mirror of
https://github.com/molstar/molstar.git
synced 2026-06-04 21:34:23 +08:00
Compare commits
46 Commits
v1.3.1
...
v2.0.0-dev
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6c5224f33e |
@@ -31,7 +31,14 @@
|
||||
"no-unsafe-finally": "warn",
|
||||
"no-var": "error",
|
||||
"spaced-comment": "error",
|
||||
"semi": "warn"
|
||||
"semi": "warn",
|
||||
"no-restricted-syntax": [
|
||||
"error",
|
||||
{
|
||||
"selector": "ExportDefaultDeclaration",
|
||||
"message": "Default exports are not allowed"
|
||||
}
|
||||
]
|
||||
},
|
||||
"overrides": [
|
||||
{
|
||||
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||||
@@ -177,4 +177,4 @@ Funding sources include but are not limited to:
|
||||
* [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
|
||||
* [PDBe, EMBL-EBI](https://pdbe.org)
|
||||
* [CEITEC](https://www.ceitec.eu/)
|
||||
* [EntosAI](https://www.entos.ai) (``alpha-orbitals`` extension)
|
||||
* [EntosAI](https://www.entos.ai)
|
||||
|
||||
@@ -26,3 +26,4 @@
|
||||
* Protein (1BRR, 5Z6Y)
|
||||
* DNA (5D3G)
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||||
* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
|
||||
* Long linear sugar chain (4HG6)
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||||
|
||||
442
package-lock.json
generated
442
package-lock.json
generated
@@ -1,11 +1,11 @@
|
||||
{
|
||||
"name": "molstar",
|
||||
"version": "1.3.0",
|
||||
"version": "2.0.0-dev.7",
|
||||
"lockfileVersion": 2,
|
||||
"requires": true,
|
||||
"packages": {
|
||||
"": {
|
||||
"version": "1.2.15",
|
||||
"version": "2.0.0-dev.4",
|
||||
"license": "MIT",
|
||||
"dependencies": {
|
||||
"@types/argparse": "^1.0.38",
|
||||
@@ -24,14 +24,14 @@
|
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"cors": "^2.8.5",
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"express": "^4.17.1",
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"h264-mp4-encoder": "^1.0.12",
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"immer": "^8.0.0",
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"immer": "^8.0.1",
|
||||
"immutable": "^3.8.2",
|
||||
"node-fetch": "^2.6.1",
|
||||
"react": "^17.0.1",
|
||||
"react-dom": "^17.0.1",
|
||||
"rxjs": "^6.6.3",
|
||||
"rxjs": "^6.6.6",
|
||||
"swagger-ui-dist": "^3.37.2",
|
||||
"tslib": "^2.0.3",
|
||||
"tslib": "^2.1.0",
|
||||
"util.promisify": "^1.0.1",
|
||||
"xhr2": "^0.2.0"
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||||
},
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@@ -74,7 +74,7 @@
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"style-loader": "^2.0.0",
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|
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"typescript": "^4.2.3",
|
||||
"webpack": "^4.44.1",
|
||||
"webpack-cli": "^3.3.12",
|
||||
"webpack-version-file-plugin": "^0.4.0"
|
||||
@@ -92,6 +92,12 @@
|
||||
"node": ">=8"
|
||||
}
|
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},
|
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"dev": true
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"version": "7.10.4",
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"resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.10.4.tgz",
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@@ -1217,6 +1223,12 @@
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|
||||
}
|
||||
},
|
||||
"node_modules/@graphql-codegen/add/node_modules/tslib": {
|
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"version": "2.0.3",
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"dev": true
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"node_modules/@graphql-codegen/cli": {
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"version": "1.19.4",
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"resolved": "https://registry.npmjs.org/@graphql-codegen/cli/-/cli-1.19.4.tgz",
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@@ -1324,6 +1336,12 @@
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"dev": true
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"node_modules/@graphql-codegen/cli/node_modules/tslib": {
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"version": "2.0.3",
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"resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz",
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"dev": true
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"version": "1.17.9",
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"resolved": "https://registry.npmjs.org/@graphql-codegen/core/-/core-1.17.9.tgz",
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||||
@@ -1339,6 +1357,12 @@
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}
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"dev": true
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"node_modules/@graphql-codegen/time": {
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"version": "2.0.2",
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"resolved": "https://registry.npmjs.org/@graphql-codegen/time/-/time-2.0.2.tgz",
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@@ -1449,6 +1479,12 @@
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"graphql": "^0.8.0 || ^0.9.0 || ^0.10.0 || ^0.11.0 || ^0.12.0 || ^0.13.0 || ^14.0.0 || ^15.0.0"
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||||
}
|
||||
},
|
||||
"node_modules/@graphql-codegen/typescript-graphql-files-modules/node_modules/tslib": {
|
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"version": "2.0.3",
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"resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz",
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"dev": true
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"node_modules/@graphql-codegen/typescript-graphql-request": {
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"version": "2.0.3",
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"resolved": "https://registry.npmjs.org/@graphql-codegen/typescript-graphql-request/-/typescript-graphql-request-2.0.3.tgz",
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@@ -1465,6 +1501,12 @@
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"graphql-tag": "^2.0.0"
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"node_modules/@graphql-codegen/typescript-graphql-request/node_modules/tslib": {
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"version": "2.0.3",
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"resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz",
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"dev": true
|
||||
},
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"node_modules/@graphql-codegen/typescript-operations": {
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"version": "1.17.12",
|
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"resolved": "https://registry.npmjs.org/@graphql-codegen/typescript-operations/-/typescript-operations-1.17.12.tgz",
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@@ -1481,6 +1523,18 @@
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"graphql": "^0.8.0 || ^0.9.0 || ^0.10.0 || ^0.11.0 || ^0.12.0 || ^0.13.0 || ^14.0.0 || ^15.0.0"
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}
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},
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"node_modules/@graphql-codegen/typescript-operations/node_modules/tslib": {
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"dev": true
|
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},
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"node_modules/@graphql-codegen/typescript/node_modules/tslib": {
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"version": "2.0.3",
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"dev": true
|
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},
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"node_modules/@graphql-codegen/visitor-plugin-common": {
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"version": "1.17.21",
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"resolved": "https://registry.npmjs.org/@graphql-codegen/visitor-plugin-common/-/visitor-plugin-common-1.17.21.tgz",
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@@ -1518,6 +1572,12 @@
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"dev": true
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"node_modules/@graphql-codegen/visitor-plugin-common/node_modules/tslib": {
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"version": "2.0.3",
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"resolved": "https://registry.npmjs.org/tslib/-/tslib-2.0.3.tgz",
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"dev": true
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"node_modules/@graphql-tools/apollo-engine-loader": {
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"version": "6.2.5",
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"resolved": "https://registry.npmjs.org/@graphql-tools/apollo-engine-loader/-/apollo-engine-loader-6.2.5.tgz",
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@@ -1546,6 +1606,12 @@
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"graphql": "^14.0.0 || ^15.0.0"
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},
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"node_modules/@graphql-tools/apollo-engine-loader/node_modules/tslib": {
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"version": "2.0.3",
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"node_modules/@graphql-tools/batch-execute": {
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"version": "7.0.0",
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"resolved": "https://registry.npmjs.org/@graphql-tools/batch-execute/-/batch-execute-7.0.0.tgz",
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@@ -1575,6 +1641,12 @@
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"graphql": "^14.0.0 || ^15.0.0"
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},
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"node_modules/@graphql-tools/batch-execute/node_modules/tslib": {
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"version": "2.0.3",
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"dev": true
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"node_modules/@graphql-tools/code-file-loader": {
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"version": "6.2.6",
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"resolved": "https://registry.npmjs.org/@graphql-tools/code-file-loader/-/code-file-loader-6.2.6.tgz",
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@@ -1603,6 +1675,12 @@
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"graphql": "^14.0.0 || ^15.0.0"
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},
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@@ -1635,15 +1713,21 @@
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"dev": true
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"node_modules/@graphql-tools/git-loader": {
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"version": "6.2.6",
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"dev": true,
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"tslib": "~2.0.1"
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"peerDependencies": {
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"graphql": "^14.0.0 || ^15.0.0"
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@@ -1663,6 +1747,12 @@
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@@ -1692,6 +1782,12 @@
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"dev": true
