icn3d 3.30.4 → 3.30.6

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Files changed (4) hide show
  1. package/icn3d.js +90 -77
  2. package/icn3d.min.js +3 -3
  3. package/icn3d.module.js +90 -77
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -11983,17 +11983,17 @@ class SetDialog {
11983
11983
 
11984
11984
  setTemplateMenu() { let me = this.icn3dui; me.icn3d;
11985
11985
  let group2tpl = {};
11986
- group2tpl['V'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PDL1_4z18B_human_V-n1', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
11987
- group2tpl['C1'] = ['B2Microglobulin_7phrL_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
11988
- group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
11989
- group2tpl['I'] = ['BTLA_2aw2A_human_Iset', 'CD19_6al5A_human_C2orV-n1', 'JAM1_1nbqA_human_VorIset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152'];
11990
- group2tpl['E'] = ['ASF1A_2iijA_human', 'CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'TEAD1_3kysC_human'];
11986
+ group2tpl['IgV'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
11987
+ group2tpl['IgC1'] = ['B2Microglobulin_7phrL_human_C1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'LAG3_7tzgD_human_C1-n2', 'MHCIa_7phrH_human_C1', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_C1-n2'];
11988
+ group2tpl['IgC2'] = ['CD2_1hnfA_human_C2-n2', 'CD3g_6jxrg_human_C2'];
11989
+ group2tpl['IgI'] = ['BTLA_2aw2A_human_Iset', 'Contactin1_3s97C_human_Iset-n2', 'JAM1_1nbqA_human_Iset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152'];
11990
+ group2tpl['IgE'] = ['CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria'];
11991
11991
 
11992
- group2tpl['FN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
11992
+ group2tpl['IgFN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
11993
11993
 
11994
- group2tpl['FN3-like'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
11994
+ group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TEAD1_3kysC_human'];
11995
11995
 
11996
- group2tpl['Other'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];
11996
+ group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];
11997
11997
 
