pub_soft/molstar
3
0
Fork 0
mirror of https://github.com/molstar/molstar.git synced 2026-06-04 13:30:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'upstream/master' into seqres-to-sequence-toolbar

Browse Source
This commit is contained in:
Ryan DiRisio
2026-03-18 12:01:10 -04:00
parent 71a484586f 6d61745f0f
commit c53940e67e
3 changed files with 32 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
CHANGELOG.md
View File

@@ -8,6 +8,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add `putty` as a mol-view-spec representation.
- Fix detecting sidechain-only structures as coarse-grained (#1420)
- Fix clip-object transform due to missing axis normalization
- Sequence alignment: Fix return type & improve scoring for unknown residues
- Use PDB SEQRES block to show unresolved residues in Sequence toolbar
## [v5.7.0] - 2026-02-28

4
src/mol-model/sequence/alignment/_spec/alignment.spec.ts
View File

@@ -19,8 +19,8 @@ describe('Alignment', () => {
substMatrix: 'blosum62'
});
expect(aliA).toEqual('------------------------------------------------------------------------------------------------------------------------------------------------MNGTEGPNFYVPFSNKTGVVRSPFEA---PQYYLAEPWQFSM--LAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH---GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMS-NFRFGENHAIMGVAFTWVMA-LACAAPPLVGWSRYI-PEGMQC----SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLV----------------FTVKEAAAQQQESATTQ----------KAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA');
expect(aliB).toEqual('DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS-RWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFG---NVLVITAIAKFERLQTVTNYFITSLACADLVM---GLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETC-CDFFT------NQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMG-TFTLCWLPFF-IVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIY-CRSPDFRIAFQELLCLRRSSL--KAYGNGYSSNGNTGEQSG');
expect(aliA.join('')).toEqual('------------------------------------------------------------------------------------------------------------------------------------------------MNGTEGPNFYVPFSNKTGVVRSPFEA---PQYYLAEPWQFSM--LAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH---GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMS-NFRFGENHAIMGVAFTWVMA-LACAAPPLVGWSRYI-PEGMQC----SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLV----------------FTVKEAAAQQQESATTQ----------KAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA');
expect(aliB.join('')).toEqual('DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS-RWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFG---NVLVITAIAKFERLQTVTNYFITSLACADLVM---GLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETC-CDFFT------NQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMG-TFTLCWLPFF-IVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIY-CRSPDFRIAFQELLCLRRSSL--KAYGNGYSSNGNTGEQSG');
expect(score).toEqual(118);
});
});

48
src/mol-model/sequence/alignment/alignment.ts
View File

@@ -1,9 +1,11 @@
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2020-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Ryan DiRisio <rjdiris@gmail.com>
*/
import { isDebugMode } from '../../../mol-util/debug';
import { SubstitutionMatrix, SubstitutionMatrices, SubstitutionMatrixData } from './substitution-matrix';
const DefaultAlignmentOptions = {
@@ -67,7 +69,11 @@ class Alignment {
return function score(i: number, j: number) {
const cA = seqA[i];
const cB = seqB[j];
return substMatrix[cA]?.[cB] ?? -4;
const val = substMatrix[cA]?.[cB];
if (isDebugMode && val === undefined) {
console.warn(`Substitution matrix has no entry for residue pair ('${cA}', '${cB}') (seqA[${i}], seqB[${j}]). Non-standard residues are not supported with BLOSUM matrices.`);
}
return val ?? 0;
};
} else {
return function scoreNoSubstMat(i: number, j: number) {
@@ -109,7 +115,7 @@ class Alignment {
}
}
trace(): { aliA: ArrayLike<string>, aliB: ArrayLike<string>, score: number } {
trace(): { aliA: string[], aliB: string[], score: number } {
const scoreFn = this.makeScoreFn();
const { V, H, S, seqA, seqB, gapExtensionPenalty, gapPenalty } = this;
@@ -118,8 +124,8 @@ class Alignment {
let mat: 'S' | 'V' | 'H';
let score: number;
let aliA = '';
let aliB = '';
const aliA: string[] = [];
const aliB: string[] = [];
if (S[i][j] >= V[i][j]) {
mat = 'S';
@@ -135,8 +141,8 @@ class Alignment {
while (i > 0 && j > 0) {
if (mat === 'S') {
if (S[i][j] === S[i - 1][j - 1] + scoreFn(i - 1, j - 1)) {
aliA = seqA[i - 1] + aliA;
aliB = seqB[j - 1] + aliB;
aliA.push(seqA[i - 1]);
aliB.push(seqB[j - 1]);
--i;
--j;
mat = 'S';
@@ -150,13 +156,13 @@ class Alignment {
}
} else if (mat === 'V') {
if (V[i][j] === V[i - 1][j] + gapExtensionPenalty) {
aliA = seqA[i - 1] + aliA;
aliB = '-' + aliB;
aliA.push(seqA[i - 1]);
aliB.push('-');
--i;
mat = 'V';
} else if (V[i][j] === S[i - 1][j] + gapPenalty) {
aliA = seqA[i - 1] + aliA;
aliB = '-' + aliB;
aliA.push(seqA[i - 1]);
aliB.push('-');
--i;
mat = 'S';
} else {
@@ -164,13 +170,13 @@ class Alignment {
}
} else if (mat === 'H') {
if (H[i][j] === H[i][j - 1] + gapExtensionPenalty) {
aliA = '-' + aliA;
aliB = seqB[j - 1] + aliB;
aliA.push('-');
aliB.push(seqB[j - 1]);
--j;
mat = 'H';
} else if (H[i][j] === S[i][j - 1] + gapPenalty) {
aliA = '-' + aliA;
aliB = seqB[j - 1] + aliB;
aliA.push('-');
aliB.push(seqB[j - 1]);
--j;
mat = 'S';
} else {
@@ -180,17 +186,21 @@ class Alignment {
}
while (i > 0) {
aliA = seqA[i - 1] + aliA;
aliB = '-' + aliB;
aliA.push(seqA[i - 1]);
aliB.push('-');
--i;
}
while (j > 0) {
aliA = '-' + aliA;
aliB = seqB[j - 1] + aliB;
aliA.push('-');
aliB.push(seqB[j - 1]);
--j;
}
// The traceback builds arrays in reverse order; reverse them in place.
aliA.reverse();
aliB.reverse();
return { aliA, aliB, score };
}
}