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@@ -1754,6 +1856,12 @@
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@@ -1794,6 +1908,12 @@
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@@ -1828,6 +1948,12 @@
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@@ -1856,6 +1982,12 @@
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@@ -1868,6 +2000,12 @@
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@@ -1916,6 +2054,12 @@
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@@ -1944,6 +2088,12 @@
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@@ -1971,6 +2121,12 @@
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@@ -2013,6 +2169,12 @@
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@@ -2073,6 +2241,12 @@
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@@ -8454,9 +8628,9 @@
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@@ -13532,9 +13706,9 @@
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@@ -15663,9 +15837,9 @@
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@@ -15773,9 +15947,9 @@
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@@ -17571,6 +17745,14 @@
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@@ -18522,6 +18704,14 @@
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@@ -18628,6 +18818,12 @@
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@@ -18641,6 +18837,14 @@
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@@ -18714,6 +18918,12 @@
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@@ -18737,6 +18947,14 @@
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@@ -18747,6 +18965,14 @@
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@@ -18759,6 +18985,14 @@
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@@ -18772,6 +19006,14 @@
|
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"auto-bind": "~4.0.0",
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@@ -18809,6 +19051,12 @@
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"dev": true
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@@ -18833,6 +19081,12 @@
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@@ -18858,6 +19112,12 @@
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@@ -18882,6 +19142,12 @@
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@@ -18910,18 +19176,24 @@
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@@ -18934,6 +19206,12 @@
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@@ -18959,6 +19237,12 @@
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@@ -18983,6 +19267,12 @@
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@@ -19010,6 +19300,12 @@
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"dev": true
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@@ -19021,6 +19317,14 @@
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@@ -19043,6 +19347,12 @@
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@@ -19073,6 +19383,12 @@
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@@ -19097,6 +19413,12 @@
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@@ -19107,6 +19429,14 @@
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"@graphql-tools/prisma-loader": {
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@@ -19150,6 +19480,12 @@
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@@ -19174,6 +19510,12 @@
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@@ -19197,6 +19539,12 @@
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@@ -19235,6 +19583,12 @@
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"dev": true
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@@ -19266,6 +19620,12 @@
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@@ -19292,6 +19652,12 @@
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"dev": true
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@@ -24455,9 +24821,9 @@
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"immutable": {
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@@ -28461,9 +28827,9 @@
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@@ -30176,9 +30542,9 @@
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@@ -30264,9 +30630,9 @@
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"ua-parser-js": {
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10
package.json
10
package.json
@@ -1,6 +1,6 @@
|
||||
{
|
||||
"name": "molstar",
|
||||
"version": "1.3.0",
|
||||
"version": "2.0.0-dev.7",
|
||||
"description": "A comprehensive macromolecular library.",
|
||||
"homepage": "https://github.com/molstar/molstar#readme",
|
||||
"repository": {
|
||||
@@ -115,7 +115,7 @@
|
||||
"simple-git": "^2.25.0",
|
||||
"style-loader": "^2.0.0",
|
||||
"ts-jest": "^26.4.4",
|
||||
"typescript": "^4.1.2",
|
||||
"typescript": "^4.2.3",
|
||||
"webpack": "^4.44.1",
|
||||
"webpack-cli": "^3.3.12",
|
||||
"webpack-version-file-plugin": "^0.4.0"
|
||||
@@ -137,14 +137,14 @@
|
||||
"cors": "^2.8.5",
|
||||
"express": "^4.17.1",
|
||||
"h264-mp4-encoder": "^1.0.12",
|
||||
"immer": "^8.0.0",
|
||||
"immer": "^8.0.1",
|
||||
"immutable": "^3.8.2",
|
||||
"node-fetch": "^2.6.1",
|
||||
"react": "^17.0.1",
|
||||
"react-dom": "^17.0.1",
|
||||
"rxjs": "^6.6.3",
|
||||
"rxjs": "^6.6.6",
|
||||
"swagger-ui-dist": "^3.37.2",
|
||||
"tslib": "^2.0.3",
|
||||
"tslib": "^2.1.0",
|
||||
"util.promisify": "^1.0.1",
|
||||
"xhr2": "^0.2.0"
|
||||
}
|
||||
|
||||
@@ -6,7 +6,8 @@
|
||||
*/
|
||||
|
||||
import '../../mol-util/polyfill';
|
||||
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPlugin } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import './index.html';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
@@ -69,9 +70,10 @@ class Viewer {
|
||||
viewportShowSelectionMode: false,
|
||||
viewportShowAnimation: false,
|
||||
} };
|
||||
const defaultSpec = DefaultPluginSpec();
|
||||
|
||||
const spec: PluginSpec = {
|
||||
actions: [...DefaultPluginSpec.actions],
|
||||
actions: [...defaultSpec.actions],
|
||||
behaviors: [
|
||||
PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
|
||||
PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
|
||||
@@ -81,8 +83,8 @@ class Viewer {
|
||||
PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
|
||||
PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
|
||||
],
|
||||
animations: [...DefaultPluginSpec.animations || []],
|
||||
customParamEditors: DefaultPluginSpec.customParamEditors,
|
||||
animations: [...defaultSpec.animations || []],
|
||||
customParamEditors: defaultSpec.customParamEditors,
|
||||
layout: {
|
||||
initial: {
|
||||
isExpanded: o.layoutIsExpanded,
|
||||
@@ -90,14 +92,14 @@ class Viewer {
|
||||
controlsDisplay: o.layoutControlsDisplay,
|
||||
},
|
||||
controls: {
|
||||
...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
|
||||
...defaultSpec.layout && defaultSpec.layout.controls,
|
||||
top: o.layoutShowSequence ? undefined : 'none',
|
||||
bottom: o.layoutShowLog ? undefined : 'none',
|
||||
left: o.layoutShowLeftPanel ? undefined : 'none',
|
||||
}
|
||||
},
|
||||
components: {
|
||||
...DefaultPluginSpec.components,
|
||||
...defaultSpec.components,
|
||||
remoteState: o.layoutShowRemoteState ? 'default' : 'none',
|
||||
viewport: {
|
||||
view: ViewportComponent
|
||||
|
||||
@@ -48,16 +48,10 @@
|
||||
var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
|
||||
if (debugMode) molstar.setDebugMode(debugMode, debugMode);
|
||||
|
||||
var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
|
||||
var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
|
||||
var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
|
||||
var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
|
||||
var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
|
||||
var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
|
||||
var viewer = new molstar.Viewer('app', {
|
||||
disableAntialiasing: disableAntialiasing,
|
||||
pixelScale: pixelScale,
|
||||
enableWboit: !disableWboit,
|
||||
layoutShowControls: !hideControls,
|
||||
viewportShowExpand: false,
|
||||
pdbProvider: pdbProvider || 'pdbe',
|
||||
|
||||
@@ -6,7 +6,8 @@
|
||||
*/
|
||||
|
||||
import '../../mol-util/polyfill';
|
||||
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPlugin } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import './index.html';
|
||||
import './embedded.html';
|
||||
import './favicon.ico';
|
||||
@@ -89,15 +90,16 @@ export class Viewer {
|
||||
|
||||
constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
|
||||
const o = { ...DefaultViewerOptions, ...options };
|
||||
const defaultSpec = DefaultPluginSpec();
|
||||
|
||||
const spec: PluginSpec = {
|
||||
actions: [...DefaultPluginSpec.actions],
|
||||
actions: [...defaultSpec.actions],
|
||||
behaviors: [
|
||||
...DefaultPluginSpec.behaviors,
|
||||
...defaultSpec.behaviors,
|
||||
...o.extensions.map(e => Extensions[e]),
|
||||
],
|
||||
animations: [...DefaultPluginSpec.animations || []],
|
||||
customParamEditors: DefaultPluginSpec.customParamEditors,
|
||||
animations: [...defaultSpec.animations || []],
|
||||
customParamEditors: defaultSpec.customParamEditors,
|
||||
customFormats: o?.customFormats,
|
||||
layout: {
|
||||
initial: {
|
||||
@@ -106,14 +108,14 @@ export class Viewer {
|
||||
controlsDisplay: o.layoutControlsDisplay,
|
||||
},
|
||||
controls: {
|
||||
...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
|
||||
...defaultSpec.layout && defaultSpec.layout.controls,
|
||||
top: o.layoutShowSequence ? undefined : 'none',
|
||||
bottom: o.layoutShowLog ? undefined : 'none',
|
||||
left: o.layoutShowLeftPanel ? undefined : 'none',
|
||||
}
|
||||
},
|
||||
components: {
|
||||
...DefaultPluginSpec.components,
|
||||
...defaultSpec.components,
|
||||
remoteState: o.layoutShowRemoteState ? 'default' : 'none',
|
||||
},
|
||||
config: [
|
||||
|
||||
@@ -70,7 +70,7 @@ function classify(name: string, field: CifField): CifWriter.Field {
|
||||
}
|
||||
}
|
||||
|
||||
export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
|
||||
export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
|
||||
return Task.create<Uint8Array>('BinaryCIF', async ctx => {
|
||||
const encodingProvider: BinaryEncodingProvider = hints
|
||||
? CifWriter.createEncodingProviderFromJsonConfig(hints)
|
||||
|
||||
@@ -10,7 +10,7 @@ import * as argparse from 'argparse';
|
||||
import * as util from 'util';
|
||||
import * as fs from 'fs';
|
||||
import * as zlib from 'zlib';
|
||||
import convert from './converter';
|
||||
import { convert } from './converter';
|
||||
|
||||
require('util.promisify').shim();
|
||||
|
||||
|
||||
@@ -12,7 +12,7 @@ import fetch from 'node-fetch';
|
||||
|
||||
import { parseCsv } from '../../mol-io/reader/csv/parser';
|
||||
import { CifFrame, CifBlock } from '../../mol-io/reader/cif';
|
||||
import parseText from '../../mol-io/reader/cif/text/parser';
|
||||
import { parseCifText } from '../../mol-io/reader/cif/text/parser';
|
||||
import { generateSchema } from './util/cif-dic';
|
||||
import { generate } from './util/generate';
|
||||
import { Filter, Database } from './util/schema';
|
||||
@@ -28,19 +28,19 @@ function getDicNamespace(block: CifBlock) {
|
||||
|
||||
async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
|
||||
await ensureMmcifDicAvailable();
|
||||
const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
|
||||
const mmcifDic = await parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
|
||||
if (mmcifDic.isError) throw mmcifDic;
|
||||
|
||||
await ensureIhmDicAvailable();
|
||||
const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
|
||||
const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
|
||||
if (ihmDic.isError) throw ihmDic;
|
||||
|
||||
await ensureCarbBranchDicAvailable();
|
||||
const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