11998
11998
  let tpl2strandsig = {};
11999
11999
  tpl2strandsig['ASF1A_2iijA_human'] = "A A' B C C' E F G G+";
@@ -12001,33 +12001,33 @@ class SetDialog {
12001
12001
  tpl2strandsig['BArrestin1_4jqiA_rat_n1'] = "A- A A' B C C' E F G";
12002
12002
  tpl2strandsig['BTLA_2aw2A_human_Iset'] = "A A' B C C' D E F G";
12003
12003
  tpl2strandsig['C3_2qkiD_human_n1'] = "A A' B C C' E F G";
12004
- tpl2strandsig['CD19_6al5A_human_C2orV-n1'] = "A' B C C' D E F G";
12004
+ tpl2strandsig['CD19_6al5A_human-n1'] = "A' B C C' D E F G";
12005
12005
  tpl2strandsig['CD28_1yjdC_human_V'] = "A A' B C C' C'' D E F G";
12006
12006
  tpl2strandsig['CD2_1hnfA_human_C2-n2'] = "A B C C' E F G";
12007
12007
  tpl2strandsig['CD2_1hnfA_human_V-n1'] = "A' B C C' C'' D E F G";
12008
- tpl2strandsig['CD3d_6jxrd_human_Iset'] = "A B C D E F G";
12009
- tpl2strandsig['CD3e_6jxrf_human_Iset'] = "A B C C' D E F G";
12010
- tpl2strandsig['CD3g_6jxrg_human_Iset'] = "A B C C' E F G G+";
12008
+ tpl2strandsig['CD3d_6jxrd_human_C1'] = "A B C D E F G";
12009
+ tpl2strandsig['CD3e_6jxrf_human_C1'] = "A B C C' D E F G";
12010
+ tpl2strandsig['CD3g_6jxrg_human_C2'] = "A B C C' E F G G+";
12011
12011
  tpl2strandsig['CD8a_1cd8A_human_V'] = "A A' B C C' C'' D E F G";
12012
12012
  tpl2strandsig['CoAtomerGamma1_1r4xA_human'] = "A- A B C D E F G";
12013
12013
  tpl2strandsig['Contactin1_2ee2A_human_FN3-n9'] = "A A' B C C' E F G";
12014
- tpl2strandsig['Contactin1_3s97C_human_C2-n2'] = "A A' B C D E F G";
12014
+ tpl2strandsig['Contactin1_3s97C_human_Iset-n2'] = "A A' B C D E F G";
12015
12015
  tpl2strandsig['CuZnSuperoxideDismutase_1hl5C_human'] = "A- A B C C' E F G";
12016
12016
  tpl2strandsig['ECadherin_4zt1A_human_n2'] = "A' B C D E F G";
12017
12017
  tpl2strandsig['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = "A--- A-- A- A B C C' C'' D E F G";
12018
12018
  tpl2strandsig['FAB-HEAVY_5esv_C1-n2'] = "A B C D E F G";
12019
12019
  tpl2strandsig['FAB-HEAVY_5esv_V-n1'] = "A B C C' C'' D E F G";
12020
- tpl2strandsig['FAB-LIGHT_5esv_C1-n2'] = "A B C C' E F G";
12020
+ tpl2strandsig['FAB-LIGHT_5esv_C1-n2'] = "A B C C' D E F G";
12021
12021
  tpl2strandsig['FAB-LIGHT_5esv_V-n1'] = "A A' B C C' C'' D E F G";
12022
- tpl2strandsig['GHR_1axiB_human_FN3-n1'] = "A B C C' D E F G";
12022
+ tpl2strandsig['GHR_1axiB_human_C1-n1'] = "A B C C' D E F G";
12023
12023
  tpl2strandsig['ICOS_6x4gA_human_V'] = "A B C C' C'' D E F G";
12024
12024
  tpl2strandsig['IL6Rb_1bquB_human_FN3-n2'] = "A B C C' E F G";
12025
12025
  tpl2strandsig['IL6Rb_1bquB_human_FN3-n3'] = "A B C C' E F G";
12026
12026
  tpl2strandsig['InsulinR_8guyE_human_FN3-n1'] = "A B C C' E F G";
12027
12027
  tpl2strandsig['InsulinR_8guyE_human_FN3-n2'] = "A B C C' E F G";
12028
12028
  tpl2strandsig['IsdA_2iteA_bacteria'] = "A- A B C C' D E F G";
12029
- tpl2strandsig['JAM1_1nbqA_human_VorIset-n2'] = "A A' B C C' D E F G";
12030
- tpl2strandsig['LAG3_7tzgD_human_C2-n2'] = "A A' B C C' D E F G";
12029
+ tpl2strandsig['JAM1_1nbqA_human_Iset-n2'] = "A A' B C C' D E F G";
12030
+ tpl2strandsig['LAG3_7tzgD_human_C1-n2'] = "A A' B C C' D E F G";
12031
12031
  tpl2strandsig['LAG3_7tzgD_human_V-n1'] = "A' B C C' D E F G";
12032
12032
  tpl2strandsig['LaminAC_1ifrA_human'] = "A- A B C C' E E+ F G";
12033
12033
  tpl2strandsig['MHCIa_7phrH_human_C1'] = "A B C C' D E F G";
@@ -12041,16 +12041,16 @@ class SetDialog {
12041
12041
  tpl2strandsig['RBPJ_6py8C_human_Unk-n1'] = "A A' B C C' E F G";
12042
12042
  tpl2strandsig['RBPJ_6py8C_human_Unk-n2'] = "A B C D E F G";
12043
12043
  tpl2strandsig['Sidekick2_1wf5A_human_FN3-n7'] = "A B C C' E F G";
12044
- tpl2strandsig['Siglec3_5j0bB_human_C2-n2'] = "A A' B C D E F G";
12044
+ tpl2strandsig['Siglec3_5j0bB_human_C1-n2'] = "A A' B C D E F G";
12045
12045
  tpl2strandsig['TCRa_6jxrm_human_C1-n2'] = "A B C D E F G";
12046
12046
  tpl2strandsig['TCRa_6jxrm_human_V-n1'] = "A A' B C C' C'' D E F G";
12047
12047
  tpl2strandsig['TEAD1_3kysC_human'] = "A A+ A' B C C' E F G G+";
12048
12048
  tpl2strandsig['TP34_2o6cA_bacteria'] = "A- A B C C' D E F G";
12049
12049
  tpl2strandsig['TP47_1o75A_bacteria'] = "A B C C' D E F G";
12050
- tpl2strandsig['Titin_4uowM_human_Unk-n152'] = "A A' B C C' D E F G";
12050
+ tpl2strandsig['Titin_4uowM_human_Iset-n152'] = "A A' B C C' D E F G";
12051
12051
  tpl2strandsig['VISTA_6oilA_human_V'] = "A A' B C C' C'' D E F G G+";
12052
12052
  tpl2strandsig['VNAR_1t6vN_shark_V'] = "A A' B C C' D E F G";
12053
- tpl2strandsig['VTCN1_Q7Z7D3_human_V-n2'] = "A B C C' D E F G G+";
12053
+ tpl2strandsig['VTCN1_Q7Z7D3_human_C1-n2'] = "A B C C' D E F G G+";
12054
12054
 
