icn3d 3.25.9 → 3.25.10

package/icn3d.js

@@ -7309,14 +7309,14 @@ class ClickMenu {
             thisClass.setLogCmd('ig refnum on', true);
             await ic.refnumCls.showIgRefNum();
 
-            if(ic.bShowRefnum) {
-               ic.opts.color = 'ig strand';
-               ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+            // if(ic.bShowRefnum) {
+            //    ic.opts.color = 'ig strand';
+            //    ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
    
-               ic.selectionCls.selectAll_base();
-               ic.hlUpdateCls.updateHlAll();
-               ic.drawCls.draw();
-            }
+            //    ic.selectionCls.selectAll_base();
+            //    ic.hlUpdateCls.updateHlAll();
+            //    ic.drawCls.draw();
+            // }
          });
 
          me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; e.preventDefault();
@@ -9396,8 +9396,8 @@ class SetMenu {
             //}
 
             //!!!
-            // html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            // html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -34674,25 +34674,27 @@ class SetColor {
             case 'ig strand':
                 if(ic.bShowRefnum) {
                     let color;
-                    for(let resid in ic.residues) {
-                        if(!ic.resid2refnum[resid]) {
+                    let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
+
+                    for(let resid in residueHash) {
+                        if(!ic.resid2refnum[resid]) {              
                             color = me.parasCls.thr('#FFFFFF');
                         }
                         else {
                             let refnumLabel = ic.resid2refnum[resid];
                             
-                            if(!refnumLabel) {
-                                color = me.parasCls.thr(me.htmlCls.GREYB);
-                            }
-                            else {
-                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
+                            // if(!refnumLabel) {
+                            //     color = me.parasCls.thr(me.htmlCls.GREYB);
+                            // }
+                            // else {
+                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
                                 let currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                                 color = ic.showSeqCls.getRefnumColor(currStrand);
 
-                                if(ic.residIgLoop.hasOwnProperty(resid)) {
+                                if(ic.residIgLoop.hasOwnProperty(resid)) {                            
                                     color = me.parasCls.thr(me.htmlCls.GREYB);
                                 }
-                            }
+                            // }
                         }
                             
                         for (let i in ic.residues[resid]) {
@@ -34709,7 +34711,8 @@ class SetColor {
             case 'ig protodomain':
                 if(ic.bShowRefnum) {
                     let color;
-                    for(let resid in ic.residues) {
+                    let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
+                    for(let resid in residueHash) {
                         if(!ic.resid2refnum[resid]) {
                             color = me.parasCls.thr('#FFFFFF');
                         }
@@ -34720,7 +34723,7 @@ class SetColor {
                                 color = me.parasCls.thr(me.htmlCls.GREYB);
                             }
                             else {
-                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
+                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
                                 let currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                                 color = ic.showSeqCls.getProtodomainColor(currStrand);
 
@@ -35662,9 +35665,9 @@ class SetOption {
         let html = '';
 
         const name2color = {
-            //"A^ Strand": "FF00FF", 
+            //"A- Strand": "FF00FF", 
             "A Strand": "663399",
-            //"A* Strand": "663399", //"FFC0CB",
+            //"A+ Strand": "663399", //"FFC0CB",
             "A' Strand": "663399", //"9370db",
             "B Strand": "ba55d3",
             "C Strand": "0000FF",
@@ -35674,7 +35677,7 @@ class SetOption {
             "E Strand": "FFFF00", //"F0E68C",
             "F Strand": "FFA500",
             "G Strand": "FF0000",
-            //"G* Strand": "8B0000",
+            //"G+ Strand": "8B0000",
             "Loop": "CCCCCC"
         };
 
@@ -40852,10 +40855,12 @@ class ShowAnno {
 
         if(ic.bShowRefnum) {
             ic.opts.color = 'ig strand';
-            ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+            //ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+            ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
 
             ic.selectionCls.selectAll_base();
             ic.hlUpdateCls.updateHlAll();
+            //ic.drawCls.draw();
         }
     }
 
@@ -41941,7 +41946,7 @@ class ShowSeq {
                 }
 
                 if(refnumLabel) {                        
-                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
+                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
                     currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
                     refnumStr_ori.substr(0, 1);
 
@@ -42047,7 +42052,7 @@ class ShowSeq {
                     currStrand = strandArray[strandCnt].strand;
 
                     if(refnumLabel) {
-                        refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
+                        refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
                         currRefnum = parseInt(refnumStr);
                         refnumLabelNoPostfix = currStrand + currRefnum;
                         
@@ -42128,6 +42133,9 @@ class ShowSeq {
                             }
                         }
                         else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
+                            // not in loop any more if you assign ref numbers multiple times
+                            delete ic.residIgLoop[residueid];
+
                             bBeforeAstrand = false;
 
                             if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
@@ -42216,7 +42224,7 @@ class ShowSeq {
                 let bHidelabel = false;
 
                 if(refnumLabel) {                        
-                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
+                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
                     currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
                     currStrand_ori = currStrand;
 