|
||||
const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
|
||||
if (carbBranchDic.isError) throw carbBranchDic;
|
||||
|
||||
await ensureCarbCompDicAvailable();
|
||||
const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
|
||||
const carbCompDic = await parseCifText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
|
||||
if (carbCompDic.isError) throw carbCompDic;
|
||||
|
||||
const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
|
||||
@@ -56,7 +56,7 @@ async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, type
|
||||
|
||||
async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
|
||||
await ensureCifCoreDicAvailable();
|
||||
const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
|
||||
const cifCoreDic = await parseCifText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
|
||||
if (cifCoreDic.isError) throw cifCoreDic;
|
||||
|
||||
const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
|
||||
@@ -80,7 +80,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
|
||||
if (!file) continue;
|
||||
if (imports.has(file)) continue;
|
||||
|
||||
const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
|
||||
const dic = await parseCifText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
|
||||
if (dic.isError) throw dic;
|
||||
|
||||
imports.set(file, [...dic.result.blocks[0].saveFrames]);
|
||||
@@ -92,7 +92,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
|
||||
}
|
||||
|
||||
async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
|
||||
const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
|
||||
const dic = await parseCifText(fs.readFileSync(dicPath, 'utf8')).run();
|
||||
if (dic.isError) throw dic;
|
||||
|
||||
const dicVersion = getDicVersion(dic.result.blocks[0]);
|
||||
|
||||
@@ -22,7 +22,23 @@
|
||||
left: 8px;
|
||||
top: 8px;
|
||||
width: 300px;
|
||||
}
|
||||
}
|
||||
#sponsor {
|
||||
position: absolute;
|
||||
left: 8px;
|
||||
bottom: 8px;
|
||||
font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
|
||||
font-size: 12px;
|
||||
text-align: center;
|
||||
}
|
||||
#sponsor svg {
|
||||
fill: #128EA4;
|
||||
width: 100px;
|
||||
}
|
||||
#sponsor a {
|
||||
text-decoration: none;
|
||||
color: #128EA4;
|
||||
}
|
||||
</style>
|
||||
<link rel="stylesheet" type="text/css" href="molstar.css" />
|
||||
<script type="text/javascript" src="./index.js"></script>
|
||||
@@ -30,6 +46,14 @@
|
||||
<body>
|
||||
<div id="app"></div>
|
||||
<div id='controls'></div>
|
||||
<div id='sponsor'>
|
||||
<a href='https://www.entos.ai/envision' target="_blank" rel="noopener">
|
||||
<svg class="makeStyles-root-46" viewBox="0 0 190 36" xmlns="http://www.w3.org/2000/svg"><path d="M32.2591 28.6707C32.2591 32.3914 29.2421 35.407 25.5214 35.407C22.0752 35.407 19.2338 32.8206 18.8325 29.4831V29.4775C18.8143 29.3312 18.8018 29.1835 18.7934 29.0344C18.7934 29.0316 18.7921 29.0274 18.7921 29.0246V29.0177C18.7865 28.902 18.7837 28.7864 18.7837 28.6707C18.7837 26.2557 20.0532 24.1389 21.9609 22.9503C21.9623 22.9489 21.9651 22.9489 21.9665 22.9475C22.0933 22.8666 22.2243 22.7914 22.3581 22.7203C22.3581 22.7203 22.3595 22.7203 22.3595 22.7189C23.3029 22.2173 24.3787 21.933 25.5214 21.933C29.2421 21.933 32.2591 24.9486 32.2591 28.6707Z"></path><path d="M25.5214 14.0692C29.2421 14.0692 32.2591 11.0522 32.2591 7.33146C32.2591 3.61074 29.2421 0.59375 25.5214 0.59375C22.0529 0.59375 19.1962 3.21637 18.8255 6.58592C18.8185 6.67092 18.8116 6.75454 18.8018 6.83815C18.7893 7.00119 18.7837 7.16563 18.7837 7.33146C18.7837 9.73669 20.0434 11.8465 21.94 13.038C22.0891 13.116 22.2355 13.201 22.3776 13.2916C22.3783 13.2923 22.379 13.2926 22.3797 13.293C22.3804 13.2933 22.3811 13.2937 22.3818 13.2944C23.3196 13.7891 24.3871 14.0692 25.5214 14.0692Z"></path><path d="M19.3645 12.4113C20.2926 12.4113 21.1694 12.638 21.94 13.038C20.0434 11.8465 18.7837 9.73669 18.7837 7.33146C18.7837 7.16563 18.7893 7.00119 18.8018 6.83815C18.4688 9.76455 16.1385 12.0866 13.2065 12.4044C13.8545 13.1193 14.3785 13.9484 14.745 14.857C15.7497 13.3798 17.4443 12.4113 19.3645 12.4113Z"></path><path d="M14.7312 21.1249V21.1236C14.1279 20.2331 13.7767 19.1587 13.7767 18.0007V17.9728C13.7767 15.3084 12.2285 13.0035 9.9835 11.911C9.98141 11.9103 9.97967 11.9096 9.97793 11.9089C9.97619 11.9082 9.97444 11.9075 9.97235 11.9068C9.96817 11.904 9.96538 11.9026 9.9612 11.9012C9.95981 11.9012 9.95981 11.8998 9.95981 11.8998C9.9417 11.8915 9.92394 11.8831 9.90618 11.8747C9.8884 11.8664 9.87063 11.858 9.85251 11.8497C9.82046 11.8343 9.78701 11.819 9.75357 11.8051L9.74521 11.8009C8.91745 11.4372 8.0019 11.2351 7.03898 11.2351C3.31826 11.2351 0.30127 14.2521 0.30127 17.9728C0.30127 21.6935 3.31826 24.7105 7.03898 24.7105C7.98797 24.7105 8.89098 24.514 9.71037 24.1601C9.71246 24.1594 9.7142 24.1583 9.71594 24.1573C9.71768 24.1562 9.71943 24.1552 9.72152 24.1545C9.8107 24.1169 9.8985 24.0765 9.9849 24.0333L9.98629 24.0319C10.7625 23.6919 11.6181 23.5037 12.5197 23.5037C12.7524 23.5037 12.9824 23.5163 13.2081 23.54C13.2082 23.5399 13.2081 23.54 13.2081 23.54C15.0168 23.7365 16.5971 24.695 17.6185 26.0885C17.9195 25.1688 18.3752 24.3201 18.9563 23.5732C17.1964 23.4464 15.6635 22.5058 14.7312 21.1249Z"></path><g clip-path="url(#clip0)"><path d="M106.391 18.0021C106.391 11.3724 101.039 6 94.4389 6H88.4585C81.8581 6 76.5061 11.3724 76.5061 18.0021V30.0042H81.2845V18.0021C81.2845 14.0268 84.4941 10.8008 88.4585 10.8008H94.4347C98.395 10.8008 101.609 14.0226 101.609 18.0021V30.0042H106.391V18.0021Z"></path><path d="M149.432 6H142.258C135.653 6 130.301 11.3724 130.301 18.0021C130.301 24.6319 135.653 30.0042 142.258 30.0042H149.432C156.036 30.0042 161.388 24.6319 161.388 18.0021C161.388 11.3724 156.032 6 149.432 6ZM149.432 25.1992H142.258C138.297 25.1992 135.084 21.9774 135.084 17.9979C135.084 14.0183 138.293 10.7966 142.258 10.7966H149.432C153.392 10.7966 156.606 14.0183 156.606 17.9979C156.606 21.9774 153.392 25.1992 149.432 25.1992Z"></path><path d="M74.1151 25.1992H58.5736C55.4526 25.1992 52.804 23.1924 51.8171 20.3983H74.1151V17.9979C74.1151 17.1808 74.1868 16.3807 74.3175 15.5975H51.8171C52.804 12.8033 55.4526 10.7966 58.5736 10.7966H76.0383C77.1475 8.87458 78.6911 7.22773 80.5299 6H58.5736C51.969 6 46.6169 11.3724 46.6169 18.0021C46.6169 24.6276 51.969 30 58.5736 30H74.1151V25.1992Z"></path><path d="M120.74 6H115.958H102.369C104.212 7.22773 105.751 8.87458 106.861 10.8008H115.958V30H120.74V10.8008H129.838C130.947 8.87458 132.486 7.22773 134.329 6H120.74Z"></path><path d="M182.906 15.6017H169.756C168.436 15.6017 167.365 14.5264 167.365 13.2013C167.365 11.8762 168.436 10.8008 169.756 10.8008H188.882V6H169.756C165.796 6 162.582 9.22173 162.582 13.2013C162.582 17.1808 165.791 20.4025 169.756 20.4025H182.906C184.226 20.4025 185.297 21.4779 185.297 22.803C185.297 24.1281 184.226 25.2034 182.906 25.2034H161.852C160.743 27.1297 159.199 28.7765 157.361 30.0042H182.906C186.866 30.0042 190.08 26.7825 190.08 22.803C190.08 18.8234 186.866 15.6017 182.906 15.6017Z"></path></g><defs><clipPath id="clip0"><rect width="190" height="24" fill="white" transform="translate(0 6)"></rect></clipPath></defs></svg>
|
||||
<div>
|
||||
Entos Envision
|
||||
</div>
|
||||
</a>
|
||||
</div>
|
||||
<script>
|
||||
AlphaOrbitalsExample.init('app')
|
||||
</script>
|
||||
|
||||
@@ -6,7 +6,8 @@
|
||||
|
||||
import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
|
||||
import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
|
||||
import { createPluginAsync, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPluginAsync } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { PluginConfig } from '../../mol-plugin/config';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
@@ -52,8 +53,9 @@ export class AlphaOrbitalsExample {
|
||||
plugin: PluginContext;
|
||||
|
||||
async init(target: string | HTMLElement) {
|
||||
const defaultSpec = DefaultPluginSpec();
|
||||
this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
|
||||
...DefaultPluginSpec,
|
||||
...defaultSpec,
|
||||
layout: {
|
||||
initial: {
|
||||
isExpanded: false,
|
||||
@@ -61,6 +63,15 @@ export class AlphaOrbitalsExample {
|
||||
},
|
||||
controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
|
||||
},
|
||||
components: {
|
||||
viewport: {
|
||||
canvas3d: {
|
||||
camera: {
|
||||
helper: { axes: { name: 'off', params: { } } }
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
config: [
|
||||
[PluginConfig.Viewport.ShowExpand, false],
|
||||
[PluginConfig.Viewport.ShowControls, false],
|
||||
|
||||
@@ -86,7 +86,7 @@
|
||||
|
||||
// adjust this number to make the animation faster or slower
|
||||
// requires to "restart" the animation if changed
|
||||
BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
|
||||
BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
|
||||
|
||||
addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
|
||||
addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());
|
||||
|
||||
@@ -6,7 +6,8 @@
|
||||
|
||||
import { EmptyLoci } from '../../mol-model/loci';
|
||||
import { StructureSelection } from '../../mol-model/structure';
|
||||
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPlugin } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
|
||||
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
@@ -28,7 +29,7 @@ class BasicWrapper {
|
||||
|
||||
init(target: string | HTMLElement) {
|
||||
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
|
||||
...DefaultPluginSpec,
|
||||
...DefaultPluginSpec(),
|
||||
layout: {
|
||||
initial: {
|
||||
isExpanded: false,
|
||||
@@ -82,13 +83,17 @@ class BasicWrapper {
|
||||
if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
|
||||
}
|
||||
|
||||
private animateModelIndexTargetFps() {
|
||||
return Math.max(1, this.animate.modelIndex.targetFps | 0);
|
||||
}
|
||||
|
||||
animate = {
|
||||
modelIndex: {
|
||||
maxFPS: 8,
|
||||
onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
|
||||
onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
|
||||
palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
|
||||
loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
|
||||
targetFps: 8,
|
||||
onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
|
||||
onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
|
||||
palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
|
||||
loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
|
||||
stop: () => this.plugin.managers.animation.stop()
|
||||
}
|
||||
}
|
||||
|
||||
@@ -10,7 +10,7 @@ import { superpose } from '../../mol-model/structure/structure/util/superpositio
|
||||
import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
|
||||
import Expression from '../../mol-script/language/expression';
|
||||
import { Expression } from '../../mol-script/language/expression';
|
||||
import { compile } from '../../mol-script/runtime/query/compiler';
|
||||
import { StateObjectRef } from '../../mol-state';
|
||||
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
|
||||
|
||||
@@ -9,7 +9,7 @@ import { CifWriter } from '../../mol-io/writer/cif';
|
||||
import * as S from './schemas';
|
||||
// import { getCategoryInstanceProvider } from './utils'
|
||||
|
||||
export default function create(allData: any) {
|
||||
export function createMapping(allData: any) {
|
||||
const mols = Object.keys(allData);
|
||||
const enc = CifWriter.createEncoder();
|
||||
enc.startDataBlock(mols[0]);
|
||||
|
||||
@@ -6,7 +6,7 @@
|
||||
|
||||
import express from 'express';
|
||||
import fetch from 'node-fetch';
|
||||
import createMapping from './mapping';
|
||||
import { createMapping } from './mapping';
|
||||
|
||||
async function getMappings(id: string) {
|
||||
const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import fetch from 'node-fetch';
|
||||
import createMapping from './mapping';
|
||||
import { createMapping } from './mapping';
|
||||
|
||||
(async function () {
|
||||
const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');
|
||||
|
||||
@@ -12,18 +12,18 @@
|
||||
}
|
||||
#app {
|
||||
position: absolute;
|
||||
left: 160px;
|
||||
top: 100px;
|
||||
width: 600px;
|
||||
height: 600px;
|
||||
border: 1px solid #ccc;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
}
|
||||
|
||||
#controls {
|
||||
position: absolute;
|
||||
width: 150px;
|
||||
top: 100px;
|
||||
left: 780px;
|
||||
bottom: 100px;
|
||||
right: 50px;
|
||||
z-index: 10;
|
||||
font-family: sans-serif;
|
||||
font-size: smaller;
|
||||
}
|
||||
|
||||
#controls > button {
|
||||
@@ -46,13 +46,13 @@
|
||||
<div id="app"></div>
|
||||
<script>
|
||||
LightingDemo.init('app')
|
||||
LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
|
||||
LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
|
||||
|
||||
addHeader('Example PDB IDs');
|
||||
addControl('1M07', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' }));
|
||||
addControl('6HY0', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6HY0.cif', assemblyId: '1' }));
|
||||
addControl('6QVK', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6QVK.cif', assemblyId: '1' }));
|
||||
addControl('1RB8', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1RB8.cif', assemblyId: '1' }));
|
||||
addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
|
||||
addControl('5FJ5', () => LightingDemo.load({ url: 'https://models.rcsb.org/5FJ5.bcif', assemblyId: '1' }, 8, 1.8));
|
||||
addControl('1UPN', () => LightingDemo.load({ url: 'https://models.rcsb.org/1UPN.bcif', assemblyId: '1' }, 7, 1.6));
|
||||
addControl('1RB8', () => LightingDemo.load({ url: 'https://models.rcsb.org/1RB8.bcif', assemblyId: '1' }, 6, 1.3));
|
||||
|
||||
addSeparator()
|
||||
|
||||
|
||||
@@ -5,7 +5,8 @@
|
||||
*/
|
||||
|
||||
import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
|
||||
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPlugin } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
@@ -24,12 +25,11 @@ const Canvas3DPresets = {
|
||||
mode: 'temporal' as Canvas3DProps['multiSample']['mode']
|
||||
},
|
||||
postprocessing: {
|
||||
occlusion: { name: 'on', params: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
|
||||
outline: { name: 'on', params: { scale: 1, threshold: 0.33 } }
|
||||
occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
|
||||
outline: { name: 'on', params: { scale: 1, threshold: 0.1 } }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 1,
|
||||
lightIntensity: 0,
|
||||
style: { name: 'flat', params: {} }
|
||||
}
|
||||
},
|
||||
occlusion: <Preset> {
|
||||
@@ -37,12 +37,11 @@ const Canvas3DPresets = {
|
||||
mode: 'temporal' as Canvas3DProps['multiSample']['mode']
|
||||
},
|
||||
postprocessing: {
|
||||
occlusion: { name: 'on', params: { samples: 64, radius: 8, bias: 1.0, blurKernelSize: 13 } },
|
||||
occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
|
||||
outline: { name: 'off', params: { } }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 0.4,
|
||||
lightIntensity: 0.6,
|
||||
style: { name: 'matte', params: {} }
|
||||
}
|
||||
},
|
||||
standard: <Preset> {
|
||||
@@ -54,20 +53,24 @@ const Canvas3DPresets = {
|
||||
outline: { name: 'off', params: { } }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 0.4,
|
||||
lightIntensity: 0.6,
|
||||
style: { name: 'matte', params: {} }
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
type Canvas3DPreset = keyof typeof Canvas3DPresets
|
||||
|
||||
class LightingDemo {
|
||||
plugin: PluginContext;
|
||||
|
||||
private radius = 5;
|
||||
private bias = 1.1;
|
||||
private preset: Canvas3DPreset = 'illustrative';
|
||||
|
||||
init(target: string | HTMLElement) {
|
||||
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
|
||||
...DefaultPluginSpec,
|
||||
...DefaultPluginSpec(),
|
||||
layout: {
|
||||
initial: {
|
||||
isExpanded: false,
|
||||
@@ -82,6 +85,10 @@ class LightingDemo {
|
||||
|
||||
setPreset(preset: Canvas3DPreset) {
|
||||
const props = Canvas3DPresets[preset];
|
||||
if (props.postprocessing.occlusion?.name === 'on') {
|
||||
props.postprocessing.occlusion.params.radius = this.radius;
|
||||
props.postprocessing.occlusion.params.bias = this.bias;
|
||||
}
|
||||
PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
|
||||
...props,
|
||||
multiSample: {
|
||||
@@ -99,7 +106,7 @@ class LightingDemo {
|
||||
}});
|
||||
}
|
||||
|
||||
async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
|
||||
async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
|
||||
await this.plugin.clear();
|
||||
|
||||
const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
|
||||
@@ -111,7 +118,11 @@ class LightingDemo {
|
||||
if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });
|
||||
|
||||
const ligand = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand');
|
||||
if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
|
||||
if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
|
||||
|
||||
this.radius = radius;
|
||||
this.bias = bias;
|
||||
this.setPreset(this.preset);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -147,7 +147,7 @@
|
||||
|
||||
// adjust this number to make the animation faster or slower
|
||||
// requires to "restart" the animation if changed
|
||||
PluginWrapper.animate.modelIndex.maxFPS = 30;
|
||||
PluginWrapper.animate.modelIndex.targetFps = 30;
|
||||
|
||||
addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
|
||||
addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());
|
||||
|
||||
@@ -6,7 +6,8 @@
|
||||
|
||||
import * as ReactDOM from 'react-dom';
|
||||
import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
|
||||
import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
|
||||
import { createPlugin } from '../../mol-plugin';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
|
||||
import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
|
||||
import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
|
||||
@@ -46,7 +47,7 @@ class MolStarProteopediaWrapper {
|
||||
customColorList?: number[]
|
||||
}) {
|
||||
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
|
||||
...DefaultPluginSpec,
|
||||
...DefaultPluginSpec(),
|
||||
animations: [
|
||||
AnimateModelIndex
|
||||
],
|
||||
@@ -271,13 +272,17 @@ class MolStarProteopediaWrapper {
|
||||
resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
|
||||
}
|
||||
|
||||
private animateModelIndexTargetFps() {
|
||||
return Math.max(1, this.animate.modelIndex.targetFps | 0);
|
||||
}
|
||||
|
||||
animate = {
|
||||
modelIndex: {
|
||||
maxFPS: 8,
|
||||
onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
|
||||
onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
|
||||
palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
|
||||
loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
|
||||
targetFps: 8,
|
||||
onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
|
||||
onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
|
||||
palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
|
||||
loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: { direction: 'forward' } } }); },
|
||||
stop: () => this.plugin.managers.animation.stop()
|
||||
}
|
||||
}
|
||||
|
||||
@@ -54,13 +54,13 @@ export function computeANVIL(structure: Structure, props: ANVILProps) {
|
||||
});
|
||||
}
|
||||
|
||||
const l = StructureElement.Location.create(void 0);
|
||||
|
||||
const centroidHelper = new CentroidHelper();
|
||||
function initialize(structure: Structure, props: ANVILProps): ANVILContext {
|
||||
const l = StructureElement.Location.create(structure);
|
||||
const { label_atom_id, x, y, z } = StructureProperties.atom;
|
||||
const elementCount = structure.polymerResidueCount;
|
||||
centroidHelper.reset();
|
||||
l.structure = structure;
|
||||
|
||||
let offsets = new Int32Array(elementCount);
|
||||
let exposed = new Array<boolean>(elementCount);
|
||||
@@ -328,6 +328,7 @@ namespace HphobHphil {
|
||||
const testPoint = Vec3();
|
||||
export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
|
||||
const { offsets, exposed, structure } = ctx;
|
||||
const l = StructureElement.Location.create(structure);
|
||||
const { x, y, z } = StructureProperties.atom;
|
||||
let hphob = 0;
|
||||
let hphil = 0;
|
||||
|
||||
@@ -15,7 +15,7 @@ import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/ac
|
||||
import { Vec3 } from '../../mol-math/linear-algebra';
|
||||
import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
|
||||
import { CustomPropSymbol } from '../../mol-script/language/symbol';
|
||||
import Type from '../../mol-script/language/type';
|
||||
import { Type } from '../../mol-script/language/type';
|
||||
|
||||
export const MembraneOrientationParams = {
|
||||
...ANVILParams
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import msgpackDecode from '../../mol-io/common/msgpack/decode';
|
||||
import { decodeMsgPack } from '../../mol-io/common/msgpack/decode';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { Task } from '../../mol-task';
|
||||
import { inflate } from '../../mol-util/zip/zip';
|
||||
@@ -41,7 +41,7 @@ export async function getG3dHeader(ctx: PluginContext, urlOrData: string | Uint8
|
||||
for (; last >= 0; last--) {
|
||||
if (data[last] !== 0) break;
|
||||
}
|
||||
const header = msgpackDecode(data.slice(0, last + 1));
|
||||
const header = decodeMsgPack(data.slice(0, last + 1));
|
||||
return header;
|
||||
}
|
||||
|
||||
@@ -53,7 +53,7 @@ export async function getG3dDataBlock(ctx: PluginContext, header: G3dHeader, url
|
||||
return {
|
||||
header,
|
||||
resolution,
|
||||
data: msgpackDecode(unzipped)
|
||||
data: decodeMsgPack(unzipped)
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
@@ -16,7 +16,7 @@ import { MoleculeType } from '../../mol-model/structure/model/types';
|
||||
import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
|
||||
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
|
||||
import { CustomPropSymbol } from '../../mol-script/language/symbol';
|
||||
import Type from '../../mol-script/language/type';
|
||||
import { Type } from '../../mol-script/language/type';
|
||||
import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
|
||||
import { RuntimeContext, Task } from '../../mol-task';
|
||||
import { objectForEach } from '../../mol-util/object';
|
||||
|
||||
@@ -13,7 +13,7 @@ import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-m
|
||||
import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
|
||||
import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
|
||||
import { CustomPropSymbol } from '../../../mol-script/language/symbol';
|
||||
import Type from '../../../mol-script/language/type';
|
||||
import { Type } from '../../../mol-script/language/type';
|
||||
import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { arraySetAdd } from '../../../mol-util/array';
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphql/types';
|
||||
import query from '../graphql/symmetry.gql';
|
||||
import { symmetry_gql } from '../graphql/symmetry.gql';
|
||||
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
|
||||
@@ -66,7 +66,7 @@ export namespace AssemblySymmetry {
|
||||
assembly_id: structure.units[0].conformation.operator.assembly?.id || '',
|
||||
entry_id: structure.units[0].model.entryId
|
||||
};
|
||||
const result = await client.request(ctx.runtime, query, variables);
|
||||
const result = await client.request(ctx.runtime, symmetry_gql, variables);
|
||||
let value: AssemblySymmetryDataValue = [];