12055
12055
  let html = '';
12056
12056
  for(let group in group2tpl) {
@@ -37993,7 +37993,7 @@ class AnnoIg {
37993
37993
  // titleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
37994
37994
  // fullTitleArray.push(igType + confidance + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
37995
37995
 
37996
- let igType = (parseFloat(tmscore) < 0.75 ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
37996
+ let igType = (parseFloat(tmscore) < ic.refnumCls.TMThreshold ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
37997
37997
  titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
37998
37998
  fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
37999
37999
 
@@ -65828,6 +65828,8 @@ class Dssp {
65828
65828
  class Refnum {
65829
65829
  constructor(icn3d) {
65830
65830
  this.icn3d = icn3d;
65831
+ this.TMThreshold = 0.85;
65832
+ this.topClusters = 5;
65831
65833
  }
65832
65834
 
65833
65835
  async hideIgRefNum() { let ic = this.icn3d; ic.icn3dui;
@@ -65862,7 +65864,7 @@ class Dssp {
65862
65864
 
65863
65865
  setRefPdbs() { let ic = this.icn3d; ic.icn3dui;
65864
65866
  // round 1, 16 templates
65865
- ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_Iset', '1CD28_1yjdC_human_V', '1CD19_6al5A_human_C2orV-n1'];
65867
+ ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_C2', '1CD28_1yjdC_human_V', '1CD19_6al5A_human-n1'];
65866
65868
 
65867
65869
  // round 2
65868
65870
  ic.refpdbHash = {};
@@ -65872,19 +65874,19 @@ class Dssp {
65872
65874
  ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
65873
65875
  ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
65874
65876
  ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
65875
- ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
65876
- ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
65877
+ ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_C1-n1', 'VTCN1_Q7Z7D3_human_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
65878
+ ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C1-n2'];
65877
65879
  ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2'];
65878
65880
  ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
65879
65881
  ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V'];
65880
65882
  ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
65881
- ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'LAG3_7tzgD_human_C2-n2', 'JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2'];
65882
- ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_Iset'];
65883
- ic.refpdbHash['1CD3g_6jxrg_human_Iset'] = ['CD3g_6jxrg_human_Iset', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
65884
- ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_Iset'];
65885
- ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
65883
+ ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Iset-n152', 'LAG3_7tzgD_human_C1-n2', 'JAM1_1nbqA_human_Iset-n2', 'Contactin1_3s97C_human_Iset-n2'];
65884
+ ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_C1'];
65885
+ ic.refpdbHash['1CD3g_6jxrg_human_C2'] = ['CD3g_6jxrg_human_C2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
65886
+ ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_C1'];
65887
+ ic.refpdbHash['1CD19_6al5A_human-n1'] = ['CD19_6al5A_human-n1'];
65886
65888
 
