain is a supersecondary structure <br>that by its duplication, symmetry operations <br>can generate a structural domain.<br><br>";
35584
35633
  for (let name in name2color) {
35585
35634
  let color = name2color[name];
35586
35635
  html += "<span>";
35587
- html += "<div style='width: 10px; height: 10px; background-color:#" + color + "; border: 0px;display:inline-block;' ></div> ";
35636
+ if(color) html += "<div style='width: 10px; height: 10px; background-color:#" + color + "; border: 0px;display:inline-block;' ></div> ";
35588
35637
  html += name;
35589
35638
  html += "</span><br>";
35590
35639
  }
@@ -37832,7 +37881,7 @@ class Domain3d {
37832
37881
  this.nc_fact = 0.0; // size factor for internal contacts
37833
37882
 
37834
37883
  // added by Jiyao
37835
- this.min_contacts = 10; // minimum number of contacts to be considered as neighbors
37884
+ this.min_contacts = 3; // minimum number of contacts to be considered as neighbors
37836
37885
 
37837
37886
  //let this.elements[2*this.MAX_SSE]; // sets of this.elements to be split
37838
37887
  this.elements = [];
@@ -38887,7 +38936,7 @@ class Domain3d {
38887
38936
  }
38888
38937
  }
38889
38938
  }
38890
-
38939
+
38891
38940
  return {subdomains: subdomains, substruct: substruct, pos2resi:pos2resi };
38892
38941
  } // end c2b_NewSplitChain
38893
38942
 
@@ -41787,7 +41836,7 @@ class ShowSeq {
41787
41836
  let strand2len_start_stop = {};
41788
41837
  let prevRefnumStr, prevPostfix, prevRefnum;
41789
41838
 
41790
- // sometimes one chain may have several Ig domains,set a index for each IgDomain
41839
+ // sometimes one chain may have several Ig domains,set an index for each IgDomain
41791
41840
  let index = 1, prevStrandPostfix = '', bStart = false;
41792
41841
  for(let i = 0, il = giSeq.length; i < il; ++i) {
41793
41842
  let currResi = ic.ParserUtilsCls.getResi(chnid, i);
@@ -51701,7 +51750,7 @@ class ParserUtils {
51701
51750
  me.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: " + rmsd.toPrecision(4), false);
51702
51751
  let html = "<br><b>Realignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br><br>";
51703
51752
  if(ic.bAfMem) {
51704
- //if(window.dialog) window.dialog.dialog( "close" );
51753
+ //if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
51705
51754
  html += me.utilsCls.getMemDesc();
51706
51755
  }
51707
51756
  $("#" + ic.pre + "dl_rmsd_html").html(html);
@@ -56515,6 +56564,11 @@ class ApplyCommand {
56515
56564
 
56516
56565
  ic.drawCls.draw();
56517
56566
  }
56567
+ else if(command == 'add reference number labels') {
56568
+ ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
56569
+
56570
+ ic.drawCls.draw();
56571
+ }
56518
56572
  else if(command == 'add atom labels') {
56519
56573
  ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
56520
56574
 
@@ -61961,7 +62015,8 @@ class Dssp {
61961
62015
  let startResi = segArray[m];
61962
62016
  let endResi = segArray[m+1];
61963
62017
  for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
61964
- let resid = chainid + '_' + n;
62018
+ let residNCBI = chainid + '_' + n;
62019
+ let resid = ic.ncbi2resid[residNCBI];
61965
62020
  domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
61966
62021
  ic.resid2domainid[resid] = chainid + '-' + k;
61967
62022
  }
@@ -64465,14 +64520,17 @@ class Diagram2d {
64465
64520
 
64466
64521
  ic.hlUpdateCls.updateHlAll();
64467
64522
 
64523
+ ic.transformCls.zoominSelection();
64524
+
64468
64525
  me.htmlCls.clickMenuCls.setLogCmd(select, true);
64469
64526
  });
64470
64527
 
64471
64528
  //$("#" + ic.pre + "dl_scatterplot .icn3d-interaction", "click", function(e) { let ic = this.icn3d, me = ic.icn3dui;
64472
- $(document).on("click", "#" + ic.pre + "dl_scatterplot .icn3d-interaction", function(e) { thisClass.icn3d;
64529
+ $(document).on("click", "#" + ic.pre + "dl_scatterplot .icn3d-interaction", function(e) { let ic = thisClass.icn3d;
64473
64530
  e.stopImmediatePropagation();
64474
64531
 
