npm - molstar - Versions diffs - 3.4.0 → 3.6.1 - Mend

molstar 3.4.0 → 3.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (401) hide show

package/build/viewer/molstar.js.LICENSE.txt CHANGED Viewed

@@ -1,9 +1,3 @@
-/*
-object-assign
-(c) Sindre Sorhus
-@license MIT
-*/
 /*!
  * The buffer module from node.js, for the browser.
  *
@@ -30,8 +24,9 @@ PERFORMANCE OF THIS SOFTWARE.
 /*! safe-buffer. MIT License. Feross Aboukhadijeh <https://feross.org/opensource> */
-/** @license React v0.20.2
- * scheduler.production.min.js
+/**
+ * @license React
+ * react-dom.production.min.js
  *
  * Copyright (c) Facebook, Inc. and its affiliates.
  *
@@ -39,8 +34,9 @@ PERFORMANCE OF THIS SOFTWARE.
  * LICENSE file in the root directory of this source tree.
  */
-/** @license React v17.0.2
- * react-dom.production.min.js
+/**
+ * @license React
+ * react-jsx-runtime.production.min.js
  *
  * Copyright (c) Facebook, Inc. and its affiliates.
  *
@@ -48,8 +44,9 @@ PERFORMANCE OF THIS SOFTWARE.
  * LICENSE file in the root directory of this source tree.
  */
-/** @license React v17.0.2
- * react-jsx-runtime.production.min.js
+/**
+ * @license React
+ * react.production.min.js
  *
  * Copyright (c) Facebook, Inc. and its affiliates.
  *
@@ -57,8 +54,9 @@ PERFORMANCE OF THIS SOFTWARE.
  * LICENSE file in the root directory of this source tree.
  */
-/** @license React v17.0.2
- * react.production.min.js
+/**
+ * @license React
+ * scheduler.production.min.js
  *
  * Copyright (c) Facebook, Inc. and its affiliates.
  *

package/lib/apps/docking-viewer/index.html CHANGED Viewed

@@ -1,37 +1,37 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <title>Mol* Docking Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
-            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
-            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
-                viewer.loadStructuresFromUrlsAndMerge([
-                    { url: pdbqt, format: 'pdbqt' },
-                    { url: mol2, format: 'mol2' }
-                ]);
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Docking Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
+            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
+            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
+                viewer.loadStructuresFromUrlsAndMerge([
+                    { url: pdbqt, format: 'pdbqt' },
+                    { url: mol2, format: 'mol2' }
+                ]);
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/docking-viewer/index.js CHANGED Viewed

@@ -7,7 +7,7 @@
 import { __assign, __awaiter, __generator } from "tslib";
 import { Structure } from '../../mol-model/structure';
 import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginBehaviors } from '../../mol-plugin/behavior';
 import { PluginCommands } from '../../mol-plugin/commands';

package/lib/apps/viewer/app.js CHANGED Viewed

@@ -25,7 +25,7 @@ import { PresetStructureRepresentations, StructureRepresentationPresetProvider }
 import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
-import { createPluginUI } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui/react18';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';

package/lib/apps/viewer/embedded.html CHANGED Viewed

@@ -1,44 +1,44 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Embedded Mol* Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            molstar.Viewer.create('app', {
-                layoutIsExpanded: true,
-                layoutShowControls: false,
-                layoutShowRemoteState: false,
-                layoutShowSequence: true,
-                layoutShowLog: false,
-                layoutShowLeftPanel: true,
-                viewportShowExpand: true,
-                viewportShowSelectionMode: false,
-                viewportShowAnimation: false,
-                pdbProvider: 'rcsb',
-                emdbProvider: 'rcsb',
-            }).then(viewer => {
-                viewer.loadPdb('7bv2');
-                viewer.loadEmdb('EMD-30210', { detail: 6 });
-                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/index.html CHANGED Viewed

