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Checkpoint mmtf replacement.
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Still several regressions.
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@dkoes
dkoes committed Jul 6, 2024
1 parent 2120a2b commit 5edfb1a
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Showing 4 changed files with 114 additions and 92 deletions.
181 changes: 101 additions & 80 deletions src/parsers/BCIF.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ declare var MMTF: MMTFobj;
*/
export function BCIF(bindata: any, options: ParserOptionsSpec) {

//var noH = !options.keepH; // suppress hydrogens by default
var noH = !options.keepH; // suppress hydrogens by default
//var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present
var computeStruct = !options.noComputeSecondaryStructure;
//var assemblyIndex = options.assemblyIndex ? options.assemblyIndex : 0;
Expand Down Expand Up @@ -77,50 +77,87 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
//helices
let sslookup = {}; //chain to residue range
let sshelix = cats.struct_conf;
let htypes = sshelix.getField('conf_type_id');
let hchain = sshelix.getField('beg_label_asym_id');
let hstart = sshelix.getField('beg_label_seq_id');
let hend = sshelix.getField('end_label_seq_id');

for (let i = 0; i < htypes.length; i++) {
if (htypes[i].startsWith('H')) {
let ch = hchain[i];
let startResi = hstart[i];
let endResi = hend[i];
if (sshelix) {
let htypes = sshelix.getField('conf_type_id');
let hchain = sshelix.getField('beg_label_asym_id');
let hstart = sshelix.getField('beg_label_seq_id');
let hend = sshelix.getField('end_label_seq_id');

for (let i = 0; i < htypes.length; i++) {
if (htypes[i].startsWith('H')) {
let ch = hchain[i];
let startResi = hstart[i];
let endResi = hend[i];
if (!(ch in sslookup)) {
sslookup[ch] = {};
}
sslookup[ch][startResi] = "h1";
for (let res = startResi + 1; res < endResi; res++) {
sslookup[ch][res] = "h";
}
sslookup[ch][endResi] = "h2";
}
}
}
//sheets
let sssheet = cats.struct_sheet_range;
if (sssheet) {
let sids = sssheet.getField('id');
let schain = sssheet.getField('beg_label_asym_id');
let sstart = sssheet.getField('beg_label_seq_id');
let send = sssheet.getField('end_label_seq_id');

for (let i = 0; i < sids.length; i++) {
let ch = schain[i];
let startResi = sstart[i];
let endResi = send[i];
if (!(ch in sslookup)) {
sslookup[ch] = {};
}
sslookup[ch][startResi] = "h1";
sslookup[ch][startResi] = "s1";
for (let res = startResi + 1; res < endResi; res++) {
sslookup[ch][res] = "h";
sslookup[ch][res] = "s";
}
sslookup[ch][endResi] = "h2";
}
}
sslookup[ch][endResi] = "s2";

//sheets
let sssheet = cats.struct_sheet_range;
let sids = sssheet.getField('id');
let schain = sssheet.getField('beg_label_asym_id');
let sstart = sssheet.getField('beg_label_seq_id');
let send = sssheet.getField('end_label_seq_id');

for (let i = 0; i < sids.length; i++) {
let ch = schain[i];
let startResi = sstart[i];
let endResi = send[i];
if (!(ch in sslookup)) {
sslookup[ch] = {};
}
sslookup[ch][startResi] = "s1";
for (let res = startResi + 1; res < endResi; res++) {
sslookup[ch][res] = "s";
}
sslookup[ch][endResi] = "s2";

}

//symmetry operations
let structops = cats.pdbx_struct_oper_list;
let opids = structops.getField('id');
if (opids && !noAssembly) {
let matrix11 = structops.getField('matrix[1][1]');
let matrix12 = structops.getField('matrix[1][2]');
let matrix13 = structops.getField('matrix[1][3]');
let matrix21 = structops.getField('matrix[2][1]');
let matrix22 = structops.getField('matrix[2][2]');
let matrix23 = structops.getField('matrix[2][3]');
let matrix31 = structops.getField('matrix[3][1]');
let matrix32 = structops.getField('matrix[3][2]');
let matrix33 = structops.getField('matrix[3][3]');
let vector1 = structops.getField('vector[1]');
let vector2 = structops.getField('vector[2]');
let vector3 = structops.getField('vector[3]');

for (let i = 0; i < opids.length; i++) {
const matrix = new Matrix4(
matrix11[i],
matrix12[i],
matrix13[i],
vector1[i],
matrix21[i],
matrix22[i],
matrix23[i],
vector2[i],
matrix31[i],
matrix32[i],
matrix33[i],
vector3[i]
);
modelData[modelData.length - 1].symmetries.push(matrix);
}
}
//atom info

let asites = cats.atom_site;
Expand All @@ -141,13 +178,27 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
let bfactors = asites.getField("B_iso_or_equiv");
let serials = asites.getField('id');
let icodes = asites.getField('label_alt_id');
let modelnums = asites.getField('pdbx_PDB_model_num');
let curmodel = modelnums ? modelnums[0] : 0;

for (let i = 0; i < atomCount; i++) {
if (
group_pdb !== undefined &&
if (group_pdb !== undefined &&
group_pdb[i] === "TER"
)
continue;

if (modelnums && modelnums[i] != curmodel) {
curmodel = modelnums[i];
if (options.multimodel) {
if (!options.onemol) {
atoms.push([]);
modelData.push(modelData[modelData.length-1]);
}
} else {
break; //first model only
}
}

const atom: AtomSpec = {};
atom.x = cartn_x[i];
atom.y = cartn_y[i];
Expand All @@ -159,16 +210,16 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
? label_asym_id[i]
: undefined;
atom.lchain = label_asym_id
? label_asym_id[i]
: undefined;
? label_asym_id[i]
: undefined;
atom.resi = auth_seq_id
? auth_seq_id[i]
: label_seq_id
? label_seq_id[i]
: undefined;
atom.lresi = label_seq_id
? label_seq_id[i]
: undefined;
? label_seq_id[i]
: undefined;
atom.resn = auth_comp_id
? auth_comp_id[i].trim()
: label_comp_id
Expand All @@ -193,6 +244,10 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
atom.elem = elem[0].toUpperCase() + elem.substring(1, 2).toLowerCase();
if (bfactors) atom.b = bfactors[i];

if(noH && atom.elem == 'H') {
continue;
}

atom.bonds = [];
atom.ss = "c";
atom.serial = serials[i];
Expand All @@ -203,43 +258,6 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
}



//symmetry operations
let structops = cats.pdbx_struct_oper_list;
let opids = structops.getField('id');
if (opids && !noAssembly) {
let matrix11 = structops.getField('matrix[1][1]');
let matrix12 = structops.getField('matrix[1][2]');
let matrix13 = structops.getField('matrix[1][3]');
let matrix21 = structops.getField('matrix[2][1]');
let matrix22 = structops.getField('matrix[2][2]');
let matrix23 = structops.getField('matrix[2][3]');
let matrix31 = structops.getField('matrix[3][1]');
let matrix32 = structops.getField('matrix[3][2]');
let matrix33 = structops.getField('matrix[3][3]');
let vector1 = structops.getField('vector[1]');
let vector2 = structops.getField('vector[2]');
let vector3 = structops.getField('vector[3]');

for (let i = 0; i < opids.length; i++) {
const matrix = new Matrix4(
matrix11[i],
matrix12[i],
matrix13[i],
vector1[i],
matrix21[i],
matrix22[i],
matrix23[i],
vector2[i],
matrix31[i],
matrix32[i],
matrix33[i],
vector3[i]
);
modelData[modelData.length - 1].symmetries.push(matrix);
}
}

// Assign secondary structures from pdb file
if (!isEmpty(sslookup)) {
let matoms = atoms[atoms.length - 1];
Expand All @@ -257,8 +275,11 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
}
}

if (options.multimodel) {
if (!options.onemol) atoms.push([]);
if (options.multimodel && m < numModels - 1) {
if (!options.onemol) {
atoms.push([]);
modelData.push({ symmetries: [] });
}
}
}

Expand Down
21 changes: 11 additions & 10 deletions src/utilities.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -405,7 +405,6 @@ export function getbin(uri, callback?, request?, postdata?) {
export function download(query, viewer, options, callback?) {
var type = "";
var pdbUri = "";
var mmtfUri = "";
var uri = "";
var promise = null;
var m = viewer.addModel();
Expand All @@ -420,18 +419,21 @@ export function download(query, viewer, options, callback?) {
query = 'url:' + query;
}
}
if (query.substring(0, 5) === 'mmtf:') {
pdbUri = options && options.pdbUri ? options.pdbUri : "https://mmtf.rcsb.org/v1.0/full/";
if (query.substring(0,5) == 'mmtf:') {
console.log('WARNING: MMTF now deprecated. Reverting to bcif.');
query = 'bcif:' + query.slice(5);
}
if (query.substring(0, 5) === 'bcif:') {
query = query.substring(5).toUpperCase();
uri = pdbUri + query;
uri = "https://models.rcsb.org/" + query + '.bcif.gz';
if (options && typeof options.noComputeSecondaryStructure === 'undefined') {
//when fetch directly from pdb, trust structure annotations
options.noComputeSecondaryStructure = true;
}
promise = new Promise(function (resolve) {
getbin(uri)
.then(function (ret) {
m.addMolData(ret, 'mmtf', options);
m.addMolData(ret, 'bcif.gz', options);
viewer.zoomTo();
viewer.render();
resolve(m);
Expand All @@ -440,7 +442,7 @@ export function download(query, viewer, options, callback?) {
}
else {
if (query.substring(0, 4) === 'pdb:') {
type = 'mmtf';
type = 'pdb';
if (options && options.format) {
type = options.format; //can override and require pdb
}
Expand All @@ -454,9 +456,8 @@ export function download(query, viewer, options, callback?) {
alert("Wrong PDB ID");
return;
}
if (type == 'mmtf') {
mmtfUri = options && options.mmtfUri ? options.mmtfUri : 'https://mmtf.rcsb.org/v1.0/full/';
uri = mmtfUri + query.toUpperCase();
if (type == 'bcif') {
uri = 'https://models.rcsb.org/' + query.toUpperCase() + '.bcif.gz';
}
else {
pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/";
Expand All @@ -482,7 +483,7 @@ export function download(query, viewer, options, callback?) {
viewer.render();
};
promise = new Promise(function (resolve) {
if (type == 'mmtf') { //binary data
if (type == 'bcif') { //binary data
getbin(uri)
.then(function (ret) {
handler(ret);
Expand Down
2 changes: 1 addition & 1 deletion tests/auto/tests/test60.js
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@


$3Dmol.download('pdb:1pfl',viewer,{},function(m) {
$3Dmol.download('bcif:1pfl',viewer,{},function(m) {
m.setStyle({'cartoon':{colorscheme:'ssPyMol'}});
viewer.zoomTo();
viewer.render();
Expand Down
2 changes: 1 addition & 1 deletion tests/auto/tests/test94.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

$3Dmol.download("pdb:2V0E",viewer,{multimodel:true, frames:true})
$3Dmol.download("bcif:2V0E",viewer,{multimodel:true, frames:true})
.then(function(m1){
$3Dmol.download("mmtf:4HHB",viewer,{multimodel:true, frames:true})
.then(function(m2){
Expand Down

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