|
||||
|
||||
if (!result.data.assembly?.rcsb_struct_symmetry) {
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default /* GraphQL */ `
|
||||
export const symmetry_gql = /* GraphQL */ `
|
||||
query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
|
||||
assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
|
||||
rcsb_struct_symmetry {
|
||||
|
||||
@@ -19,7 +19,7 @@ import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
|
||||
import { Vec3 } from '../../../mol-math/linear-algebra';
|
||||
import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
|
||||
import { CustomPropSymbol } from '../../../mol-script/language/symbol';
|
||||
import Type from '../../../mol-script/language/type';
|
||||
import { Type } from '../../../mol-script/language/type';
|
||||
import { Asset } from '../../../mol-util/assets';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
|
||||
|
||||
@@ -8,14 +8,14 @@
|
||||
import { BehaviorSubject, Subscription } from 'rxjs';
|
||||
import { now } from '../mol-util/now';
|
||||
import { Vec3, Vec2 } from '../mol-math/linear-algebra';
|
||||
import InputObserver, { ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
|
||||
import Renderer, { RendererStats, RendererParams } from '../mol-gl/renderer';
|
||||
import { InputObserver, ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
|
||||
import { Renderer, RendererStats, RendererParams } from '../mol-gl/renderer';
|
||||
import { GraphicsRenderObject } from '../mol-gl/render-object';
|
||||
import { TrackballControls, TrackballControlsParams } from './controls/trackball';
|
||||
import { Viewport } from './camera/util';
|
||||
import { createContext, WebGLContext, getGLContext } from '../mol-gl/webgl/context';
|
||||
import { Representation } from '../mol-repr/representation';
|
||||
import Scene from '../mol-gl/scene';
|
||||
import { Scene } from '../mol-gl/scene';
|
||||
import { PickingId } from '../mol-geo/geometry/picking';
|
||||
import { MarkerAction } from '../mol-util/marker-action';
|
||||
import { Loci, EmptyLoci, isEmptyLoci } from '../mol-model/loci';
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
|
||||
import { Viewport } from '../camera/util';
|
||||
import InputObserver, { DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
|
||||
import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { Camera } from '../camera';
|
||||
import { absMax } from '../../mol-math/misc';
|
||||
|
||||
@@ -9,7 +9,7 @@ import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
|
||||
import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
|
||||
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { Sphere3D } from '../../mol-math/geometry';
|
||||
import { Color } from '../../mol-util/color';
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { Camera, ICamera } from '../camera';
|
||||
import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
|
||||
import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
|
||||
import { Vec3, Mat4, Mat3 } from '../../mol-math/linear-algebra';
|
||||
import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { BoundingSphereHelper, DebugHelperParams } from './bounding-sphere-helper';
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
|
||||
import { PickingId } from '../../mol-geo/geometry/picking';
|
||||
import { Representation } from '../../mol-repr/representation';
|
||||
import InputObserver, { ModifiersKeys, ButtonsType } from '../../mol-util/input/input-observer';
|
||||
import { InputObserver, ModifiersKeys, ButtonsType } from '../../mol-util/input/input-observer';
|
||||
import { RxEventHelper } from '../../mol-util/rx-event-helper';
|
||||
import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
|
||||
import { Camera } from '../camera';
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
* @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
|
||||
@@ -7,8 +7,8 @@
|
||||
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { createNullRenderTarget, RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
import Renderer from '../../mol-gl/renderer';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Renderer } from '../../mol-gl/renderer';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { Texture } from '../../mol-gl/webgl/texture';
|
||||
import { Camera, ICamera } from '../camera';
|
||||
import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
|
||||
@@ -20,8 +20,8 @@ import { ValueCell } from '../../mol-util';
|
||||
import { Vec2 } from '../../mol-math/linear-algebra';
|
||||
import { Helper } from '../helper/helper';
|
||||
|
||||
import quad_vert from '../../mol-gl/shader/quad.vert';
|
||||
import depthMerge_frag from '../../mol-gl/shader/depth-merge.frag';
|
||||
import { quad_vert } from '../../mol-gl/shader/quad.vert';
|
||||
import { depthMerge_frag } from '../../mol-gl/shader/depth-merge.frag';
|
||||
import { copy_frag } from '../../mol-gl/shader/copy.frag';
|
||||
import { StereoCamera } from '../camera/stereo';
|
||||
import { WboitPass } from './wboit';
|
||||
@@ -100,7 +100,7 @@ export class DrawPass {
|
||||
}
|
||||
|
||||
constructor(private webgl: WebGLContext, width: number, height: number, enableWboit: boolean) {
|
||||
const { extensions, resources } = webgl;
|
||||
const { extensions, resources, isWebGL2 } = webgl;
|
||||
|
||||
this.drawTarget = createNullRenderTarget(webgl.gl);
|
||||
|
||||
@@ -113,8 +113,8 @@ export class DrawPass {
|
||||
this.depthTargetPrimitives = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
|
||||
this.depthTargetVolumes = this.packedDepth ? webgl.createRenderTarget(width, height) : null;
|
||||
|
||||
this.depthTexturePrimitives = this.depthTargetPrimitives ? this.depthTargetPrimitives.texture : resources.texture('image-depth', 'depth', 'ushort', 'nearest');
|
||||
this.depthTextureVolumes = this.depthTargetVolumes ? this.depthTargetVolumes.texture : resources.texture('image-depth', 'depth', 'ushort', 'nearest');
|
||||
this.depthTexturePrimitives = this.depthTargetPrimitives ? this.depthTargetPrimitives.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
|
||||
this.depthTextureVolumes = this.depthTargetVolumes ? this.depthTargetVolumes.texture : resources.texture('image-depth', 'depth', isWebGL2 ? 'float' : 'ushort', 'nearest');
|
||||
if (!this.packedDepth) {
|
||||
this.depthTexturePrimitives.define(width, height);
|
||||
this.depthTextureVolumes.define(width, height);
|
||||
|
||||
@@ -14,8 +14,8 @@ import { Texture } from '../../mol-gl/webgl/texture';
|
||||
import { Vec2 } from '../../mol-math/linear-algebra';
|
||||
import { ValueCell } from '../../mol-util';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import quad_vert from '../../mol-gl/shader/quad.vert';
|
||||
import fxaa_frag from '../../mol-gl/shader/fxaa.frag';
|
||||
import { quad_vert } from '../../mol-gl/shader/quad.vert';
|
||||
import { fxaa_frag } from '../../mol-gl/shader/fxaa.frag';
|
||||
import { Viewport } from '../camera/util';
|
||||
import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
|
||||
|
||||
@@ -6,8 +6,8 @@
|
||||
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
import Renderer from '../../mol-gl/renderer';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Renderer } from '../../mol-gl/renderer';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { DrawPass } from './draw';
|
||||
import { PostprocessingParams } from './postprocessing';
|
||||
|
||||
@@ -18,13 +18,13 @@ import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
import { Camera } from '../../mol-canvas3d/camera';
|
||||
import { PostprocessingProps } from './postprocessing';
|
||||
import { DrawPass } from './draw';
|
||||
import Renderer from '../../mol-gl/renderer';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Renderer } from '../../mol-gl/renderer';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { Helper } from '../helper/helper';
|
||||
import { StereoCamera } from '../camera/stereo';
|
||||
|
||||
import quad_vert from '../../mol-gl/shader/quad.vert';
|
||||
import compose_frag from '../../mol-gl/shader/compose.frag';
|
||||
import { quad_vert } from '../../mol-gl/shader/quad.vert';
|
||||
import { compose_frag } from '../../mol-gl/shader/compose.frag';
|
||||
|
||||
const ComposeSchema = {
|
||||
...QuadSchema,
|
||||
|
||||
@@ -5,8 +5,8 @@
|
||||
*/
|
||||
|
||||
import { PickingId } from '../../mol-geo/geometry/picking';
|
||||
import Renderer from '../../mol-gl/renderer';
|
||||
import Scene from '../../mol-gl/scene';
|
||||
import { Renderer } from '../../mol-gl/renderer';
|
||||
import { Scene } from '../../mol-gl/scene';
|
||||
import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
|
||||
import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
|
||||
@@ -18,11 +18,11 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
||||
import { DrawPass } from './draw';
|
||||
import { ICamera } from '../../mol-canvas3d/camera';
|
||||
import quad_vert from '../../mol-gl/shader/quad.vert';
|
||||
import outlines_frag from '../../mol-gl/shader/outlines.frag';
|
||||
import ssao_frag from '../../mol-gl/shader/ssao.frag';
|
||||
import ssao_blur_frag from '../../mol-gl/shader/ssao-blur.frag';
|
||||
import postprocessing_frag from '../../mol-gl/shader/postprocessing.frag';
|
||||
import { quad_vert } from '../../mol-gl/shader/quad.vert';
|
||||
import { outlines_frag } from '../../mol-gl/shader/outlines.frag';
|
||||
import { ssao_frag } from '../../mol-gl/shader/ssao.frag';
|
||||
import { ssaoBlur_frag } from '../../mol-gl/shader/ssao-blur.frag';
|
||||
import { postprocessing_frag } from '../../mol-gl/shader/postprocessing.frag';
|
||||
import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
|
||||
import { Color } from '../../mol-util/color';
|
||||
import { FxaaParams, FxaaPass } from './fxaa';
|
||||
@@ -143,7 +143,7 @@ function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, dir
|
||||
};
|
||||
|
||||
const schema = { ...SsaoBlurSchema };
|
||||
const shaderCode = ShaderCode('ssao_blur', quad_vert, ssao_blur_frag);
|
||||
const shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
|
||||
const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
|
||||
|
||||
return createComputeRenderable(renderItem, values);
|
||||
|
||||
@@ -13,8 +13,8 @@ import { WebGLContext } from '../../mol-gl/webgl/context';
|
||||
import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
|
||||
import { Texture } from '../../mol-gl/webgl/texture';
|
||||
import { ValueCell } from '../../mol-util';
|
||||
import quad_vert from '../../mol-gl/shader/quad.vert';
|
||||
import evaluate_wboit_frag from '../../mol-gl/shader/evaluate-wboit.frag';
|
||||
import { quad_vert } from '../../mol-gl/shader/quad.vert';
|
||||
import { evaluateWboit_frag } from '../../mol-gl/shader/evaluate-wboit.frag';
|
||||
import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
|
||||
import { Vec2 } from '../../mol-math/linear-algebra';
|
||||
import { isDebugMode } from '../../mol-util/debug';
|
||||
@@ -25,7 +25,7 @@ const EvaluateWboitSchema = {
|
||||
tWboitB: TextureSpec('texture', 'rgba', 'float', 'nearest'),
|
||||
uTexSize: UniformSpec('v2'),
|
||||
};
|
||||
const EvaluateWboitShaderCode = ShaderCode('evaluate-wboit', quad_vert, evaluate_wboit_frag);
|
||||
const EvaluateWboitShaderCode = ShaderCode('evaluate-wboit', quad_vert, evaluateWboit_frag);
|
||||
type EvaluateWboitRenderable = ComputeRenderable<Values<typeof EvaluateWboitSchema>>
|
||||
|
||||
function getEvaluateWboitRenderable(ctx: WebGLContext, wboitATexture: Texture, wboitBTexture: Texture): EvaluateWboitRenderable {
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Iterator from '../iterator';
|
||||
import { Iterator } from '../iterator';