@@ -1,107 +1,107 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Mol* Viewer</title>
-        <style>
-            * {
-                margin: 0;
-                padding: 0;
-                box-sizing: border-box;
-            }
-            html, body {
-                width: 100%;
-                height: 100%;
-                overflow: hidden;
-            }
-            hr {
-                margin: 10px;
-            }
-            h1, h2, h3, h4, h5 {
-                margin-top: 5px;
-                margin-bottom: 3px;
-            }
-            button {
-                padding: 2px;
-            }
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
-            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
-            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
-            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
-            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
-            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
-            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
-            var pickScale = getParam('pick-scale', '[^&]+').trim();
-            var pickPadding = getParam('pick-padding', '[^&]+').trim();
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
-            molstar.Viewer.create('app', {
-                layoutShowControls: !hideControls,
-                viewportShowExpand: false,
-                collapseLeftPanel: collapseLeftPanel,
-                pdbProvider: pdbProvider || 'pdbe',
-                emdbProvider: emdbProvider || 'pdbe',
-                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
-                    ? 'https://maps.rcsb.org'
-                    : 'https://www.ebi.ac.uk/pdbe/densities',
-                pixelScale: parseFloat(pixelScale) || 1,
-                pickScale: parseFloat(pickScale) || 0.25,
-                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
-                preferWebgl1: preferWebgl1,
-            }).then(viewer => {
-                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
-                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
-                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
-                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
-                var structureUrl = getParam('structure-url', '[^&]+').trim();
-                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
-                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
-                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
-                var pdb = getParam('pdb', '[^&]+').trim();
-                if (pdb) viewer.loadPdb(pdb);
-                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-                if (pdbDev) viewer.loadPdbDev(pdbDev);
-                var emdb = getParam('emdb', '[^&]+').trim();
-                if (emdb) viewer.loadEmdb(emdb);
-                var afdb = getParam('afdb', '[^&]+').trim();
-                if (afdb) viewer.loadAlphaFoldDb(afdb);
-                var modelArchive = getParam('model-archive', '[^&]+').trim();
-                if (modelArchive) viewer.loadModelArchive(modelArchive);
-            });
-        </script>
-        <!-- __MOLSTAR_ANALYTICS__ -->
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Viewer</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            html, body {
+                width: 100%;
+                height: 100%;
+                overflow: hidden;
+            }
+            hr {
+                margin: 10px;
+            }
+            h1, h2, h3, h4, h5 {
+                margin-top: 5px;
+                margin-bottom: 3px;
+            }
+            button {
+                padding: 2px;
+            }
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            molstar.Viewer.create('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
+                preferWebgl1: preferWebgl1,
+            }).then(viewer => {
+                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+                var structureUrl = getParam('structure-url', '[^&]+').trim();
+                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) viewer.loadPdb(pdb);
+                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
+                var emdb = getParam('emdb', '[^&]+').trim();
+                if (emdb) viewer.loadEmdb(emdb);
+                var afdb = getParam('afdb', '[^&]+').trim();
+                if (afdb) viewer.loadAlphaFoldDb(afdb);
+                var modelArchive = getParam('model-archive', '[^&]+').trim();
+                if (modelArchive) viewer.loadModelArchive(modelArchive);
+            });
+        </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
+    </body>
 </html>

package/lib/cli/chem-comp-dict/util.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -26,12 +26,12 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -47,9 +47,9 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -57,13 +57,13 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };
@@ -84,7 +84,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -94,12 +94,12 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -115,9 +115,9 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -125,13 +125,13 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };

package/lib/cli/cif2bcif/converter.js CHANGED Viewed

@@ -96,7 +96,7 @@ function classify(name, field) {
 export function convert(path, asText, hints, filter) {
     var _this = this;
     if (asText === void 0) { asText = false; }
-    return Task.create('BinaryCIF', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+    return Task.create('Convert CIF', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
         var encodingProvider, cif, encoder, maxProgress, _i, _a, b, _b, _c, c, current, _d, _e, b, _f, _g, c, cat, fields, _h, _j, f, ret;
         return __generator(this, function (_k) {
             switch (_k.label) {

package/lib/cli/cif2bcif/index.js CHANGED Viewed

@@ -20,7 +20,7 @@ function process(srcPath, outPath, configPath, filterPath) {
                 case 0:
                     config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
                     filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
-                    return [4 /*yield*/, convert(srcPath, false, config, filter)];
+                    return [4 /*yield*/, convert(srcPath, srcPath.toLowerCase().indexOf('.bcif') > 0, config, filter)];
                 case 1:
                     res = _a.sent();
                     return [4 /*yield*/, write(outPath, res)];
@@ -56,13 +56,13 @@ function run(args) {
 }
 var parser = new argparse.ArgumentParser({
     add_help: true,
-    description: 'Convert any CIF file to a BCIF file'
+    description: 'Convert any BCIF file to a CIF file or vice versa'
 });
 parser.add_argument('src', {
-    help: 'Source CIF path'
+    help: 'Source file path'
 });
 parser.add_argument('out', {
-    help: 'Output BCIF path'
+    help: 'Output file path'
 });
 parser.add_argument('-c', '--config', {
     help: 'Optional encoding strategy/precision config path',

package/lib/cli/cifschema/util/cif-dic.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */