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Pull request #594: Fixed a bug in relaigning structures.
Merge in STRUC/icn3d from release3251 to master * commit '791ad473cecca53e37a77e3e72fac60602e137a5': Fixed a bug in relaigning structures.
2 parents 126eb88 + 791ad47 commit 99f58c5

28 files changed

Lines changed: 499 additions & 128 deletions

‎CHANGELOG.md‎

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,6 @@
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## Change Log
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[icn3d-3.25.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.25.1.zip) was release on May 3, 2023. Fixed a bug in relaigning structures.
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[icn3d-3.25.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.25.0.zip) was release on April 26, 2023. To improve the performance of embedding several structures in a single page, added the URL parameter "imageonly=1" to render the structure into a static image instead of interactive 3D view. The image is clickable to launch an interactive 3D view.
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[icn3d-3.24.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.24.2.zip) was release on April 24, 2023. Fixed the secondary structures of mutant in the mutation analysis; fixed the lower case in the sequences of VAST+ alignment.

‎build/icn3d.js‎

Lines changed: 92 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -39530,12 +39530,12 @@ var icn3d = (function (exports) {
3953039530

3953139531
if (nsse <= 3)
3953239532
// too small, can't split or trim
39533-
return {subdomains: subdomains, substruct: substruct};
39533+
return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
3953439534

3953539535
if (nsse > this.MAX_SSE) {
3953639536
// we have a problem...
3953739537

39538-
return {subdomains: subdomains, substruct: substruct};
39538+
return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
3953939539
}
3954039540

3954139541
let seqLen = residueArray.length; // + resiOffset;
@@ -39807,7 +39807,7 @@ var icn3d = (function (exports) {
3980739807
let k = prts[i] - 1;
3980839808

3980939809
if ((k < 0) || (k >= substruct.length)) {
39810-
return {subdomains: subdomains, substruct: substruct};
39810+
return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
3981139811
}
3981239812

3981339813
//SSE_Rec sserec = substruct[k];
@@ -39924,7 +39924,7 @@ var icn3d = (function (exports) {
3992439924
}
3992539925
}
3992639926

39927-
return {subdomains: subdomains, substruct: substruct, pos2resi:pos2resi };
39927+
return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
3992839928
} // end c2b_NewSplitChain
3992939929

3993039930
getDomainJsonForAlign(atoms) { let ic = this.icn3d, me = ic.icn3dui;
@@ -42826,10 +42826,10 @@ var icn3d = (function (exports) {
4282642826
// sometimes one chain may have several Ig domains,set an index for each IgDomain
4282742827
let index = 1, bStart = false;
4282842828

42829-
// get the range of each strand excluding loops
42830-
let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0;
42829+
// 1. get the range of each strand excluding loops
42830+
let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0, resCntAtAnchor = 0;
4283142831
if(!bCustom && !kabat_or_imgt) {
42832-
for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt) {
42832+
for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor, ++resCntAtAnchor) {
4283342833
let currResi = ic.ParserUtilsCls.getResi(chnid, i);
4283442834
let residueid = chnid + '_' + currResi;
4283542835
refnumLabel = ic.resid2refnum[residueid];
@@ -42858,6 +42858,8 @@ var icn3d = (function (exports) {
4285842858

4285942859
if(currStrand && currStrand != ' ') {
4286042860
if(refnum3c.substr(0,1) != '9') {
42861+
let lastTwo = parseInt(refnum.toString().substr(refnum.toString().length - 2, 2));
42862+
4286142863
if(currStrand != prevStrand) { // reset currCnt
4286242864
if(strandHash[currStrand + postfix]) {
4286342865
++index;
@@ -42869,10 +42871,19 @@ var icn3d = (function (exports) {
4286942871
strandArray[strandCnt] = {};
4287042872
strandArray[strandCnt].startResi = currResi;
4287142873
strandArray[strandCnt].startRefnum = refnum; // 1250 in A1250a
42874+
42875+
resCntBfAnchor = 0;
4287242876