|
||||
|
||||
function iteratorToArray<T>(it: Iterator<T>): T[] {
|
||||
const ret = [];
|
||||
|
||||
@@ -5,9 +5,9 @@
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import Database from './db/database';
|
||||
import Table from './db/table';
|
||||
import Column from './db/column';
|
||||
import { Database } from './db/database';
|
||||
import { Table } from './db/table';
|
||||
import { Column } from './db/column';
|
||||
import * as ColumnHelpers from './db/column-helpers';
|
||||
|
||||
type DatabaseCollection<T extends Database.Schema> = { [name: string]: Database<T> }
|
||||
|
||||
@@ -6,8 +6,8 @@
|
||||
*/
|
||||
|
||||
import * as ColumnHelpers from '../column-helpers';
|
||||
import Column from '../column';
|
||||
import Table from '../table';
|
||||
import { Column } from '../column';
|
||||
import { Table } from '../table';
|
||||
|
||||
describe('column', () => {
|
||||
const cc = Column.ofConst(10, 2, Column.Schema.int);
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Column from './column';
|
||||
import { Column } from './column';
|
||||
|
||||
export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams<any>) {
|
||||
const start = params && typeof params.start !== 'undefined' ? Math.max(Math.min(params.start, rowCount - 1), 0) : 0;
|
||||
|
||||
@@ -230,7 +230,7 @@ namespace Column {
|
||||
}
|
||||
}
|
||||
|
||||
export default Column;
|
||||
export { Column };
|
||||
|
||||
function createFirstIndexMapOfColumn<T>(c: Column<T>): Map<T, number> {
|
||||
const map = new Map<T, number>();
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Table from './table';
|
||||
import { Table } from './table';
|
||||
|
||||
/** A collection of tables */
|
||||
type Database<Schema extends Database.Schema> = {
|
||||
@@ -41,4 +41,4 @@ namespace Database {
|
||||
}
|
||||
}
|
||||
|
||||
export default Database;
|
||||
export { Database };
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Column from './column';
|
||||
import { Column } from './column';
|
||||
import { sortArray } from '../util/sort';
|
||||
import { StringBuilder } from '../../mol-util';
|
||||
|
||||
@@ -280,4 +280,4 @@ namespace Table {
|
||||
}
|
||||
}
|
||||
|
||||
export default Table;
|
||||
export { Table };
|
||||
@@ -6,7 +6,7 @@
|
||||
|
||||
import * as DB from './db';
|
||||
import * as Int from './int';
|
||||
import Iterator from './iterator';
|
||||
import { Iterator } from './iterator';
|
||||
import * as Util from './util';
|
||||
import * as Generic from './generic';
|
||||
|
||||
|
||||
@@ -4,13 +4,13 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Interval from './int/interval';
|
||||
import OrderedSet from './int/ordered-set';
|
||||
import Segmentation from './int/segmentation';
|
||||
import SortedArray from './int/sorted-array';
|
||||
import Tuple from './int/tuple';
|
||||
import LinkedIndex from './int/linked-index';
|
||||
import IntMap from './int/map';
|
||||
import Iterator from './iterator';
|
||||
import { Interval } from './int/interval';
|
||||
import { OrderedSet } from './int/ordered-set';
|
||||
import { Segmentation } from './int/segmentation';
|
||||
import { SortedArray } from './int/sorted-array';
|
||||
import { IntTuple as Tuple } from './int/tuple';
|
||||
import { LinkedIndex } from './int/linked-index';
|
||||
import { IntMap } from './int/map';
|
||||
import { Iterator } from './iterator';
|
||||
|
||||
export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, LinkedIndex, IntMap, Iterator };
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Interval from '../interval';
|
||||
import { Interval } from '../interval';
|
||||
|
||||
describe('interval', () => {
|
||||
function testI(name: string, a: Interval, b: Interval) {
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import LinkedIndex from '../linked-index';
|
||||
import { LinkedIndex } from '../linked-index';
|
||||
|
||||
describe('linked-index', () => {
|
||||
it('initial state', () => {
|
||||
|
||||
@@ -4,9 +4,9 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import OrderedSet from '../ordered-set';
|
||||
import Interval from '../interval';
|
||||
import SortedArray from '../sorted-array';
|
||||
import { OrderedSet } from '../ordered-set';
|
||||
import { Interval } from '../interval';
|
||||
import { SortedArray } from '../sorted-array';
|
||||
|
||||
describe('ordered set', () => {
|
||||
function ordSetToArray(set: OrderedSet) {
|
||||
|
||||
@@ -4,9 +4,9 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import OrderedSet from '../ordered-set';
|
||||
import Interval from '../interval';
|
||||
import Segmentation from '../segmentation';
|
||||
import { OrderedSet } from '../ordered-set';
|
||||
import { Interval } from '../interval';
|
||||
import { Segmentation } from '../segmentation';
|
||||
|
||||
describe('segments', () => {
|
||||
const data = OrderedSet.ofSortedArray([4, 9, 10, 11, 14, 15, 16]);
|
||||
|
||||
@@ -4,8 +4,8 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Interval from '../interval';
|
||||
import SortedArray from '../sorted-array';
|
||||
import { Interval } from '../interval';
|
||||
import { SortedArray } from '../sorted-array';
|
||||
|
||||
describe('sortedArray', () => {
|
||||
function testI(name: string, a: Interval, b: Interval) {
|
||||
|
||||
@@ -4,9 +4,9 @@
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import SortedRanges from '../sorted-ranges';
|
||||
import OrderedSet from '../ordered-set';
|
||||
import SortedArray from '../sorted-array';
|
||||
import { SortedRanges } from '../sorted-ranges';
|
||||
import { OrderedSet } from '../ordered-set';
|
||||
import { SortedArray } from '../sorted-array';
|
||||
|
||||
describe('rangesArray', () => {
|
||||
function test(name: string, a: any, b: any) {
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import IntTuple from '../tuple';
|
||||
import { IntTuple } from '../tuple';
|
||||
|
||||
describe('int pair', () => {
|
||||
it('works', () => {
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Tuple from '../tuple';
|
||||
import { IntTuple as Tuple } from '../tuple';
|
||||
|
||||
export const Empty = Tuple.Zero;
|
||||
export function ofRange(min: number, max: number) { return max < min ? Tuple.create(min, min) : Tuple.create(min, max + 1); }
|
||||
|
||||
@@ -4,8 +4,8 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import S from '../sorted-array';
|
||||
import I from '../interval';
|
||||
import { SortedArray as S } from '../sorted-array';
|
||||
import { Interval as I } from '../interval';
|
||||
|
||||
type OrderedSetImpl = I | S
|
||||
type Nums = ArrayLike<number>
|
||||
|
||||
@@ -4,11 +4,11 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Iterator from '../../iterator';
|
||||
import OrderedSet from '../ordered-set';
|
||||
import Interval from '../interval';
|
||||
import SortedArray from '../sorted-array';
|
||||
import Segs from '../segmentation';
|
||||
import { Iterator } from '../../iterator';
|
||||
import { OrderedSet } from '../ordered-set';
|
||||
import { Interval } from '../interval';
|
||||
import { SortedArray } from '../sorted-array';
|
||||
import { Segmentation as Segs } from '../segmentation';
|
||||
|
||||
interface Segmentation {
|
||||
/** Segments stored as a sorted array */
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import { sortArray, hash3, hash4, createRangeArray } from '../../util';
|
||||
import Interval from '../interval';
|
||||
import { Interval } from '../interval';
|
||||
|
||||
type Nums = ArrayLike<number>
|
||||
|
||||
|
||||
@@ -60,4 +60,4 @@ namespace Interval {
|
||||
/** Interval describing a range [min, max] of values */
|
||||
interface Interval<T extends number = number> { '@type': 'int-interval' }
|
||||
|
||||
export default Interval;
|
||||
export { Interval };
|
||||
@@ -55,4 +55,4 @@ class LinkedIndexImpl implements LinkedIndex {
|
||||
}
|
||||
}
|
||||
|
||||
export default LinkedIndex;
|
||||
export { LinkedIndex };
|
||||
@@ -58,4 +58,4 @@ namespace IntMap {
|
||||
}
|
||||
}
|
||||
|
||||
export default IntMap;
|
||||
export { IntMap };
|
||||
@@ -5,8 +5,8 @@
|
||||
*/
|
||||
|
||||
import * as Base from './impl/ordered-set';
|
||||
import Interval from './interval';
|
||||
import SortedArray from './sorted-array';
|
||||
import { Interval } from './interval';
|
||||
import { SortedArray } from './sorted-array';
|
||||
|
||||
namespace OrderedSet {
|
||||
export const Empty: OrderedSet = Base.Empty as any;
|
||||
@@ -82,4 +82,4 @@ namespace OrderedSet {
|
||||
|
||||
type OrderedSet<T extends number = number> = SortedArray<T> | Interval<T>
|
||||
|
||||
export default OrderedSet;
|
||||
export { OrderedSet };
|
||||
@@ -4,8 +4,8 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import Interval from './interval';
|
||||
import OrderedSet from './ordered-set';
|
||||
import { Interval } from './interval';
|
||||
import { OrderedSet } from './ordered-set';
|
||||
import * as Impl from './impl/segmentation';
|
||||
|
||||
namespace Segmentation {
|
||||
@@ -33,4 +33,4 @@ interface Segmentation<T extends number = number, I extends number = number> {
|
||||
readonly count: number
|
||||
}
|
||||
|
||||
export default Segmentation;
|
||||
export { Segmentation };
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import * as Impl from './impl/sorted-array';
|
||||
import Interval from './interval';
|
||||
import { Interval } from './interval';
|
||||
|
||||
namespace SortedArray {
|
||||
export const Empty: SortedArray = Impl.Empty as any;
|
||||
@@ -54,4 +54,4 @@ namespace SortedArray {
|
||||
|
||||
interface SortedArray<T extends number = number> extends ArrayLike<T> { '@type': 'int-sorted-array' }
|
||||
|
||||
export default SortedArray;
|
||||
export { SortedArray };
|
||||
@@ -5,7 +5,7 @@
|
||||
*/
|
||||
|
||||
import { Segmentation, OrderedSet, SortedArray, Interval } from '../int';
|
||||
import _Iterator from '../iterator';
|
||||
import { Iterator as _Iterator } from '../iterator';
|
||||
|
||||
/** Pairs of min and max indices of sorted, non-overlapping ranges */
|
||||
type SortedRanges<T extends number = number> = SortedArray<T>
|
||||
@@ -115,4 +115,4 @@ namespace SortedRanges {
|
||||
}
|
||||
}
|
||||
|
||||
export default SortedRanges;
|
||||
export { SortedRanges };
|
||||
@@ -80,4 +80,4 @@ namespace IntTuple {
|
||||
}
|
||||
}
|
||||
|
||||
export default IntTuple;
|
||||
export { IntTuple };
|
||||
@@ -117,4 +117,4 @@ namespace Iterator {
|
||||
}
|
||||
}
|
||||
|
||||
export default Iterator;
|
||||
export { Iterator };
|
||||
@@ -6,7 +6,7 @@
|
||||
|
||||
// adpated from https://github.com/dankogai/js-combinatorics, MIT 2013-2016 Dan Kogai
|
||||
|
||||
import Iterator from '../iterator';
|
||||
import { Iterator } from '../iterator';
|
||||
|
||||
function P(m: number, n: number) {
|
||||
let p = 1;
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import Iterator from '../iterator';
|
||||
import { Iterator } from '../iterator';
|
||||
import { OrderedSet, Interval, Segmentation } from '../int';
|
||||
|
||||
/** Emits a segment of length one for each element in the interval that is also in the set */
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
@@ -36,11 +36,36 @@ export interface TextureMesh {
|
||||
readonly vertexTexture: ValueCell<Texture>,
|
||||
readonly groupTexture: ValueCell<Texture>,
|
||||
readonly normalTexture: ValueCell<Texture>,
|
||||
readonly doubleBuffer: TextureMesh.DoubleBuffer
|
||||
|
||||
readonly boundingSphere: Sphere3D
|
||||
}
|
||||
|
||||
export namespace TextureMesh {
|
||||
export class DoubleBuffer {
|
||||
private index = 0;
|
||||
private textures: ({ vertex: Texture, group: Texture, normal: Texture } | undefined)[] = []
|
||||
|
||||