65887
- ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_Iset', 'CD3e_6jxrf_human_Iset', 'CD3g_6jxrg_human_Iset', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_C2-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_FN3-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C2-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
65889
+ ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_C1', 'CD3e_6jxrf_human_C1', 'CD3g_6jxrg_human_C2', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_Iset-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_C1-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_Iset-n2', 'LAG3_7tzgD_human_C1-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C1-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Iset-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_C1-n2'];
65888
65890
 
65889
65891
  // use known ref structure
65890
65892
  ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -65892,7 +65894,7 @@ class Dssp {
65892
65894
  ic.refpdbHash['8GUY_E'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2'];
65893
65895
  ic.refpdbHash['6JXR_m'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
65894
65896
  ic.refpdbHash['1HNF_A'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
65895
- ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C2-n2'];
65897
+ ic.refpdbHash['7TZG_D'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C1-n2'];
65896
65898
  ic.refpdbHash['6PY8_C'] = ['RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
65897
65899
  ic.refpdbHash['1BQU_B'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
65898
65900
 
@@ -65902,7 +65904,7 @@ class Dssp {
65902
65904
  ic.refpdbHash['1I8A_A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
65903
65905
  ic.refpdbHash['2FWU_A'] = ['NaCaExchanger_2fwuA_dog_n2'];
65904
65906
  ic.refpdbHash['4JQI_A'] = ['BArrestin1_4jqiA_rat_n1'];
65905
- ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_VorIset-n2'];
65907
+ ic.refpdbHash['1NBQ_A'] = ['JAM1_1nbqA_human_Iset-n2'];
65906
65908
  ic.refpdbHash['1O75_A'] = ['TP47_1o75A_bacteria'];
65907
65909
  ic.refpdbHash['7PHR_H'] = ['MHCIa_7phrH_human_C1'];
65908
65910
  ic.refpdbHash['2IIJ_A'] = ['ASF1A_2iijA_human'];
@@ -65914,9 +65916,9 @@ class Dssp {
65914
65916
  ic.refpdbHash['2AW2_A'] = ['BTLA_2aw2A_human_Iset'];
65915
65917
  ic.refpdbHash['1HL5_C'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
65916
65918
  ic.refpdbHash['1WF5_A'] = ['Sidekick2_1wf5A_human_FN3-n7'];
65917
- ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C2-n2'];
65919
+ ic.refpdbHash['5J0B_B'] = ['Siglec3_5j0bB_human_C1-n2'];
65918
65920
  ic.refpdbHash['1IFR_A'] = ['LaminAC_1ifrA_human'];
65919
- ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_V-n2'];
65921
+ ic.refpdbHash['Q7Z7D3_A'] = ['VTCN1_Q7Z7D3_human_C1-n2'];
65920
65922
  ic.refpdbHash['4ZQK_B'] = ['PD1_4zqkB_human_V'];
65921
65923
  ic.refpdbHash['2DM3_A'] = ['Palladin_2dm3A_human_Iset-n1'];
65922
65924
  ic.refpdbHash['2ITE_A'] = ['IsdA_2iteA_bacteria'];
@@ -65924,17 +65926,17 @@ class Dssp {
65924
65926
  ic.refpdbHash['4ZT1_A'] = ['ECadherin_4zt1A_human_n2'];
65925
65927
  ic.refpdbHash['1LMI_A'] = ['MPT63_1lmiA_bacteria'];
65926
65928
  ic.refpdbHash['1CD8_A'] = ['CD8a_1cd8A_human_V'];
65927
- ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_C2-n2'];
65928
- ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_FN3-n1'];
65929
+ ic.refpdbHash['3S97_C'] = ['Contactin1_3s97C_human_Iset-n2'];
65930
+ ic.refpdbHash['1AXI_B'] = ['GHR_1axiB_human_C1-n1'];
65929
65931
  ic.refpdbHash['6X4G_A'] = ['ICOS_6x4gA_human_V'];
65930
65932
  ic.refpdbHash['2EE2_A'] = ['Contactin1_2ee2A_human_FN3-n9'];
65931
- ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Unk-n152'];
65932
- ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human_C2orV-n1'];
65933
+ ic.refpdbHash['4UOW_M'] = ['Titin_4uowM_human_Iset-n152'];
65934
+ ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human-n1'];
65933
65935
  ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
65934
65936
  ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
65935
- ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_Iset'];
65936
- ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_Iset'];
65937
- ic.refpdbHash['6JXR_g'] = ['CD3g_6jxrg_human_Iset'];
65937
+ ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_C1'];
65938
+ ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_C1'];
65939
+ ic.refpdbHash['6JXR_g'] = ['CD3g_6jxrg_human_C2'];
65938
65940
 
