chem_comp_bond and struct_conn to mmcif exporter

+ fix argparse config for Model/Volume servers

CHANGELOG.md

@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v2.3.1] - 2021-09-28
+
 - Add Charmm saccharide names
 - Treat missing occupancy column as occupany of 1
 - Fix line shader not accounting for aspect ratio
@@ -15,6 +17,8 @@ Note that since we don't clearly distinguish between a public and private interf
     - Set ``pointSizeAttenuation`` to false by default
     - Set ``sizeTheme`` to ``uniform`` by default
 - Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
+- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
+- Model and VolumeServer: fix argparse config
 
 ## [v2.3.0] - 2021-09-06
 

package-lock.json

@@ -5,7 +5,6 @@
   "requires": true,
   "packages": {
     "": {
-      "name": "molstar",
       "version": "2.3.0",
       "license": "MIT",
       "dependencies": {
@@ -4314,6 +4313,7 @@
       "dependencies": {
         "anymatch": "~3.1.2",
         "braces": "~3.0.2",
+        "fsevents": "~2.3.2",
         "glob-parent": "~5.1.2",
         "is-binary-path": "~2.1.0",
         "is-glob": "~4.0.1",
@@ -5627,7 +5627,8 @@
         "esprima": "^4.0.1",
         "estraverse": "^5.2.0",
         "esutils": "^2.0.2",
-        "optionator": "^0.8.1"
+        "optionator": "^0.8.1",
+        "source-map": "~0.6.1"
       },
       "bin": {
         "escodegen": "bin/escodegen.js",
@@ -8250,6 +8251,7 @@
         "@types/node": "*",
         "anymatch": "^3.0.3",
         "fb-watchman": "^2.0.0",
+        "fsevents": "^2.3.2",
         "graceful-fs": "^4.2.4",
         "jest-regex-util": "^27.0.6",
         "jest-serializer": "^27.0.6",
@@ -8917,6 +8919,7 @@
       "integrity": "sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==",
       "dev": true,
       "dependencies": {
+        "graceful-fs": "^4.1.6",
         "universalify": "^2.0.0"
       },
       "optionalDependencies": {

src/mol-model/structure/export/categories/misc.ts

@@ -22,6 +22,18 @@ export const _chem_comp: CifCategory<CifExportContext> = {
     }
 };
 
+export const _chem_comp_bond: CifCategory<CifExportContext> = {
+    name: 'chem_comp_bond',
+    instance({ firstModel, structures, cache }) {
+        const chem_comp_bond = getModelMmCifCategory(structures[0].model, 'chem_comp_bond');
+        if (!chem_comp_bond) return CifCategory.Empty;
+        const { comp_id } = chem_comp_bond;
+        const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNamesFromStructures(structures));
+        const indices = Column.indicesOf(comp_id, id => names.has(id));
+        return CifCategory.ofTable(chem_comp_bond, indices);
+    }
+};
+
 export const _pdbx_chem_comp_identifier: CifCategory<CifExportContext> = {
     name: 'pdbx_chem_comp_identifier',
     instance({ firstModel, structures, cache }) {

src/mol-model/structure/export/mmcif.ts

@@ -11,7 +11,7 @@ import { Structure } from '../structure';
 import { _atom_site } from './categories/atom_site';
 import CifCategory = CifWriter.Category
 import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
-import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
+import { _chem_comp, _chem_comp_bond, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
 import { Model } from '../model';
 import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
 import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
@@ -81,9 +81,12 @@ const Categories = [
     copy_mmCif_category('pdbx_entity_branch_link'),
     copy_mmCif_category('pdbx_branch_scheme'),
 
+    // Struct conn
+    copy_mmCif_category('struct_conn'),
+
     // Misc
-    // TODO: filter for actual present residues?
     _chem_comp,
+    _chem_comp_bond,
     _pdbx_chem_comp_identifier,
     copy_mmCif_category('atom_sites'),
 

src/servers/model/CHANGELOG.md

@@ -1,3 +1,6 @@
+# 0.9.8
+* fix support for chem_comp_bond and struct_conn categories
+
 # 0.9.7
 * add Surrounding Ligands query
 

src/servers/model/config.ts

@@ -229,10 +229,11 @@ function addJsonConfigArgs(parser: argparse.ArgumentParser) {
             'JSON config file path',
             'If a property is not specified, cmd line param/OS variable/default value are used.'
         ].join('\n'),
-        required: false
+        required: false,
+        action: 'store_true'
     });
-    parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
-    parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+    parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, action: 'store_true' });
+    parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, action: 'store_true' });
 }
 
 function setConfig(config: ModelServerConfig) {
@@ -271,7 +272,7 @@ function parseConfigArguments() {
 export function configureServer() {
     const config = parseConfigArguments();
 
-    if (config.cfgTemplate !== null) {
+    if (!!config.cfgTemplate) {
         console.log(JSON.stringify(ModelServerConfigTemplate, null, 2));
         process.exit(0);
     }
@@ -284,7 +285,7 @@ export function configureServer() {
             setConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (!!config.printCfg) {
             console.log(JSON.stringify(ModelServerConfig, null, 2));
             process.exit(0);
         }

src/servers/model/version.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export const VERSION = '0.9.7';
+export const VERSION = '0.9.8';

src/servers/volume/config.ts

@@ -89,10 +89,11 @@ function addJsonConfigArgs(parser: argparse.ArgumentParser) {
             'JSON config file path',
             'If a property is not specified, cmd line param/OS variable/default value are used.'
         ].join('\n'),
-        required: false
+        required: false,
+        action: 'store_true'
     });
-    parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
-    parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+    parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, action: 'store_true' });
+    parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, action: 'store_true' });
 }
 
 export interface ServerJsonConfig {
@@ -165,7 +166,7 @@ export function configureServer() {
     addLimitsArgs(parser);
     const config = parser.parse_args() as FullServerConfig & ServerJsonConfig;
 
-    if (config.cfgTemplate !== null) {
+    if (!!config.cfgTemplate) {
         console.log(JSON.stringify(ServerConfigTemplate, null, 2));
         process.exit(0);
     }
@@ -178,7 +179,7 @@ export function configureServer() {
             setConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (config.printCfg) {
             console.log(JSON.stringify({ ...ServerConfig, ...LimitsConfig }, null, 2));
             process.exit(0);
         }