@@ -42329,15 +42337,14 @@ class ShowSeq {
     }
 
     getRefnumColor(currStrand, bText) {  let ic = this.icn3d, me = ic.icn3dui;
-        // if(currStrand == "A^") { 
-        //     return '#FF00FF'; 
-        // }
-        // else 
-        
-        if(currStrand == "A") { 
+        if(currStrand == "A-") { 
             return '#663399'; 
         }
-        else if(currStrand == "A*") { 
+        else if(currStrand == "A") { 
+            return '#663399'; 
+        }
+        //else if(currStrand == "A*") { 
+        else if(currStrand == "A+") { 
             return '#663399'; //'#FFC0CB'; 
         }
         else if(currStrand == "A'") { 
@@ -42367,7 +42374,7 @@ class ShowSeq {
         else if(currStrand == "G") { 
             return '#FF0000'; 
         }
-        else if(currStrand == "G*") { 
+        else if(currStrand == "G+") { 
             return '#8B0000'; 
         }
         else {
@@ -47790,7 +47797,7 @@ class ChainalignParser {
                 // reset annotations
                 $("#" + ic.pre + "dl_annotations").html("");
                 ic.bAnnoShown = false;
-                if($('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
+                if($('#' + me.pre + 'dl_selectannotations').hasClass('ui-dialog-content') && $('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
                     $('#' + ic.pre + 'dl_selectannotations').dialog( 'close' );
                 }
            //});
@@ -62069,10 +62076,15 @@ class Dssp {
             await thisClass.parseRefPdbData(ic.pdbDataArray);
         }
         else {
-            //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1t6v_vnar', '1wio_c2', '1wio_igv', '2atp_a', '2atp_b', '2dm3_iset', '5esv_vh', '5esv_vl', '6al5_cd19', '7bz5_cl1', '7bz5_vh', '7bz5_vl'];
             //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1cdh_cd4', '1dr9_cd80', '1hnf_cd2', '1hxm_d', '1hxm_g', '1ifr_lamin', '1ncn_cd86', '1t6v_vnar', '1yjd_cd28', '2atp_a', '2atp_b', '2dm3_iset', '3kys_tead1', '3pv7_ncr', '4f9l_cd277', '4gos_vtc', '4i0k_cd276', '4jqi_b', '4z18_cd274', '4zqk_pd1', '4zt1_e', '5esv_vh', '5esv_vl', '6al5_cd19', '6jxr_a', '6jxr_b', '6jxr_d', '6jxr_e', '6jxr_g', '6oil_vista', '6rp8_at', '6rp8_t', '6umt_cd273', '6x4g_cd275', '6x4g_icos', '7xq8_a', '7xq8_b', 'q71h61_ild', 'q9um44_hhl', 'p42081_cd86', 'q7z7d3_vtc', '1bqu_x', '1cdh_x', '1hnf_x', '1hxm_dx', '1hxm_gx', '4jqi_x', '4zt1_x', '5esv_vhx', '5esv_vlx', '6jxr_ax', '6jxr_bx', '1dr9_x', '3pv7_x', '4f9l_x', '4iok_x', '4z18_x', '6x4g_cd275x', 'q9um44_x'];
             
-            ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1cdh_cd4', '1dr9_cd80', '1hnf_cd2', '1hxm_d', '1hxm_g', '1ifr_lamin', '1ncn_cd86', '1t6v_vnar', '1yjd_cd28', '2atp_a', '2atp_b', '2dm3_iset', '3kys_tead1', '3pv7_ncr', '4f9l_cd277', '4gos_vtc', '4i0k_cd276', '4jqi_b', '4z18_cd274', '4zqk_pd1', '4zt1_e', '5esv_vh', '5esv_vl', '6al5_cd19', '6jxr_a', '6jxr_b', '6jxr_d', '6jxr_e', '6jxr_g', '6oil_vista', '6rp8_at', '6rp8_t', '6umt_cd273', '6x4g_cd275', '6x4g_icos', '7xq8_a', '7xq8_b', 'q71h61_ild', 'q9um44_hhl'];
+            //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1cdh_cd4', '1dr9_cd80', '1hnf_cd2', '1hxm_d', '1hxm_g', '1ifr_lamin', '1ncn_cd86', '1t6v_vnar', '1yjd_cd28', '2atp_a', '2atp_b', '2dm3_iset', '3kys_tead1', '3pv7_ncr', '4f9l_cd277', '4gos_vtc', '4i0k_cd276', '4jqi_b', '4z18_cd274', '4zqk_pd1', '4zt1_e', '5esv_vh', '5esv_vl', '6al5_cd19', '6jxr_a', '6jxr_b', '6jxr_d', '6jxr_e', '6jxr_g', '6oil_vista', '6rp8_at', '6rp8_t', '6umt_cd273', '6x4g_cd275', '6x4g_icos', '7xq8_a', '7xq8_b', 'q71h61_ild', 'q9um44_hhl'];
+
+            //ic.refpdbArray = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', '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', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
+
+            //ic.refpdbArray2 = ['B2Microglobulin_7phrL_human_C1.pdb', 'Contactin1_2ee2A_human_FN3-n9.pdb', 'IL6Rb_1bquB_human_FN3-n3.pdb', 'InsulinR_8guyE_human_FN3-n1.pdb', 'JAM1_1nbqA_human_VorIset-n2.pdb', 'NaCaExchanger_2fwuA_dog_n2.pdb', 'ORF7a_1xakA_virus.pdb', 'Sidekick2_1wf5A_human_FN3-n7.pdb', 'Siglec3_5j0bB_human_C2-n2.pdb', 'TP47_1o75A_bacteria.pdb'];
+
+            ic.refpdbArray = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', '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', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1.pdb', 'Contactin1_2ee2A_human_FN3-n9.pdb', 'IL6Rb_1bquB_human_FN3-n3.pdb', 'InsulinR_8guyE_human_FN3-n1.pdb', 'JAM1_1nbqA_human_VorIset-n2.pdb', 'NaCaExchanger_2fwuA_dog_n2.pdb', 'ORF7a_1xakA_virus.pdb', 'Sidekick2_1wf5A_human_FN3-n7.pdb', 'Siglec3_5j0bB_human_C2-n2.pdb', 'TP47_1o75A_bacteria.pdb'];
 
