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Pull request #542: Enabled users to add custom reference residue numb…
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…er with the menu "Analysis > Ref.Number", add (transparent) spheres or cubes for any sets with the menu "Style > Cartoon for a Set", add a line between two sets with the menu "Style > Line btw. Two Sets".

Merge in STRUC/icn3d from release3190b to master

* commit '4275ca5d1068e69c7cb6d3b69b582a0e82eb7cd2':
  Enabled users to add custom reference residue number with the menu "Analysis > Ref. Number", add (transparent) spheres or cubes for any sets with the menu "Style > Cartoon for a Set", add a line between two sets with the menu "Style > Line btw. Two Sets". Also improved the color legends.
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@jiywang3
jiywang3 committed Nov 19, 2022
2 parents 80e354e + 4275ca5 commit b709fcb
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Showing 18 changed files with 658 additions and 193 deletions.
169 changes: 131 additions & 38 deletions build/icn3d.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4988,6 +4988,57 @@ var icn3d = (function (exports) {
'GLN': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.58 + 1.85)/2.5)
};

this.hydrophobicValues = {
// charged residues
' G': 3, ' A': 3, ' T': 3,
' C': 3, ' U': 3, ' DG': 3,
' DA': 3, ' DT': 3, ' DC': 3,
' DU': 3, 'G': 3, 'A': 3,
'T': 3, 'C': 3, 'U': 3,
'DG': 3, 'DA': 3, 'DT': 3,
'DC': 3, 'DU': 3, 'ARG': 1,
'LYS': 1, 'ASP': 3, 'GLU': 3,
'HIS': 2,

// + 0.81)/(1.14 + 0.81)),
// hydrophobic
// https://en.m.wikipedia.org/wiki/Hydrophobicity_scales#Wimley%E2%80%93White_whole_residue_hydrophobicity_scales
// 0.65 ~ -1.85: white ~ green
'TRP': -1.85,
'PHE': -1.13,
'TYR': -0.94,
'LEU': -0.56,
'ILE': -0.31,
'CYS': -0.24,
'MET': -0.23,

// polar
'GLY': 0.01,
'VAL': 0.07,
'SER': 0.13,
'THR': 0.14,
'ALA': 0.17,
'ASN': 0.42,
'PRO': 0.45,
'GLN': 0.58
};

this.residueAbbrev = {
ALA: "A (Ala)", ARG: "R (Arg)", ASN: "N (Asn)",
ASP: "D (Asp)", CYS: "C (Cys)", GLN: "Q (Gln)",
GLU: "E (Glu)", GLY: "G (Gly)", HIS: "H (His)",
ILE: "I (Ile)", LEU: "L (Leu)", LYS: "K (Lys)",
MET: "M (Met)", PHE: "F (Phe)", PRO: "P (Pro)",
SER: "S (Ser)", THR: "T (Thr)", TRP: "W (Trp)",
TYR: "Y (Tyr)", VAL: "V (Val)",
//ASX: "B (Asx)", GLX: "Z (Glx)",
ASX: "X (Asx)", GLX: "X (Glx)",
'G': "Guanine", 'A': "Adenine",
'T': "Thymine", 'C': "Cytosine", 'U': "Uracil",
'DG': "deoxy-Guanine", 'DA': "deoxy-Adenine", 'DT': "deoxy-Thymine",
'DC': "deoxy-Cytosine", 'DU': 'deoxy-Uracil'
};

this.ssColors = {
helix: this.thr(0xFF0000),
sheet: this.thr(0x008000),
Expand Down Expand Up @@ -6934,7 +6985,8 @@ var icn3d = (function (exports) {
for(let i in atomsHash) {
if((ic.atoms[i].name == 'CA' && ic.proteins.hasOwnProperty(i)) || !ic.proteins.hasOwnProperty(i)) {
let residueid = ic.atoms[i].structure + '_' + ic.atoms[i].chain + '_' + ic.atoms[i].resi;
residuesHash[residueid] = 1;
//residuesHash[residueid] = 1;
residuesHash[residueid] = ic.atoms[i].resn;
}
}

Expand Down Expand Up @@ -9301,11 +9353,11 @@ var icn3d = (function (exports) {
if (atom.ss === 'sheet') beta[atom.serial] = atom;
if (atom.name !== 'CA') continue;
if (atom.ss === 'helix' && atom.ssend) {
if (start !== null && currentChain === atom.chain && currentResi < atom.resi) {
if (start !== null && currentChain === atom.chain && parseInt(currentResi) < parseInt(atom.resi)) {
if(bHighlight === 1 || bHighlight === 2) {
this.createCylinder(start.coord, atom.coord, radius, ic.hColor, bHighlight);
}
else {
else {
this.createCylinder(start.coord, atom.coord, radius, atom.color);
}
}
Expand Down Expand Up @@ -35377,6 +35429,9 @@ var icn3d = (function (exports) {

ic.resid2specCls.selectProperty(property, from, to);
}
else if(command.indexOf('select each residue') !== -1) {
ic.selectionCls.saveEachResiInSel();
}
else if(command.indexOf('select') == 0 && command.indexOf('name') !== -1) {
let paraArray = commandOri.split(' | '); // atom names might be case-sensitive