65939
65941
  // assign Ig types
65940
65942
  ic.ref2igtype = {};
@@ -65944,17 +65946,17 @@ class Dssp {
65944
65946
  ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
65945
65947
  ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
65946
65948
  ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
65947
- ic.ref2igtype['CD19_6al5A_human_C2orV-n1'] = 'CD19';
65949
+ ic.ref2igtype['CD19_6al5A_human-n1'] = 'CD19';
65948
65950
  ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
65949
65951
  ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
65950
65952
  ic.ref2igtype['CD2_1hnfA_human_V-n1'] = 'IgV';
65951
- ic.ref2igtype['CD3d_6jxrd_human_Iset'] = 'IgI';
65952
- ic.ref2igtype['CD3e_6jxrf_human_Iset'] = 'IgI';
65953
- ic.ref2igtype['CD3g_6jxrg_human_Iset'] = 'IgI';
65953
+ ic.ref2igtype['CD3d_6jxrd_human_C1'] = 'IgI';
65954
+ ic.ref2igtype['CD3e_6jxrf_human_C1'] = 'IgI';
65955
+ ic.ref2igtype['CD3g_6jxrg_human_C2'] = 'IgI';
65954
65956
  ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
65955
65957
  ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
65956
65958
  ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
65957
- ic.ref2igtype['Contactin1_3s97C_human_C2-n2'] = 'IgC2';
65959
+ ic.ref2igtype['Contactin1_3s97C_human_Iset-n2'] = 'IgC2';
65958
65960
  ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'SOD';
65959
65961
  ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'Cadherin';
65960
65962
  ic.ref2igtype['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = 'IgE';
@@ -65962,15 +65964,15 @@ class Dssp {
65962
65964
  ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
65963
65965
  ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
65964
65966
  ic.ref2igtype['FAB-LIGHT_5esv_V-n1'] = 'IgV';
65965
- ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFN3';
65967
+ ic.ref2igtype['GHR_1axiB_human_C1-n1'] = 'IgFN3';
65966
65968
  ic.ref2igtype['ICOS_6x4gA_human_V'] = 'IgV';
65967
65969
  ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFN3';
65968
65970
  ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
65969
65971
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
65970
65972
  ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
65971
65973
  ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
65972
- ic.ref2igtype['JAM1_1nbqA_human_VorIset-n2'] = 'IgI';
65973
- ic.ref2igtype['LAG3_7tzgD_human_C2-n2'] = 'IgC2';
65974
+ ic.ref2igtype['JAM1_1nbqA_human_Iset-n2'] = 'IgI';
65975
+ ic.ref2igtype['LAG3_7tzgD_human_C1-n2'] = 'IgC2';
65974
65976
  ic.ref2igtype['LAG3_7tzgD_human_V-n1'] = 'IgV';
65975
65977
  ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
65976
65978
  ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
@@ -65984,16 +65986,16 @@ class Dssp {
65984
65986
  ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
65985
65987
  ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
65986
65988
  ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
65987
- ic.ref2igtype['Siglec3_5j0bB_human_C2-n2'] = 'IgC2';
65989
+ ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC2';
65988
65990
  ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
65989
65991
  ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
65990
65992
  ic.ref2igtype['TEAD1_3kysC_human'] = 'IgE';
65991
65993
  ic.ref2igtype['TP34_2o6cA_bacteria'] = 'IgE';
65992
65994
  ic.ref2igtype['TP47_1o75A_bacteria'] = 'IgE';
65993
- ic.ref2igtype['Titin_4uowM_human_Unk-n152'] = 'IgI';
65995
+ ic.ref2igtype['Titin_4uowM_human_Iset-n152'] = 'IgI';
65994
65996
  ic.ref2igtype['VISTA_6oilA_human_V'] = 'IgV';
65995
65997
  ic.ref2igtype['VNAR_1t6vN_shark_V'] = 'IgV';
65996
- ic.ref2igtype['VTCN1_Q7Z7D3_human_V-n2'] = 'IgV';
65998
+ ic.ref2igtype['VTCN1_Q7Z7D3_human_C1-n2'] = 'IgV';
65997
65999
  }
65998
66000
 