get() {
|
||||
return this.textures[this.index];
|
||||
}
|
||||
|
||||
set(vertex: Texture, group: Texture, normal: Texture) {
|
||||
this.textures[this.index] = Object.assign(this.textures[this.index] || {}, {
|
||||
vertex, group, normal
|
||||
});
|
||||
this.index = (this.index + 1) % 2;
|
||||
}
|
||||
|
||||
destroy() {
|
||||
for (const buffer of this.textures) {
|
||||
buffer!.vertex.destroy();
|
||||
buffer!.group.destroy();
|
||||
buffer!.normal.destroy();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
export function create(vertexCount: number, groupCount: number, vertexTexture: Texture, groupTexture: Texture, normalTexture: Texture, boundingSphere: Sphere3D, textureMesh?: TextureMesh): TextureMesh {
|
||||
const width = vertexTexture.getWidth();
|
||||
const height = vertexTexture.getHeight();
|
||||
@@ -49,7 +74,9 @@ export namespace TextureMesh {
|
||||
textureMesh.groupCount = groupCount;
|
||||
ValueCell.update(textureMesh.geoTextureDim, Vec2.set(textureMesh.geoTextureDim.ref.value, width, height));
|
||||
ValueCell.update(textureMesh.vertexTexture, vertexTexture);
|
||||
ValueCell.update(textureMesh.groupTexture, groupTexture);
|
||||
ValueCell.update(textureMesh.normalTexture, normalTexture);
|
||||
textureMesh.doubleBuffer.set(vertexTexture, groupTexture, normalTexture);
|
||||
Sphere3D.copy(textureMesh.boundingSphere, boundingSphere);
|
||||
return textureMesh;
|
||||
} else {
|
||||
@@ -61,6 +88,7 @@ export namespace TextureMesh {
|
||||
vertexTexture: ValueCell.create(vertexTexture),
|
||||
groupTexture: ValueCell.create(groupTexture),
|
||||
normalTexture: ValueCell.create(normalTexture),
|
||||
doubleBuffer: new DoubleBuffer(),
|
||||
boundingSphere: Sphere3D.clone(boundingSphere),
|
||||
};
|
||||
}
|
||||
|
||||
@@ -10,14 +10,14 @@ import { Camera } from '../../mol-canvas3d/camera';
|
||||
import { Vec3, Mat4, Vec4 } from '../../mol-math/linear-algebra';
|
||||
import { ValueCell } from '../../mol-util';
|
||||
|
||||
import Renderer from '../renderer';
|
||||
import { Renderer } from '../renderer';
|
||||
import { createValueColor } from '../../mol-geo/geometry/color-data';
|
||||
import { createValueSize } from '../../mol-geo/geometry/size-data';
|
||||
import { createContext } from '../webgl/context';
|
||||
import { RenderableState } from '../renderable';
|
||||
import { createRenderObject } from '../render-object';
|
||||
import { PointsValues } from '../renderable/points';
|
||||
import Scene from '../scene';
|
||||
import { Scene } from '../scene';
|
||||
import { createEmptyMarkers } from '../../mol-geo/geometry/marker-data';
|
||||
import { fillSerial } from '../../mol-util/array';
|
||||
import { Color } from '../../mol-util/color';
|
||||
|
||||
@@ -7,8 +7,8 @@
|
||||
import { RenderableSchema, Values, UnboxedValues, UniformSpec, TextureSpec, DefineSpec, RenderableValues } from '../renderable/schema';
|
||||
import { WebGLContext } from '../webgl/context';
|
||||
import { getRegularGrid3dDelta, RegularGrid3d } from '../../mol-math/geometry/common';
|
||||
import shader_template from '../shader/util/grid3d-template.frag';
|
||||
import quad_vert from '../shader/quad.vert';
|
||||
import { grid3dTemplate_frag } from '../shader/util/grid3d-template.frag';
|
||||
import { quad_vert } from '../shader/quad.vert';
|
||||
import { ShaderCode } from '../shader-code';
|
||||
import { UUID, ValueCell } from '../../mol-util';
|
||||
import { objectForEach } from '../../mol-util/object';
|
||||
@@ -74,7 +74,7 @@ export function createGrid3dComputeRenderable<S extends RenderableSchema, P, CS>
|
||||
if (isBound) uniforms.push(`#endif`);
|
||||
});
|
||||
|
||||
const code = shader_template
|
||||
const code = grid3dTemplate_frag
|
||||
.replace('{UNIFORMS}', uniforms.join('\n'))
|
||||
.replace('{UTILS}', spec.utilCode ?? '')
|
||||
.replace('{MAIN}', spec.mainCode)
|
||||
|
||||
@@ -16,8 +16,8 @@ import { Vec2, Vec3 } from '../../../mol-math/linear-algebra';
|
||||
import { getHistopyramidSum } from './sum';
|
||||
import { Framebuffer } from '../../../mol-gl/webgl/framebuffer';
|
||||
import { isPowerOfTwo } from '../../../mol-math/misc';
|
||||
import quad_vert from '../../../mol-gl/shader/quad.vert';
|
||||
import reduction_frag from '../../../mol-gl/shader/histogram-pyramid/reduction.frag';
|
||||
import { quad_vert } from '../../../mol-gl/shader/quad.vert';
|
||||
import { reduction_frag } from '../../../mol-gl/shader/histogram-pyramid/reduction.frag';
|
||||
import { isWebGL2 } from '../../webgl/compat';
|
||||
|
||||
const HistopyramidReductionSchema = {
|
||||
|
||||
@@ -13,8 +13,8 @@ import { ShaderCode } from '../../../mol-gl/shader-code';
|
||||
import { ValueCell } from '../../../mol-util';
|
||||
import { decodeFloatRGB } from '../../../mol-util/float-packing';
|
||||
import { QuadSchema, QuadValues } from '../util';
|
||||
import quad_vert from '../../../mol-gl/shader/quad.vert';
|
||||
import sum_frag from '../../../mol-gl/shader/histogram-pyramid/sum.frag';
|
||||
import { quad_vert } from '../../../mol-gl/shader/quad.vert';
|
||||
import { sum_frag } from '../../../mol-gl/shader/histogram-pyramid/sum.frag';
|
||||
import { isWebGL2 } from '../../webgl/compat';
|
||||
|
||||
const HistopyramidSumSchema = {
|
||||
|
||||
@@ -14,8 +14,8 @@ import { ValueCell } from '../../../mol-util';
|
||||
import { Vec3, Vec2 } from '../../../mol-math/linear-algebra';
|
||||
import { QuadSchema, QuadValues } from '../util';
|
||||
import { getTriCount } from './tables';
|
||||
import quad_vert from '../../../mol-gl/shader/quad.vert';
|
||||
import active_voxels_frag from '../../../mol-gl/shader/marching-cubes/active-voxels.frag';
|
||||
import { quad_vert } from '../../../mol-gl/shader/quad.vert';
|
||||
import { activeVoxels_frag } from '../../../mol-gl/shader/marching-cubes/active-voxels.frag';
|
||||
|
||||
const ActiveVoxelsSchema = {
|
||||
...QuadSchema,
|
||||
@@ -65,7 +65,7 @@ function createActiveVoxelsRenderable(ctx: WebGLContext, volumeData: Texture, gr
|
||||
};
|
||||
|
||||
const schema = { ...ActiveVoxelsSchema };
|
||||
const shaderCode = ShaderCode('active-voxels', quad_vert, active_voxels_frag);
|
||||
const shaderCode = ShaderCode('active-voxels', quad_vert, activeVoxels_frag);
|
||||
const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
|
||||
|
||||
return createComputeRenderable(renderItem, values);
|
||||
|
||||
@@ -15,8 +15,8 @@ import { Vec3, Vec2, Mat4 } from '../../../mol-math/linear-algebra';
|
||||
import { QuadSchema, QuadValues } from '../util';
|
||||
import { createHistogramPyramid, HistogramPyramid } from '../histogram-pyramid/reduction';
|
||||
import { getTriIndices } from './tables';
|
||||
import quad_vert from '../../../mol-gl/shader/quad.vert';
|
||||
import isosurface_frag from '../../../mol-gl/shader/marching-cubes/isosurface.frag';
|
||||
import { quad_vert } from '../../../mol-gl/shader/quad.vert';
|
||||
import { isosurface_frag } from '../../../mol-gl/shader/marching-cubes/isosurface.frag';
|
||||
import { calcActiveVoxels } from './active-voxels';
|
||||
import { isWebGL2 } from '../../webgl/compat';
|
||||
|
||||
@@ -185,7 +185,7 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
|
||||
gl.clear(gl.COLOR_BUFFER_BIT);
|
||||
renderable.render();
|
||||
|
||||
gl.flush();
|
||||
gl.finish();
|
||||
|
||||
return { vertexTexture, groupTexture, normalTexture, vertexCount: count };
|
||||
}
|
||||
|
||||
@@ -37,6 +37,7 @@ export function splitValues(schema: RenderableSchema, values: RenderableValues)
|
||||
const textureValues: TextureValues = {};
|
||||
const uniformValues: UniformValues = {};
|
||||
const materialUniformValues: UniformValues = {};
|
||||
const bufferedUniformValues: UniformValues = {};
|
||||
Object.keys(schema).forEach(k => {
|
||||
const spec = schema[k];
|
||||
if (spec.type === 'attribute') attributeValues[k] = values[k];
|
||||
@@ -45,11 +46,12 @@ export function splitValues(schema: RenderableSchema, values: RenderableValues)
|
||||
if (spec.type === 'texture' && values[k] !== undefined) textureValues[k] = values[k];
|
||||
// check if k exists in values to exclude global uniforms
|
||||
if (spec.type === 'uniform' && values[k] !== undefined) {
|
||||
if (spec.isMaterial) materialUniformValues[k] = values[k];
|
||||
if (spec.variant === 'material') materialUniformValues[k] = values[k];
|
||||
else if (spec.variant === 'buffered') bufferedUniformValues[k] = values[k];
|
||||
else uniformValues[k] = values[k];
|
||||
}
|
||||
});
|
||||
return { attributeValues, defineValues, textureValues, uniformValues, materialUniformValues };
|
||||
return { attributeValues, defineValues, textureValues, uniformValues, materialUniformValues, bufferedUniformValues };
|
||||
}
|
||||
|
||||
export type Versions<T extends RenderableValues> = { [k in keyof T]: number }
|
||||
@@ -68,9 +70,9 @@ export function AttributeSpec<K extends AttributeKind>(kind: K, itemSize: Attrib
|
||||
return { type: 'attribute', kind, itemSize, divisor };
|
||||
}
|
||||
|
||||
export type UniformSpec<K extends UniformKind> = { type: 'uniform', kind: K, isMaterial: boolean }
|
||||
export function UniformSpec<K extends UniformKind>(kind: K, isMaterial = false): UniformSpec<K> {
|
||||
return { type: 'uniform', kind, isMaterial };
|
||||
export type UniformSpec<K extends UniformKind> = { type: 'uniform', kind: K, variant?: 'material' | 'buffered' }
|
||||
export function UniformSpec<K extends UniformKind>(kind: K, variant?: 'material' | 'buffered'): UniformSpec<K> {
|
||||
return { type: 'uniform', kind, variant };
|
||||
}
|
||||
|
||||
export type TextureSpec<K extends TextureKind> = { type: 'texture', kind: K, format: TextureFormat, dataType: TextureType, filter: TextureFilter }
|
||||
@@ -180,7 +182,7 @@ export type InternalValues = Values<InternalSchema>
|
||||
|
||||
export const ColorSchema = {
|
||||
// aColor: AttributeSpec('float32', 3, 0), // TODO
|
||||
uColor: UniformSpec('v3', true),
|
||||
uColor: UniformSpec('v3', 'material'),
|
||||
uColorTexDim: UniformSpec('v2'),
|
||||
tColor: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
|
||||
dColorType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'groupInstance', 'vertex', 'vertexInstance']),
|
||||
@@ -190,7 +192,7 @@ export type ColorValues = Values<ColorSchema>
|
||||
|
||||
export const SizeSchema = {
|
||||
// aSize: AttributeSpec('float32', 1, 0), // TODO
|
||||
uSize: UniformSpec('f', true),
|
||||
uSize: UniformSpec('f', 'material'),
|
||||
uSizeTexDim: UniformSpec('v2'),
|
||||
tSize: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
|
||||
dSizeType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'groupInstance']),
|
||||
@@ -251,7 +253,7 @@ export const BaseSchema = {
|
||||
/**
|
||||
* final alpha, calculated as `values.alpha * state.alpha`
|
||||
*/
|
||||
uAlpha: UniformSpec('f', true),
|
||||
uAlpha: UniformSpec('f', 'material'),
|
||||
uVertexCount: UniformSpec('i'),
|
||||
uInstanceCount: UniformSpec('i'),
|
||||
uGroupCount: UniformSpec('i'),
|
||||
|
||||
@@ -13,7 +13,7 @@ import { ValueCell } from '../../mol-util';
|
||||
|
||||
export const TextureMeshSchema = {
|
||||
...BaseSchema,
|
||||
uGeoTexDim: UniformSpec('v2'),
|
||||
uGeoTexDim: UniformSpec('v2', 'buffered'),
|
||||
tPosition: TextureSpec('texture', 'rgb', 'float', 'nearest'),
|
||||
tGroup: TextureSpec('texture', 'alpha', 'float', 'nearest'),
|
||||
tNormal: TextureSpec('texture', 'rgb', 'float', 'nearest'),
|
||||
|
||||
@@ -6,7 +6,7 @@
|
||||
|
||||
import { Viewport } from '../mol-canvas3d/camera/util';
|
||||
import { ICamera } from '../mol-canvas3d/camera';
|
||||
import Scene from './scene';
|
||||
import { Scene } from './scene';
|
||||
import { WebGLContext } from './webgl/context';
|
||||