Expand Down Expand Up @@ -38897,7 +38952,7 @@ var icn3d = (function (exports) {
}

// not all listed residues are considered missing, e.g., PDB ID 4OR2, only the firts four residues are considered missing
if(!isNaN(resi) &&(prevMissingChain == '' ||(chain != prevMissingChain) ||(chain == prevMissingChain && resi > maxMissingResi)) ) {
if(!isNaN(resi) &&(prevMissingChain == '' ||(chain != prevMissingChain) ||(chain == prevMissingChain && parseInt(resi) > maxMissingResi)) ) {
ic.chainMissingResidueArray[chainNum].push(resObject);

maxMissingResi = resi;
Expand Down Expand Up @@ -44244,6 +44299,22 @@ var icn3d = (function (exports) {
}
}

saveEachResiInSel() { let ic = this.icn3d; ic.icn3dui;
ic.selectionCls.saveSelectionPrep();

ic.selectedResidues = {};

ic.selectedResidues = ic.firstAtomObjCls.getResiduesFromCalphaAtoms(ic.hAtoms);

for(let resid in ic.selectedResidues) {
let eachResidueHash = {};
eachResidueHash[resid] = 1;
let name = resid + '_' + ic.selectedResidues[resid];

this.selectResidueList(eachResidueHash, name, name);
}
}

removeSelection() { let ic = this.icn3d; ic.icn3dui;
if(!ic.bAnnotations) {
ic.hlUpdateCls.removeSeqChainBkgd();
Expand Down Expand Up @@ -56235,15 +56306,19 @@ var icn3d = (function (exports) {
thisClass.setLogCmd('defined sets', true);
//thisClass.setLogCmd('window defined sets', true);
});
me.myEventCls.onIds("#" + me.pre + "setOr", "click", function(e) { let ic = me.icn3d; e.preventDefault();
ic.setOperation = 'or';
$(document).on("click", "#" + me.pre + "setOr", function(e) { let ic = me.icn3d;
e.stopImmediatePropagation();
ic.setOperation = 'or';
});
me.myEventCls.onIds("#" + me.pre + "setAnd", "click", function(e) { let ic = me.icn3d; e.preventDefault();
ic.setOperation = 'and';
$(document).on("click", "#" + me.pre + "setAnd", function(e) { let ic = me.icn3d;
e.stopImmediatePropagation();
ic.setOperation = 'and';
});
me.myEventCls.onIds("#" + me.pre + "setNot", "click", function(e) { let ic = me.icn3d; e.preventDefault();
ic.setOperation = 'not';
$(document).on("click", "#" + me.pre + "setNot", function(e) { let ic = me.icn3d;
e.stopImmediatePropagation();
ic.setOperation = 'not';
});

// },
// clkMn2_pkNo: function() {
me.myEventCls.onIds("#" + me.pre + "mn2_pkNo", "click", function(e) { let ic = me.icn3d; e.preventDefault();
Expand Down Expand Up @@ -58603,6 +58678,7 @@ var icn3d = (function (exports) {

html += me.htmlCls.setHtmlCls.getLink('mn2_saveselection', 'Save Selection', 1, 1);
html += me.htmlCls.setHtmlCls.getLink('clearall', 'Clear Selection', undefined, 1);
html += me.htmlCls.setHtmlCls.getLink('mn2_saveresidue', 'Save Res. in Sel.', 1, 1);

html += me.htmlCls.setHtmlCls.getMenuSep();

Expand Down Expand Up @@ -59002,7 +59078,7 @@ var icn3d = (function (exports) {
html += "<ul>";
html += me.htmlCls.setHtmlCls.getLink('mn5_elecmap2fofc', '2Fo-Fc Map', undefined, 2);
html += me.htmlCls.setHtmlCls.getLink('mn5_elecmapfofc', 'Fo-Fc Map', undefined, 2);
html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2', undefined, undefined, 2);
html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2', undefined, 2);

html += "</ul>";
html += "</li>";
Expand Down Expand Up @@ -63945,6 +64021,16 @@ var icn3d = (function (exports) {
//var description = $("#" + me.pre + "seq_command_desc2").val();
ic.selectionCls.saveSelection(name, name);
});

me.myEventCls.onIds("#" + me.pre + "mn2_saveresidue", "click", function(e) { let ic = me.icn3d;
e.stopImmediatePropagation();
if(!me.cfg.notebook) dialog.dialog( "close" );

ic.selectionCls.saveEachResiInSel();

me.htmlCls.clickMenuCls.setLogCmd('select each residue', true);
});

// },
// clickAlignSeqSaveSelection: function() {
me.myEventCls.onIds("#" + me.pre + "alignseq_saveselection", "click", function(e) { let ic = me.icn3d;
Expand Down Expand Up @@ -65753,6 +65839,9 @@ var icn3d = (function (exports) {
else if(colorType == 'normalized hydrophobic') {
colorLabel = 'Normalized Hydrophobicity';
}
else if(colorType == 'hydrophobic') {
colorLabel = 'Hydrophobicity';
}

let html = "Color by <b>" + colorLabel + "</b><br><br>";