4287342877
strandArray[strandCnt].endResi = currResi;
4287442878
strandArray[strandCnt].endRefnum = refnum; // 1250a
4287542879

42880+
if(lastTwo == 50) {
42881+
strandArray[strandCnt].anchorRefnum = refnum;
42882+
strandArray[strandCnt].resCntBfAnchor = resCntBfAnchor;
42883+
42884+
resCntAtAnchor = 0;
42885+
}
42886+
4287642887
strandArray[strandCnt].strandPostfix = strandPostfix; // a in A1250a
4287742888
strandArray[strandCnt].strand = currStrand; // A in A1250a
4287842889

@@ -42885,8 +42896,23 @@ var icn3d = (function (exports) {
4288542896
}
4288642897
else {
4288742898
if(strandHash[currStrand + postfix]) {
42899+
if(lastTwo == 50) {
42900+
strandArray[strandCnt - 1].anchorRefnum = refnum;
42901+
strandArray[strandCnt - 1].resCntBfAnchor = resCntBfAnchor;
42902+
42903+
// update
42904+
strandArray[strandCnt - 1].startRefnum = strandArray[strandCnt - 1].anchorRefnum - strandArray[strandCnt - 1].resCntBfAnchor;
42905+
42906+
resCntAtAnchor = 0;
42907+
}
42908+
4288842909
strandArray[strandCnt - 1].endResi = currResi;
4288942910
strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
42911+
strandArray[strandCnt - 1].resCntAtAnchor = resCntAtAnchor;
42912+
42913+
if(strandArray[strandCnt - 1].anchorRefnum) {
42914+
strandArray[strandCnt - 1].endRefnum = strandArray[strandCnt - 1].anchorRefnum + strandArray[strandCnt - 1].resCntAtAnchor;
42915+
}
4289042916

4289142917
resCnt = 0;
4289242918
}
@@ -42898,13 +42924,26 @@ var icn3d = (function (exports) {
4289842924
prevStrand = currStrand;
4289942925
}
4290042926

42927+
// 2. remove strands with less than 3 residues
42928+
for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
42929+
if(strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
42930+
if(i != il - 1) { // modify
42931+
strandArray[i + 1].loopResCnt += strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
42932+
}
42933+
42934+
strandArray.splice(i, 1);
42935+
}
42936+
}
42937+
42938+
// 3. assign refnumLabel for each resid
4290142939
strandCnt = 0;
4290242940
let loopCnt = 0;
4290342941

42904-
let bNterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
42942+
let bNterminal = true, bCterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
4290542943
bStart = false;
42944+
let refnumInStrand = 0;
4290642945
if(strandArray.length > 0) {
42907-
for(let i = 0, il = giSeq.length; i < il; ++i, ++loopCnt) {
42946+
for(let i = 0, il = giSeq.length; i < il; ++i, ++loopCnt, ++refnumInStrand) {
4290842947
let currResi = ic.ParserUtilsCls.getResi(chnid, i);
4290942948
let residueid = chnid + '_' + currResi;
4291042949
refnumLabel = ic.resid2refnum[residueid];
@@ -42975,6 +43014,20 @@ var icn3d = (function (exports) {
4297543014
}
4297643015
else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
4297743016
bNterminal = false;
43017+
//bCterminal = true; // The next will be C-terminal
43018+
43019+
if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
43020+
if(currResi == strandArray[strandCnt].startResi) {
43021+
refnumInStrand = strandArray[strandCnt].anchorRefnum - strandArray[strandCnt].resCntBfAnchor;
43022+
strandArray[strandCnt].startRefnum = refnumInStrand;
43023+
}
43024+
else if(currResi == strandArray[strandCnt].endResi) {
43025+
strandArray[strandCnt].endRefnum = refnumInStrand;
43026+
}
43027+
43028+
refnumLabelNoPostfix = strandArray[strandCnt].strand + refnumInStrand;
43029+
refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
43030+
}
4297843031