import { Mat4, Vec3, Vec4, Vec2, Quat } from '../mol-math/linear-algebra';
|
||||
import { GraphicsRenderable } from './renderable';
|
||||
@@ -678,4 +678,4 @@ namespace Renderer {
|
||||
}
|
||||
}
|
||||
|
||||
export default Renderer;
|
||||
export { Renderer };
|
||||
@@ -247,4 +247,4 @@ namespace Scene {
|
||||
}
|
||||
}
|
||||
|
||||
export default Scene;
|
||||
export { Scene };
|
||||
@@ -35,38 +35,38 @@ export interface ShaderCode {
|
||||
readonly outTypes: FragOutTypes
|
||||
}
|
||||
|
||||
import apply_fog from './shader/chunks/apply-fog.glsl';
|
||||
import apply_interior_color from './shader/chunks/apply-interior-color.glsl';
|
||||
import apply_light_color from './shader/chunks/apply-light-color.glsl';
|
||||
import apply_marker_color from './shader/chunks/apply-marker-color.glsl';
|
||||
import assign_clipping_varying from './shader/chunks/assign-clipping-varying.glsl';
|
||||
import assign_color_varying from './shader/chunks/assign-color-varying.glsl';
|
||||
import assign_group from './shader/chunks/assign-group.glsl';
|
||||
import assign_marker_varying from './shader/chunks/assign-marker-varying.glsl';
|
||||
import assign_material_color from './shader/chunks/assign-material-color.glsl';
|
||||
import assign_position from './shader/chunks/assign-position.glsl';
|
||||
import assign_size from './shader/chunks/assign-size.glsl';
|
||||
import check_picking_alpha from './shader/chunks/check-picking-alpha.glsl';
|
||||
import clip_instance from './shader/chunks/clip-instance.glsl';
|
||||
import clip_pixel from './shader/chunks/clip-pixel.glsl';
|
||||
import color_frag_params from './shader/chunks/color-frag-params.glsl';
|
||||
import color_vert_params from './shader/chunks/color-vert-params.glsl';
|
||||
import common_clip from './shader/chunks/common-clip.glsl';
|
||||
import common_frag_params from './shader/chunks/common-frag-params.glsl';
|
||||
import common_vert_params from './shader/chunks/common-vert-params.glsl';
|
||||
import common from './shader/chunks/common.glsl';
|
||||
import float_to_rgba from './shader/chunks/float-to-rgba.glsl';
|
||||
import light_frag_params from './shader/chunks/light-frag-params.glsl';
|
||||
import matrix_scale from './shader/chunks/matrix-scale.glsl';
|
||||
import normal_frag_params from './shader/chunks/normal-frag-params.glsl';
|
||||
import read_from_texture from './shader/chunks/read-from-texture.glsl';
|
||||
import rgba_to_float from './shader/chunks/rgba-to-float.glsl';
|
||||
import size_vert_params from './shader/chunks/size-vert-params.glsl';
|
||||
import texture3d_from_1d_trilinear from './shader/chunks/texture3d-from-1d-trilinear.glsl';
|
||||
import texture3d_from_2d_linear from './shader/chunks/texture3d-from-2d-linear.glsl';
|
||||
import texture3d_from_2d_nearest from './shader/chunks/texture3d-from-2d-nearest.glsl';
|
||||
import wboit_params from './shader/chunks/wboit-params.glsl';
|
||||
import wboit_write from './shader/chunks/wboit-write.glsl';
|
||||
import { apply_fog } from './shader/chunks/apply-fog.glsl';
|
||||
import { apply_interior_color } from './shader/chunks/apply-interior-color.glsl';
|
||||
import { apply_light_color } from './shader/chunks/apply-light-color.glsl';
|
||||
import { apply_marker_color } from './shader/chunks/apply-marker-color.glsl';
|
||||
import { assign_clipping_varying } from './shader/chunks/assign-clipping-varying.glsl';
|
||||
import { assign_color_varying } from './shader/chunks/assign-color-varying.glsl';
|
||||
import { assign_group } from './shader/chunks/assign-group.glsl';
|
||||
import { assign_marker_varying } from './shader/chunks/assign-marker-varying.glsl';
|
||||
import { assign_material_color } from './shader/chunks/assign-material-color.glsl';
|
||||
import { assign_position } from './shader/chunks/assign-position.glsl';
|
||||
import { assign_size } from './shader/chunks/assign-size.glsl';
|
||||
import { check_picking_alpha } from './shader/chunks/check-picking-alpha.glsl';
|
||||
import { clip_instance } from './shader/chunks/clip-instance.glsl';
|
||||
import { clip_pixel } from './shader/chunks/clip-pixel.glsl';
|
||||
import { color_frag_params } from './shader/chunks/color-frag-params.glsl';
|
||||
import { color_vert_params } from './shader/chunks/color-vert-params.glsl';
|
||||
import { common_clip } from './shader/chunks/common-clip.glsl';
|
||||
import { common_frag_params } from './shader/chunks/common-frag-params.glsl';
|
||||
import { common_vert_params } from './shader/chunks/common-vert-params.glsl';
|
||||
import { common } from './shader/chunks/common.glsl';
|
||||
import { float_to_rgba } from './shader/chunks/float-to-rgba.glsl';
|
||||
import { light_frag_params } from './shader/chunks/light-frag-params.glsl';
|
||||
import { matrix_scale } from './shader/chunks/matrix-scale.glsl';
|
||||
import { normal_frag_params } from './shader/chunks/normal-frag-params.glsl';
|
||||
import { read_from_texture } from './shader/chunks/read-from-texture.glsl';
|
||||
import { rgba_to_float } from './shader/chunks/rgba-to-float.glsl';
|
||||
import { size_vert_params } from './shader/chunks/size-vert-params.glsl';
|
||||
import { texture3d_from_1d_trilinear } from './shader/chunks/texture3d-from-1d-trilinear.glsl';
|
||||
import { texture3d_from_2d_linear } from './shader/chunks/texture3d-from-2d-linear.glsl';
|
||||
import { texture3d_from_2d_nearest } from './shader/chunks/texture3d-from-2d-nearest.glsl';
|
||||
import { wboit_params } from './shader/chunks/wboit-params.glsl';
|
||||
import { wboit_write } from './shader/chunks/wboit-write.glsl';
|
||||
|
||||
const ShaderChunks: { [k: string]: string } = {
|
||||
apply_fog,
|
||||
@@ -127,36 +127,36 @@ export function ShaderCode(name: string, vert: string, frag: string, extensions:
|
||||
|
||||
// Note: `drawBuffers` need to be 'optional' for wboit
|
||||
|
||||
import points_vert from './shader/points.vert';
|
||||
import points_frag from './shader/points.frag';
|
||||
import { points_vert } from './shader/points.vert';
|
||||
import { points_frag } from './shader/points.frag';
|
||||
export const PointsShaderCode = ShaderCode('points', points_vert, points_frag, { drawBuffers: 'optional' });
|
||||
|
||||
import spheres_vert from './shader/spheres.vert';
|
||||
import spheres_frag from './shader/spheres.frag';
|
||||
import { spheres_vert } from './shader/spheres.vert';
|
||||
import { spheres_frag } from './shader/spheres.frag';
|
||||
export const SpheresShaderCode = ShaderCode('spheres', spheres_vert, spheres_frag, { fragDepth: 'required', drawBuffers: 'optional' });
|
||||
|
||||
import cylinders_vert from './shader/cylinders.vert';
|
||||
import cylinders_frag from './shader/cylinders.frag';
|
||||
import { cylinders_vert } from './shader/cylinders.vert';
|
||||
import { cylinders_frag } from './shader/cylinders.frag';
|
||||
export const CylindersShaderCode = ShaderCode('cylinders', cylinders_vert, cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' });
|
||||
|
||||
import text_vert from './shader/text.vert';
|
||||
import text_frag from './shader/text.frag';
|
||||
import { text_vert }from './shader/text.vert';
|
||||
import { text_frag } from './shader/text.frag';
|
||||
export const TextShaderCode = ShaderCode('text', text_vert, text_frag, { standardDerivatives: 'required', drawBuffers: 'optional' });
|
||||
|
||||
import lines_vert from './shader/lines.vert';
|
||||
import lines_frag from './shader/lines.frag';
|
||||
import { lines_vert } from './shader/lines.vert';
|
||||
import { lines_frag } from './shader/lines.frag';
|
||||
export const LinesShaderCode = ShaderCode('lines', lines_vert, lines_frag, { drawBuffers: 'optional' });
|
||||
|
||||
import mesh_vert from './shader/mesh.vert';
|
||||
import mesh_frag from './shader/mesh.frag';
|
||||
import { mesh_vert } from './shader/mesh.vert';
|
||||
import { mesh_frag } from './shader/mesh.frag';
|
||||
export const MeshShaderCode = ShaderCode('mesh', mesh_vert, mesh_frag, { standardDerivatives: 'optional', drawBuffers: 'optional' });
|
||||
|
||||
import direct_volume_vert from './shader/direct-volume.vert';
|
||||
import direct_volume_frag from './shader/direct-volume.frag';
|
||||
export const DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert, direct_volume_frag, { fragDepth: 'optional', drawBuffers: 'optional' });
|
||||
import { directVolume_vert } from './shader/direct-volume.vert';
|
||||
import { directVolume_frag } from './shader/direct-volume.frag';
|
||||
export const DirectVolumeShaderCode = ShaderCode('direct-volume', directVolume_vert, directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' });
|
||||
|
||||
import image_vert from './shader/image.vert';
|
||||
import image_frag from './shader/image.frag';
|
||||
import { image_vert } from './shader/image.vert';
|
||||
import { image_frag } from './shader/image.frag';
|
||||
export const ImageShaderCode = ShaderCode('image', image_vert, image_frag, { drawBuffers: 'optional' });
|
||||
|
||||
//
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const apply_fog = `
|
||||
float viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);
|
||||
float fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));
|
||||
float fogAlpha = (1.0 - fogFactor) * gl_FragColor.a;
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const apply_interior_color = `
|
||||
if (interior) {
|
||||
if (uInteriorColorFlag) {
|
||||
gl_FragColor.rgb = uInteriorColor;
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
* which under the MIT License, Copyright © 2010-2019 three.js authors
|
||||
*/
|
||||
|
||||
export default `
|
||||
export const apply_light_color = `
|
||||
// inputs
|
||||
// - vec4 material
|
||||
// - vec3 vViewPosition
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const apply_marker_color = `
|
||||
float marker = floor(vMarker * 255.0 + 0.5); // rounding required to work on some cards on win
|
||||
if (marker > 0.1) {
|
||||
if (intMod(marker, 2.0) > 0.1) {
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_clipping_varying = `
|
||||
#if dClipObjectCount != 0 && defined(dClipping)
|
||||
vClipping = readFromTexture(tClipping, aInstance * float(uGroupCount) + group, uClippingTexDim).a;
|
||||
#endif
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_color_varying = `
|
||||
#if defined(dRenderVariant_color)
|
||||
#if defined(dColorType_attribute)
|
||||
vColor.rgb = aColor;
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_group = `
|
||||
#ifdef dGeoTexture
|
||||
float group = decodeFloatRGB(readFromTexture(tGroup, VertexID, uGeoTexDim).rgb);
|
||||
#else
|
||||
|
||||
@@ -1,3 +1,3 @@
|
||||
export default `
|
||||
export const assign_marker_varying = `
|
||||
vMarker = readFromTexture(tMarker, aInstance * float(uGroupCount) + group, uMarkerTexDim).a;
|
||||
`;
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_material_color = `
|
||||
#if defined(dRenderVariant_color)
|
||||
#if defined(dColorType_uniform)
|
||||
vec4 material = vec4(uColor, uAlpha);
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_position = `
|
||||
mat4 model = uModel * aTransform;
|
||||
mat4 modelView = uView * model;
|
||||
#ifdef dGeoTexture
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const assign_size = `
|
||||
#if defined(dSizeType_uniform)
|
||||
float size = uSize;
|
||||
#elif defined(dSizeType_attribute)
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export default `
|
||||
export const check_picking_alpha = `
|
||||
float viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);
|
||||
float fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));
|
||||
float alpha = (1.0 - fogFactor) * uAlpha;
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user