             if(ic.pdbDataArray) {
                 await thisClass.parseRefPdbData(ic.pdbDataArray);
@@ -62247,15 +62259,15 @@ class Dssp {
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
 
-        // if(!ic.chainid2index) ic.chainid2index = {};
-        // if(!ic.domainid2index) ic.domainid2index = {};
-        // if(!ic.domainid2ig2kabat) ic.domainid2ig2kabat = {};
-        // if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
+        if(!ic.chainid2index) ic.chainid2index = {};
+        if(!ic.domainid2index) ic.domainid2index = {};
+        if(!ic.domainid2ig2kabat) ic.domainid2ig2kabat = {};
+        if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
 
-        ic.chainid2index = {};
-        ic.domainid2index = {};
-        ic.domainid2ig2kabat = {};
-        ic.domainid2ig2imgt = {};
+        // ic.chainid2index = {};
+        // ic.domainid2index = {};
+        // ic.domainid2ig2kabat = {};
+        // ic.domainid2ig2imgt = {};
 
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             let queryData = dataArray[i].value; //[0];
@@ -62398,10 +62410,10 @@ if(!me.bNode) {
     getLabelFromRefnum(oriRefnum, prevStrand, bCd19) { let ic = this.icn3d; ic.icn3dui;
         let refnum = parseInt(oriRefnum);
 
-        // A^: 1xx or 2xx
+        // A-: 10xx
         // A: 11xx
         // A': 12xx
-        // A*: 13xx
+        // A+: 13xx
         // B: 21xx
         // C: 32xx
         // C': 42xx
@@ -62410,7 +62422,7 @@ if(!me.bNode) {
         // E: 71xx
         // F: 82xx
         // G: 91xx, 92xx
-        // G*: 94xx
+        // G+: 94xx
 
         // if(refnum < 100) return " " + oriRefnum;
         // else if(refnum >= 100 && refnum < 1000) {
@@ -62419,10 +62431,11 @@ if(!me.bNode) {
         // }
         if(refnum < 900) return undefined;
         else if(refnum >= 900 && refnum < 1000) return " " + oriRefnum;
-
-        else if(refnum >= 1000 && refnum < 1200) return "A" + oriRefnum;
+        else if(refnum >= 1000 && refnum < 1100) return "A-" + oriRefnum;
+        else if(refnum >= 1100 && refnum < 1200) return "A" + oriRefnum;
         else if(refnum >= 1200 && refnum < 1300) return "A'" + oriRefnum;
-        else if(refnum >= 1300 && refnum < 1400) return "A*" + oriRefnum;
+        //else if(refnum >= 1300 && refnum < 1400) return "A*" + oriRefnum;
+        else if(refnum >= 1300 && refnum < 1400) return "A+" + oriRefnum;
         else if(refnum >= 1400 && refnum < 2000) {
             if(prevStrand  && prevStrand.substr(0, 1) == 'A') {
                 return prevStrand + oriRefnum;
@@ -62439,7 +62452,8 @@ if(!me.bNode) {
         else if(refnum >= 7000 && refnum < 8000) return "E" + oriRefnum;
         else if(refnum >= 8000 && refnum < 9000) return "F" + oriRefnum;
         else if(refnum >= 9000 && refnum < 9400) return "G" + oriRefnum;
-        else if(refnum >= 9400 && refnum < 9500) return "G*" + oriRefnum;
+        //else if(refnum >= 9400 && refnum < 9500) return "G*" + oriRefnum;
+        else if(refnum >= 9400 && refnum < 9500) return "G+" + oriRefnum;
         else if(refnum >= 9500) return "G" + oriRefnum;
     }