4297943032
if(currResi == strandArray[strandCnt].endResi) {
4298043033
++strandCnt; // next strand
@@ -42988,14 +43041,28 @@ var icn3d = (function (exports) {
4298843041
else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
4298943042
ic.residIgLoop[residueid] = 1;
4299043043

42991-
// C-terminal
42992-
if(!ic.resid2refnum[residueid]) {
42993-
break;
43044+
if(!bCterminal) {
43045+
refnumLabelNoPostfix = undefined;
43046+
refnumLabel = undefined;
4299443047
}
4299543048
else {
42996-
currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
42997-
refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42998-
refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
43049+
// C-terminal
43050+
if(!ic.resid2refnum[residueid]) {
43051+
//break;
43052+
43053+
bCterminal = false;
43054+
//bNterminal = true; // The next will be N-terminal
43055+
43056+
refnumLabelNoPostfix = undefined;
43057+
refnumLabel = undefined;
43058+
}
43059+
else {
43060+
bCterminal = true;
43061+
43062+
currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
43063+
refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
43064+
refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
43065+
}
4299943066
}
4300043067
}
4300143068
}
@@ -45000,7 +45067,11 @@ var icn3d = (function (exports) {
4500045067
let fontsize = '6px'; // '6';
4500145068
//let html = (bAfMap) ? "<g>" : "<g class='icn3d-node' resid='" + resid + "' >";
4500245069
let html = "<g class='icn3d-node' resid='" + resid + "' >";
45003-
html += "<title>" + node.id + "</title>";
45070+
let title = node.id;
45071+
if(ic.resid2refnum[resid]) {
45072+
title += '=>' + ic.resid2refnum[resid];
45073+
}
45074+
html += "<title>" + title + "</title>";
4500445075
if(bVertical) {
4500545076
html += "<circle cx='" + y + "' cy='" + x + "' r='" + r + "' fill='" + color + "' stroke-width='" + strokewidth + "' stroke='" + strokecolor + "' resid='" + resid + "' />";
4500645077
html += "<text x='" +(y - 20).toString() + "' y='" +(x + 2).toString() + "' fill='" + textcolor + "' stroke='none' style='font-size:" + fontsize + "; text-anchor:middle' >" + nodeName + "</text>";
@@ -51180,7 +51251,7 @@ var icn3d = (function (exports) {
5118051251

5118151252
async realignOnStructAlign() { let ic = this.icn3d, me = ic.icn3dui;
5118251253
// each 3D domain should have at least 3 secondary structures
51183-
let minSseCnt = 3;
51254+
let minSseCnt = (me.cfg.aligntool != 'tmalign') ? 3 : 0;
5118451255
let struct2domain = {};
5118551256
for(let struct in ic.structures) {
5118651257
struct2domain[struct] = {};
@@ -56268,11 +56339,13 @@ var icn3d = (function (exports) {
5626856339
}
5626956340
}
5627056341

56271-
setSsbond() { let ic = this.icn3d; ic.icn3dui;
56342+
setSsbond(chainidHash) { let ic = this.icn3d; ic.icn3dui;
5627256343
// get all Cys residues
5627356344
let structure2cys_resid = {};
5627456345

5627556346
for(let chainid in ic.chainsSeq) {
56347+
if(chainidHash && !chainidHash.hasOwnProperty(chainid)) continue;
56348+
5627656349
let seq = ic.chainsSeq[chainid];
5627756350
let structure = chainid.substr(0, chainid.indexOf('_'));
5627856351

@@ -71288,7 +71361,7 @@ var icn3d = (function (exports) {
7128871361
//even when multiple iCn3D viewers are shown together.
7128971362
this.pre = this.cfg.divid + "_";
7129071363

71291-
this.REVISION = '3.25.0';
71364+
this.REVISION = '3.25.1';
7129271365

7129371366
// In nodejs, iCn3D defines "window = {navigator: {}}"
7129471367
this.bNode = (Object.keys(window).length < 2) ? true : false;

‎build/icn3d.min.js‎

Lines changed: 2 additions & 2 deletions
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