65999
66001
  getPdbAjaxArray() { let ic = this.icn3d, me = ic.icn3dui;
@@ -66408,17 +66410,20 @@ class Dssp {
66408
66410
  if(bBstrand && bCstrand && bEstrand && bFstrand) break;
66409
66411
  }
66410
66412
 
66411
- if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
66412
- // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
66413
- if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
66414
- if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
66415
- // if(!me.bNode && (BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
66416
- if(ic.domainid2refpdbname[domainid][0] == refpdbname) {
66417
- delete ic.domainid2refpdbname[domainid];
66418
- delete ic.domainid2score[domainid];
66413
+ // if(refpdbname != 'CD19_6al5A_human-n1') { // relax for CD19
66414
+ if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
66415
+ // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
66416
+ if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
66417
+ if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
66418
+ // if(!me.bNode && (BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
66419
+ if(ic.domainid2refpdbname[domainid][0] == refpdbname) {
66420
+ delete ic.domainid2refpdbname[domainid];
66421
+ delete ic.domainid2score[domainid];
66422
+ }
66423
+ continue;
66419
66424
  }
66420
- continue;
66421
- }
66425
+ // }
66426
+
66422
66427
  }
66423
66428
 
66424
66429
  if(!bRound1) {
@@ -66447,7 +66452,8 @@ class Dssp {
66447
66452
  ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;
66448
66453
 
66449
66454
  if(bRound1) {
66450
- ic.domainid2refpdbname[domainid] = score > 0.75 ? [refpdbname] : ['all_templates'];
66455
+ // ic.domainid2refpdbname[domainid] = score > 0.75 ? [refpdbname] : ['all_templates'];
66456
+ ic.domainid2refpdbname[domainid] = score >= this.TMThreshold ? [refpdbname] : ['all_templates'];
66451
66457
  }
66452
66458
  else {
66453
66459
  ic.domainid2refpdbname[domainid] = [refpdbname];
@@ -66466,7 +66472,7 @@ class Dssp {
66466
66472
  }
66467
66473
  }
66468
66474
 
66469
- // combine the top four clusters for the 2nd round alignment
66475
+ // combine the top clusters for the 2nd round alignment
66470
66476
  if(bRound1) {
66471
66477
  for(let domainid in domainid2refpdbnamelist) {
66472
66478
  if(!me.bNode && ic.domainid2refpdbname[domainid][0] == 'all_templates') {
@@ -66475,8 +66481,8 @@ class Dssp {
66475
66481
  refpdbnameList.sort(function(a, b) {
66476
66482
  return refpdbname2score[b] - refpdbname2score[a]
66477
66483
  });
66478
- // top 4 templates
66479
- ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,4);
66484
+ // top templates
66485
+ ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0, this.topClusters);
66480
66486
  }
66481
66487
  }
66482
66488
  }
@@ -66708,13 +66714,13 @@ class Dssp {
66708
66714
 