64475
64532
  thisClass.clickInteraction(this);
64533
+ ic.transformCls.zoominSelection();
64476
64534
  });
64477
64535
 
64478
64536
  $(document).on("click", "#" + ic.pre + "dl_contactmap .icn3d-interaction", function(e) { thisClass.icn3d;
@@ -66511,7 +66569,6 @@ class SaveFile {
66511
66569
  let bMulStruc =(struArray.length > 1) ? true : false;
66512
66570
 
66513
66571
  let molNum = 1, prevStru = '', prevChain = '';
66514
- //pdbStr += '\n';
66515
66572
 
66516
66573
  let addedChainResiHash = {};
66517
66574
  for(let i in atomHash) {
@@ -66531,20 +66588,24 @@ class SaveFile {
66531
66588
 
66532
66589
  // add header
66533
66590
  let mutantInfo = (chainResi2pdb) ? "Mutated chain_residue " + Object.keys(chainResi2pdb) + '; ' : '';
66534
- if(!bNoHeader) pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, pdbid);
66591
+ if(!bNoHeader) {
66592
+ pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, pdbid);
66593
+ //pdbStr += '\n'; // separate from incomplete secondary structures
66594
+ }
66535
66595
 
66536
- prevStru = atom.structure;
66596
+ //prevStru = atom.structure;
66537
66597
  ++molNum;
66538
66598
  }
66539
- else {
66540
- if(atom.chain != prevChain) {
66599
+ //else {
66600
+ //if(atom.chain != prevChain) {
66601
+ if(atom.chain != prevChain && atom.structure == prevStru) {
66541
66602
  // add a line "TER" to work with scap/profix to add missing atoms
66542
66603
  if(prevChain) {
66543
66604
  pdbStr += 'TER\n';
66544
66605
  }
66545
- prevChain = atom.chain;
66606
+ //prevChain = atom.chain;
66546
66607
  }
66547
- }
66608
+ //}
66548
66609
 
66549
66610
  let chainResi = atom.chain + '_' + atom.resi;
66550
66611
  if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {
@@ -66709,6 +66770,9 @@ class SaveFile {
66709
66770
  }
66710
66771
 
66711
66772
  pdbStr += line + '\n';
66773
+
66774
+ prevStru = atom.structure;
66775
+ prevChain = atom.chain;
66712
66776
  }
66713
66777
 
66714
66778
  pdbStr += connStr;
@@ -66972,6 +67036,7 @@ class ShareLink {
66972
67036
  //file (the comand history) is concatenated in the URL to show the current state.
66973
67037
  async shareLink(bPngHtml, bPngOnly) { let ic = this.icn3d, me = ic.icn3dui;
66974
67038
  let url = this.shareLinkUrl();
67039
+
66975
67040
  let bTooLong =(url.length > 4000 || url.indexOf('http') !== 0) ? true : false;
66976
67041
  if(bPngHtml) url += "&random=" + parseInt(Math.random() * 1000); // generate a new shorten URL and thus image name everytime
66977
67042
  //var inputid =(ic.inputid) ? ic.inputid : "custom";
@@ -67003,40 +67068,53 @@ class ShareLink {
67003
67068
  }
67004
67069
  }
67005
67070
 
67006
- let data = await this.getShareLinkPrms(url, bPngHtml);
67007
-
67008
67071
  let shorturl = 'Problem in getting shortened URL';
67009
- if(data.shortLink !== undefined) {
67010
- shorturl = data.shortLink;
67011
- if(bPngHtml) { // save png and corresponding html
67012
- let strArray = shorturl.split("/");
67013
- let shortName = strArray[strArray.length - 1];
67014
- ic.saveFileCls.saveFile(inputid + '-' + shortName + '.png', 'png');
67015
- let text = '<div style="float:left; border: solid 1px #0000ff; padding: 5px; margin: 10px; text-align:center;">';
67016
- text += '<a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?' + shortName + '" target="_blank">';
67017
- text += '<img style="height:300px" src ="' + inputid + '-' + shortName + '.png"><br>\n';
67018
- text += '<!--Start of your comments==================-->\n';
67019
- let yournote =(ic.yournote) ? ': ' + ic.yournote.replace(/\n/g, "<br>").replace(/; /g, ", ") : '';
67020
- text += 'PDB ' + inputid.toUpperCase() + yournote + '\n';
67021
- text += '<!--End of your comments====================-->\n';
67022
- text += '</a>';
67023
- text += '</div>\n\n';
67024
- ic.saveFileCls.saveFile(inputid + '-' + shortName + '.html', 'html', text);
67025
- }
67026
- }
67027
- if(bPngHtml && data.shortLink === undefined) {
67028
- ic.saveFileCls.saveFile(inputid + '_icn3d_loadable.png', 'png');
67029
- }
67030
- //shorturl: https://icn3d.page.link/NvbAh1Vmiwc4bgX87
67031
- let urlArray = shorturl.split('page.link/');
67032
- //if(urlArray.length == 2) shorturl = me.htmlCls.baseUrl + 'icn3d/share.html?' + urlArray[1];
67033
- // When the baseURL is structure.ncbi.nlm.nih.gov, mmcifparser.cgi has a problem to past posted data in Mac/iphone
67034
- // So the base URL is still www.ncbi.nlm.nih.gov/Structure,just use short URL here
67035
- if(urlArray.length == 2) shorturl = 'https://structure.ncbi.nlm.nih.gov/icn3d/share.html?' + urlArray[1];
67072
+
67073
+ if(!me.cfg.notebook) {
67074
+ let data = await this.getShareLinkPrms(url, bPngHtml);
67075
+
67076
+ if(data.shortLink !== undefined) {
67077
+ shorturl = data.shortLink;
67078
+ if(bPngHtml) { // save png and corresponding html
67079
+ let strArray = shorturl.split("/");
67080
+ let shortName = strArray[strArray.length - 1];
67081
+ ic.saveFileCls.saveFile(inputid + '-' + shortName + '.png', 'png');
67082
+ let text = '<div style="float:left; border: solid 1px #0000ff; padding: 5px; margin: 10px; text-align:center;">';
67083
+ text += '<a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?' + shortName + '" target="_blank">';
67084
+ text += '<img style="height:300px" src ="' + inputid + '-' + shortName + '.png"><br>\n';
67085
+ text += '<!--Start of your comments==================-->\n';
67086
+ let yournote =(ic.yournote) ? ': ' + ic.yournote.replace(/\n/g, "<br>").replace(/; /g, ", ") : '';
67087
+ text += 'PDB ' + inputid.toUpperCase() + yournote + '\n';
67088
+ text += '<!--End of your comments====================-->\n';
67089
+ text += '</a>';
67090
+ text += '</div>\n\n';
67091
+ ic.saveFileCls.saveFile(inputid + '-' + shortName + '.html', 'html', text);
67092
+ }
67093
+ }
67094
+
67095
+ if(bPngHtml && data.shortLink === undefined) {
67096
+ ic.saveFileCls.saveFile(inputid + '_icn3d_loadable.png', 'png');
67097
+ }
67098
+
67099
+ //shorturl: https://icn3d.page.link/NvbAh1Vmiwc4bgX87
67100
+ let urlArray = shorturl.split('page.link/');
67101
+ //if(urlArray.length == 2) shorturl = me.htmlCls.baseUrl + 'icn3d/share.html?' + urlArray[1];
67102
+ // When the baseURL is structure.ncbi.nlm.nih.gov, mmcifparser.cgi has a problem to past posted data in Mac/iphone
67103
+ // So the base URL is still www.ncbi.nlm.nih.gov/Structure,just use short URL here
67104
+ if(urlArray.length == 2) shorturl = 'https://structure.ncbi.nlm.nih.gov/icn3d/share.html?' + urlArray[1];
67105
+
67106
+ $("#" + ic.pre + "short_url").val(shorturl);
67107
+ $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
67108
+ }
67109
+
67110
+ let outputCmd = this.shareLinkUrl(undefined, true);
67111
+ let idStr = (me.cfg.url) ? "url=" + me.cfg.url : "mmdbafid=" + ic.inputid;
67112
+ let jnCmd = "view = icn3dpy.view(q='" + idStr + "',command='" + outputCmd + "')\nview";
67113
+ $("#" + ic.pre + "jn_commands").val(jnCmd);
67114
+
67036
67115
  $("#" + ic.pre + "ori_url").val(url);
67037
- $("#" + ic.pre + "short_url").val(shorturl);
67038
- $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
67039
- if(!bPngHtml) me.htmlCls.dialogCls.openDlg('dl_copyurl', 'Copy a Share Link URL');
67116
+
67117
+ if(!bPngHtml) me.htmlCls.dialogCls.openDlg('dl_copyurl', 'Copy a Share Link URL or Jupyter Notebook Commands');
67040
67118
  }
67041
67119
 
67042
67120
  getShareLinkPrms(url, bPngHtml) { let ic = this.icn3d, me = ic.icn3dui;
@@ -67065,8 +67143,9 @@ class ShareLink {
67065
67143
  });
67066
67144
  }
67067
67145
 
67068
- shareLinkUrl(bAllCommands) { let ic = this.icn3d, me = ic.icn3dui;
67146
+ shareLinkUrl(bAllCommands, bOutputCmd) { let ic = this.icn3d, me = ic.icn3dui;
67069
67147
  let url = me.htmlCls.baseUrl + "icn3d/full.html?";
67148
+ let outputCmd = '';
67070
67149
  if(me.cfg.bSidebyside) url = me.htmlCls.baseUrl + "icn3d/full2.html?";
67071
67150
 
67072
67151
  if(ic.bInputUrlfile) {
@@ -67169,8 +67248,13 @@ class ShareLink {
67169
67248
 
67170
67249
  url += 'command=';
67171
67250
 
67172
- //let start =(inparaWithoutCommand !== undefined) ? 1 : 0;
67173
- let start = 0;
67251
+ let start;
67252
+ if(me.cfg.notebook) {
67253
+ start =(inparaWithoutCommand !== undefined) ? 1 : 0;
67254
+ }
67255
+ else {
67256
+ start = 0;
67257
+ }
67174
67258
 
67175
67259
  if(bAllCommands || ic.bInputUrlfile) start = 0;
67176
67260
 
@@ -67236,17 +67320,18 @@ class ShareLink {
67236
67320
  prevCommandStr = commandStr;
67237
67321
  }
67238
67322
 
67239
- url += tmpUrl;
67240
-
67241
67323
  // last command
67242
67324
  if(prevCommandStr) {
67243
- if(tmpUrl) url += '; ';
67244
- if(cntToggle > 0 && cntToggle %2 == 0 && prevCommandStr !== toggleStr) url += toggleStr + '; ';
67325
+ if(tmpUrl) tmpUrl += '; ';
67326
+ if(cntToggle > 0 && cntToggle %2 == 0 && prevCommandStr !== toggleStr) tmpUrl += toggleStr + '; ';
67245
67327
 
67246
- url += prevCommandStr + '|||' + ic.transformCls.getTransformationStr(transformation);
67328
+ tmpUrl += prevCommandStr + '|||' + ic.transformCls.getTransformationStr(transformation);
67247
67329
  statefile += prevCommandStr + '|||' + ic.transformCls.getTransformationStr(transformation) + '\n';
67248
67330
  }
67249
67331
 
67332
+ url += tmpUrl;
67333
+ outputCmd = tmpUrl;
67334
+
67250
67335
  statefile = statefile.replace(/!/g, Object.keys(ic.structures)[0] + '_');
67251
67336
  if((ic.bInputfile && !ic.bInputUrlfile) || (ic.bInputUrlfile && ic.bAppend) || url.length > 4000) url = statefile;
67252
67337
  let id;
@@ -67259,7 +67344,7 @@ class ShareLink {
67259
67344
  url = url.replace(new RegExp('blast_rep_id=!','g'), 'blast_rep_id=' + id + '_');
67260
67345
  }
67261
67346
 
67262
- return url;
67347
+ return (bOutputCmd) ? outputCmd : url;
67263
67348
  }
67264
67349
 
67265
67350
  getPngText() { let ic = this.icn3d; ic.icn3dui;
@@ -70503,7 +70588,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
70503
70588
 
70504
70589
  ic.loadCmd = 'load alignment ' + me.cfg.align + ' | parameters ' + me.cfg.inpara;
70505
70590
  me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
70506
- if(me.cfg.inpara.indexOf('atype=2') == -1) {
70591
+ if(me.cfg.inpara && me.cfg.inpara.indexOf('atype=2') == -1) {
70507
70592
  await ic.alignParserCls.downloadAlignment(me.cfg.align);
70508
70593
  }
70509
70594
  else {