Expand All @@ -65774,35 +65863,55 @@ var icn3d = (function (exports) {
html += this.getColorLegendForCharge(ic.hAtoms);
}
//else if (ic.legendClick == 4){
else if (colorType == 'normalized hydrophobic') {
let resSet = this.getRes2color(ic.hAtoms);
else if (colorType == 'normalized hydrophobic' || colorType == 'hydrophobic') {
let bOriResn = true;
let resSet = this.getRes2color(ic.hAtoms, bOriResn);

// polar first - most to least
// create hydrophobic table
var items = Object.keys(resSet).map(
(key) => { return [key, Object.keys(resSet[key])[0]]
//(key) => { return [key, Object.keys(resSet[key])[0]]
(key) => { return [key, me.parasCls.hydrophobicValues[key]]
});

// items.sort(
// (first, second) => {
// return ((parseInt(second[1].substring(2,4), 16) - parseInt(second[1].substring(4,6), 16)) - (parseInt(first[1].substring(2,4), 16) - parseInt(first[1].substring(4,6), 16)));
// }
// );

items.sort(
(first, second) => {
return ((parseInt(second[1].substring(2,4), 16) - parseInt(second[1].substring(4,6), 16)) - (parseInt(first[1].substring(2,4), 16) - parseInt(first[1].substring(4,6), 16))) }
return parseFloat(first[1]) - parseFloat(second[1]);
}
);

var keys = items.map(
(e) => { return [e[0], e[1]]
//(e) => { return [e[0], e[1]]
(e) => { return [e[0], Object.keys(resSet[e[0]])[0]]
});

html += "<div>";

html += "Dark green (W, F, Y, L, I, C, M): Hydrophobic<br>";
html += "Light green (G, V, S, T, A, N, P, Q): Polar<br>";
html += "Grey: Charged, not hydrophobic<br><br>";
if(colorType == 'normalized hydrophobic') {
html += "Dark green (W, F, Y, L, I, C, M): Hydrophobic<br>";
html += "Light green (G, V, S, T, A, N, P, Q): Polar<br>";
html += "Grey: Charged, not hydrophobic<br><br>";
}
else {
html += "Green (W, F, Y, L, I, C, M): Hydrophobic<br>";
html += "Yellow (G, V, S, T, A, N, P, Q): Polar<br>";
html += "Red: Negatively Charged<br>";
html += "Blue: Positively Charged<br><br>";
}

let cnt = 0;
for (let key of keys) {
if(!me.parasCls.residueAbbrev[key[0]]) continue;

html += "<div style='display:inline-block; width:100px'>";
html += "<div style='width: 10px; height: 10px; background-color:#" + key[1] + "; border: 0px;display:inline-block;' ></div> ";
html += key[0] + "</div>";
html += me.parasCls.residueAbbrev[key[0]] + "</div>";

if(cnt % 4 == 3) html += "<br>";

Expand Down Expand Up @@ -65866,31 +65975,15 @@ var icn3d = (function (exports) {
return html;
}

getRes2color(atomHash) { let ic = this.icn3d; ic.icn3dui;
getRes2color(atomHash, bOriResn) { let ic = this.icn3d, me = ic.icn3dui;
let resSet = {};

const residueAbbrev = {
ALA: "A (Ala)", ARG: "R (Arg)", ASN: "N (Asn)",
ASP: "D (Asp)", CYS: "C (Cys)", GLN: "Q (Gln)",
GLU: "E (Glu)", GLY: "G (Gly)", HIS: "H (His)",
ILE: "I (Ile)", LEU: "L (Leu)", LYS: "K (Lys)",
MET: "M (Met)", PHE: "F (Phe)", PRO: "P (Pro)",
SER: "S (Ser)", THR: "T (Thr)", TRP: "W (Trp)",
TYR: "Y (Tyr)", VAL: "V (Val)",
//ASX: "B (Asx)", GLX: "Z (Glx)",
ASX: "X (Asx)", GLX: "X (Glx)",
'G': "Guanine", 'A': "Adenine",
'T': "Thymine", 'C': "Cytosine", 'U': "Uracil",
'DG': "deoxy-Guanine", 'DA': "deoxy-Adenine", 'DT': "deoxy-Thymine",
'DC': "deoxy-Cytosine", 'DU': 'deoxy-Uracil'
};

let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atomHash);
for(let resid in residueHash){
let atomHash = ic.residues[resid];

let atom = ic.firstAtomObjCls.getFirstAtomObj(atomHash);
let resiLabel = residueAbbrev[atom.resn];
let resiLabel = (bOriResn) ? atom.resn : me.parasCls.residueAbbrev[atom.resn];
let temp = (atom === undefined || atom.color === undefined || atom.color.getHexString().toUpperCase() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();

if (resiLabel != undefined){
Expand Down
2 changes: 1 addition & 1 deletion build/icn3d.min.js
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