66709
66715
  let currStrand;
66710
66716
 
66711
- // let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
66717
+ // let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human-n1';
66712
66718
  for(let i = 0, il = segArray.length; i < il; ++i) {
66713
66719
  let seg = segArray[i];
66714
66720
  if(!seg) continue;
66715
66721
 
66716
- let qStart = seg.q_start;
66717
- parseInt(seg.q_start);
66722
+ seg.q_start;
66723
+ let qStartInt = parseInt(seg.q_start);
66718
66724
  if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
66719
66725
 
66720
66726
  // one item in "seq"
@@ -66727,7 +66733,8 @@ class Dssp {
66727
66733
  let resid = chainid + '_' + seg.t_start;
66728
66734
  //let refnum = qStartInt.toString() + postfix;
66729
66735
  //let refnum = qStart + postfix;
66730
- let refnum = qStart;
66736
+ //let refnum = qStart;
66737
+ let refnum = qStartInt;
66731
66738
 
66732
66739
  let refnumLabel = this.getLabelFromRefnum(refnum);
66733
66740
  currStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
@@ -67142,7 +67149,7 @@ class Dssp {
67142
67149
  if(!ic.chainid2refpdbname[chnid]) return false;
67143
67150
 
67144
67151
  // auto-generate ref numbers for loops
67145
- let currStrand = '', prevStrand = '';
67152
+ let currStrand = '', prevStrand = '', prevValidStrand = '';
67146
67153
  let refnumLabel, refnumStr_ori, refnumStr, postfix, strandPostfix, refnum, refnum3c, refnum2c;
67147
67154
  let bExtendedStrand = false, bSecThird9 = false;
67148
67155
 
@@ -67206,7 +67213,8 @@ class Dssp {
67206
67213
  if(!bSecThird9 || (bExtendedStrand && !bSecThird9)) {
67207
67214
  let lastTwo = parseInt(refnum.toString().substr(refnum.toString().length - 2, 2));
67208
67215
 
67209
- if(currStrand != prevStrand) { // reset currCnt
67216
+ // reset currCnt
67217
+ if(currStrand != prevStrand && currStrand != prevValidStrand) { // sometimes the same resid appear several times, e.g, 7M7B_H_135
67210
67218
  bFoundAnchor = false;
67211
67219
 
67212
67220
  if(strandHash[currStrand + postfix]) {
@@ -67308,6 +67316,8 @@ class Dssp {
67308
67316
  }
67309
67317
  }
67310
67318
  }
67319
+
67320
+ prevValidStrand = currStrand;
67311
67321
  }
67312
67322
  }
67313
67323
 
@@ -67395,6 +67405,7 @@ class Dssp {
67395
67405
  for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
67396
67406
  // let strandTmp = strandArray[i].strand.substr(0, 1);
67397
67407
  let strandTmp = strandArray[i].strand;
67408
+
67398
67409
  if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
67399
67410
  if(i != il - 1) { // modify
67400
67411
  strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
@@ -67411,7 +67422,7 @@ class Dssp {
67411
67422
  let domainid = ic.resid2domainid[resid];
67412
67423
  removeDomainidHash[domainid] = 1;
67413
67424
  continue;
67414
- }
67425
+ }
67415
67426
  }
67416
67427
  }
67417
67428
 
@@ -67528,10 +67539,12 @@ class Dssp {
67528
67539
  let halfLen = parseInt(len / 2.0 + 0.5);
67529
67540
 
67530
67541
  if(loopCnt <= halfLen) {
67531
- currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
67532
- refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
67533
- refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
67534
- domainid = strandArray[prevStrandCnt].domainid;
67542
+ if(strandArray[prevStrandCnt]) {
67543
+ currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
67544
+ refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
67545
+ refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
67546
+ domainid = strandArray[prevStrandCnt].domainid;
67547
+ }
67535
67548
  }
67536
67549
  else {
67537
67550
  currRefnum = strandArray[strandCnt].startRefnum - len + loopCnt - 1;