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Skipping atoms which are not on the ligand (#249)
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* Update package.json

- updated version number to 0.9.69

* - prelim changes

* #557 Bug? Snapshot doesn't restore precise RHS tab

* #571 [L] toggle not restored from snapshot for things on Selected Compounds tab

* - implemented first phase of discourse integration

* Squashed commit of the following:

commit 431c372
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Wed Mar 24 15:56:39 2021 +0100

    - implemented first phase of discourse integration

commit 103da7e
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Thu Mar 11 10:50:30 2021 +0100

    - prelim changes

* - updated version number to 0.10.1

* Squashed commit of the following:

commit 5761def
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Wed Feb 3 14:23:02 2021 +0100

    Fixed layout and imports

commit d9b5895
Merge: 717ad54 083cc6d
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Wed Feb 3 13:55:03 2021 +0100

    Merge branch 'allfunctionality' into #487

commit 717ad54
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Wed Feb 3 13:54:33 2021 +0100

    Removed unnecessary parts

commit 6c23110
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Wed Feb 3 13:36:29 2021 +0100

    Fixed undo

commit 19f839c
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Mon Feb 1 15:31:13 2021 +0100

    Fixed button history tracking

commit bf7b8a8
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Mon Feb 1 14:15:34 2021 +0100

    Replaced throttle with debounce for nglView tracking

commit 57b71e0
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Mon Feb 1 12:58:06 2021 +0100

    Clear history on project change

commit 419c268
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Mon Feb 1 12:10:50 2021 +0100

    Separate orientation actions

commit 272c265
Merge: f844087 bef6400
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Mon Feb 1 10:34:26 2021 +0100

    Merge branch 'allfunctionality' into #487

commit f844087
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Thu Jan 21 13:52:19 2021 +0100

    Ctreated temporary buttons

commit 9b8a2ac
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Thu Jan 21 11:54:52 2021 +0100

    Tidying up

commit cb6c477
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Thu Jan 21 11:25:23 2021 +0100

    Change ngl view on undo/redo

commit edfb571
Author: ag-m2ms <anton.gasperak@m2ms.sk>
Date:   Wed Jan 20 16:37:42 2021 +0100

    Initial implementation

* #593 Electron Density - D button behaviour

* #593 Electron Density - D button behaviour

* - implemented modal window for discourse errors

* - updated version number to 0.10.2

* - slightly updated error description

* - loading discourse links in synchronous manner to avoid net::ERR_INSUFFICIENT_RESOURCES

* - updated version number to 0.10.3

* - implemented "lazy" handling of the Discourse

* Squashed commit of the following:

commit b9205dd
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Mon Mar 29 15:13:32 2021 +0200

    - implemented "lazy" handling of the Discourse

* - updated version number to 0.10.4

* #595 Eletron Density - Settings and control panel

* - hide link to project icon if no project is loaded

* - updated version number to 0.10.5

* - updated error message

* #595 Eletron Density - Settings and control panel

* - used icon button instead of link in the target list because it behaved differently in test env from behavior in local env

* - updated version number to 0.10.6

* #595 Eletron Density - Settings and control panel

* - fixed issue when creating project from the preview and the first post for the first snapshot was not created

* - updated version number to 0.10.7

* - visual improvements

* - updated version number to 0.10.8

* #596 Atom Quality - Q button behaviour

* - visual improvements

* - updated version number to 0.10.9

* #599 Atom Quality - Bad atoms rendering

* #599 Atom Quality - Bad atoms rendering

* #599 Atom Quality - Bad atoms rendering

* #598 Atom Quality - Bad atoms identification

* #597 Atom Quality - Warning icon behaviour and representation change

* #597 Atom Quality - Warning icon behaviour and representation change

* - fix (maybe) for that sometimes a discourse post was attempted before the project and/or snapshot were created

* - updated version number to 0.10.10

* - fixed problem where snapshot post was attempted before project post was completed which caused that the snapshot post was never created

* - updated version number to 0.10.11

* #597 Atom Quality - Warning icon behaviour and representation change

* #594 Electron Density - Settings read file

* #594 Electron Density - Settings read file

* - fixed saving of the session actions

* - updated version number to 0.10.12

* - checkpoint

* - updated version number to 0.10.13

* #602 Snapshot tree and discourse posts

* #602 Snapshot tree and discourse posts

* #594 Electron Density - Settings read file

* #594 Electron Density - Settings read file

* - create discourse topic and post are disabled when creation process is ongoing
- if discourse user doesn't exists the notice is displayed

* - changed version number to 0.10.14

* - open discourse link in the new tab

* - updated version number to 0.10.15

* - minor fixes

* - updated version number to 0.10.16

* - fixed #609

* - updated version number to 0.10.17

* #594 Electron Density - Settings read file

* #594 Electron Density - Settings read file

* #594 Electron Density - Settings read file

* - updated version number to 0.10.18

* Squashed commit of the following:

commit 3361b39
Merge: 7699a37 eb1ed3b
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Thu May 6 09:03:24 2021 +0200

    Merge remote-tracking branch 'upstream/master'

commit eb1ed3b
Merge: 123071b 2d42a57
Author: Rachael Skyner <reskyner@googlemail.com>
Date:   Wed May 5 15:06:45 2021 +0100

    Merge pull request #241 from alanbchristie/master

    Supports different GitHub and Docker Hub Account names in downstream Actions

commit 2d42a57
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Wed May 5 14:38:59 2021 +0100

    - Adds STACK_GITHUB_NAMESPACE (differs from STACK_GITHUB_NAMESPACE)

commit 1c13499
Author: Alan B. Christie <alan@kaitak.org>
Date:   Wed May 5 10:30:58 2021 +0100

    Update README.md

    To trigger build

commit 7699a37
Merge: 22a978c 123071b
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Wed May 5 10:51:59 2021 +0200

    Merge remote-tracking branch 'upstream/master'

commit 123071b
Author: Rachael Skyner <reskyner@googlemail.com>
Date:   Tue Apr 27 13:50:47 2021 +0100

    Delete no.travis.yml

commit 53659c7
Author: Rachael Skyner <reskyner@googlemail.com>
Date:   Tue Apr 27 13:50:36 2021 +0100

    Update README.md

commit 5f043de
Merge: 8740211 2c8351e
Author: Rachael Skyner <reskyner@googlemail.com>
Date:   Tue Apr 27 11:46:13 2021 +0100

    Merge pull request #240 from InformaticsMatters/master

    Switch form Travis to GitHub Actions

commit 8740211
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Wed Apr 21 14:38:15 2021 +0200

    Implementation of discourse  (#239)

    * Update package.json

    - updated version number to 0.9.69

    * - prelim changes

    * #557 Bug? Snapshot doesn't restore precise RHS tab

    * #571 [L] toggle not restored from snapshot for things on Selected Compounds tab

    * - implemented first phase of discourse integration

    * Squashed commit of the following:

    commit 431c372
    Author: Boris Kovar <boris.kovar@m2ms.sk>
    Date:   Wed Mar 24 15:56:39 2021 +0100

        - implemented first phase of discourse integration

    commit 103da7e
    Author: Boris Kovar <boris.kovar@m2ms.sk>
    Date:   Thu Mar 11 10:50:30 2021 +0100

        - prelim changes

    * - updated version number to 0.10.1

    * Squashed commit of the following:

    commit 5761def
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Wed Feb 3 14:23:02 2021 +0100

        Fixed layout and imports

    commit d9b5895
    Merge: 717ad54 083cc6d
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Wed Feb 3 13:55:03 2021 +0100

        Merge branch 'allfunctionality' into #487

    commit 717ad54
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Wed Feb 3 13:54:33 2021 +0100

        Removed unnecessary parts

    commit 6c23110
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Wed Feb 3 13:36:29 2021 +0100

        Fixed undo

    commit 19f839c
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Mon Feb 1 15:31:13 2021 +0100

        Fixed button history tracking

    commit bf7b8a8
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Mon Feb 1 14:15:34 2021 +0100

        Replaced throttle with debounce for nglView tracking

    commit 57b71e0
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Mon Feb 1 12:58:06 2021 +0100

        Clear history on project change

    commit 419c268
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Mon Feb 1 12:10:50 2021 +0100

        Separate orientation actions

    commit 272c265
    Merge: f844087 bef6400
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Mon Feb 1 10:34:26 2021 +0100

        Merge branch 'allfunctionality' into #487

    commit f844087
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Thu Jan 21 13:52:19 2021 +0100

        Ctreated temporary buttons

    commit 9b8a2ac
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Thu Jan 21 11:54:52 2021 +0100

        Tidying up

    commit cb6c477
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Thu Jan 21 11:25:23 2021 +0100

        Change ngl view on undo/redo

    commit edfb571
    Author: ag-m2ms <anton.gasperak@m2ms.sk>
    Date:   Wed Jan 20 16:37:42 2021 +0100

        Initial implementation

    * - implemented modal window for discourse errors

    * - updated version number to 0.10.2

    * - slightly updated error description

    * - loading discourse links in synchronous manner to avoid net::ERR_INSUFFICIENT_RESOURCES

    * - updated version number to 0.10.3

    * - implemented "lazy" handling of the Discourse

    * Squashed commit of the following:

    commit b9205dd
    Author: Boris Kovar <boris.kovar@m2ms.sk>
    Date:   Mon Mar 29 15:13:32 2021 +0200

        - implemented "lazy" handling of the Discourse

    * - updated version number to 0.10.4

    * - hide link to project icon if no project is loaded

    * - updated version number to 0.10.5

    * - updated error message

    * - used icon button instead of link in the target list because it behaved differently in test env from behavior in local env

    * - updated version number to 0.10.6

    * - fixed issue when creating project from the preview and the first post for the first snapshot was not created

    * - updated version number to 0.10.7

    * - visual improvements

    * - updated version number to 0.10.8

    * - visual improvements

    * - updated version number to 0.10.9

    * - fix (maybe) for that sometimes a discourse post was attempted before the project and/or snapshot were created

    * - updated version number to 0.10.10

    * - fixed problem where snapshot post was attempted before project post was completed which caused that the snapshot post was never created

    * - updated version number to 0.10.11

    * - fixed saving of the session actions

    * - updated version number to 0.10.12

    * - checkpoint

    * - updated version number to 0.10.13

    * #602 Snapshot tree and discourse posts

    * #602 Snapshot tree and discourse posts

    * - create discourse topic and post are disabled when creation process is ongoing
    - if discourse user doesn't exists the notice is displayed

    * - changed version number to 0.10.14

    * - open discourse link in the new tab

    * - updated version number to 0.10.15

    * - minor fixes

    * - updated version number to 0.10.16

    * - fixed #609

    * - updated version number to 0.10.17

    Co-authored-by: Adriána Kohanová <adriana.kohanova@m2ms.sk>
    Co-authored-by: Adriána Kurillová <adriana.kurillova@m2ms.sk>

commit 2c8351e
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Tue Mar 23 00:01:22 2021 +0000

    - Use of production CI action

commit dd4ead7
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Mon Mar 22 18:36:18 2021 +0000

    - Fix for stack ref

commit 7191ae3
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Mon Mar 22 18:30:02 2021 +0000

    - Another trigger fix

commit 7f193ee
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Mon Mar 22 18:18:01 2021 +0000

    - Fix trigger logic

commit fb834c3
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Mon Mar 22 18:08:10 2021 +0000

    - Experiment with stack trigger

commit daca6eb
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Thu Mar 18 16:57:38 2021 +0000

    - Updates build badge

commit c4e8f99
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Thu Mar 18 16:54:24 2021 +0000

    - Attempt to fix action

commit c12f443
Author: Alan Christie <alan.christie@matildapeak.com>
Date:   Thu Mar 18 16:38:02 2021 +0000

    - Adds Action (disables Travis)

commit 56c0372
Merge: 663dfeb 0c9816f
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Wed Mar 3 12:17:55 2021 +0100

    Merge pull request #237 from m2ms/allfunctionality

    - #577 - implemented csv changes

commit 663dfeb
Merge: ca4517d 0c2cc4e
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Tue Mar 2 14:56:06 2021 +0100

    Merge pull request #236 from m2ms/allfunctionality

    Allfunctionality

commit ca4517d
Merge: 8b125d3 3c67748
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Thu Feb 25 16:10:30 2021 +0100

    Merge pull request #234 from m2ms/allfunctionality

    Allfunctionality

commit 8b125d3
Merge: bc9480d 8d8a70a
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Thu Feb 18 10:11:03 2021 +0100

    Merge pull request #233 from m2ms/allfunctionality

    Allfunctionality

commit bc9480d
Merge: 8b71b72 d46c222
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Wed Feb 17 10:45:51 2021 +0100

    Merge pull request #232 from m2ms/allfunctionality

    Allfunctionality

commit 8b71b72
Merge: 6d6e921 6b12b03
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Wed Feb 10 14:50:52 2021 +0100

    Merge pull request #231 from m2ms/allfunctionality

    Allfunctionality

* - updated version number to 0.10.19

* - checkpoint

* - checkpoint

* - maps stuff done

* - minor fixes

* - fixes for density maps

* - fixed saving

* - updated version number to 0.10.23

* - updated version number to 0.10.24

* Squashed commit of the following:

commit 2a66726
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Thu Jul 8 10:03:20 2021 +0200

    - fix for empty compound set

commit a88c144
Author: boriskovar-m2ms <boris.kovar@m2ms.sk>
Date:   Mon May 17 08:49:14 2021 +0200

    Update build-main.yaml

    got rid of scheduled rebuild because it's messing up data

commit 3361b39
Merge: 7699a37 eb1ed3b
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Thu May 6 09:03:24 2021 +0200

    Merge remote-tracking branch 'upstream/master'

commit 7699a37
Merge: 22a978c 123071b
Author: Boris Kovar <boris.kovar@m2ms.sk>
Date:   Wed May 5 10:51:59 2021 +0200

    Merge remote-tracking branch 'upstream/master'

* - bumped version to 0.10.25

* - double bond rendering for atom quality
- bumped version number to 0.10.26

* - added color mappings for AS, SE, I
- bumped version number to 0.10.27

* - atoms which are not on the ligand are skipped during rendering
- bumped version to 0.10.28

Co-authored-by: Adriána Kohanová <adriana.kohanova@m2ms.sk>
Co-authored-by: Adriána Kurillová <adriana.kurillova@m2ms.sk>
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1 parent b9762e0 commit 29ba7b9
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84 changes: 44 additions & 40 deletions js/components/nglView/renderingHelpers.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,31 +78,33 @@ export function loadQualityFromFile(stage, file, quality, object_name, orientati

let element1 = comp.object.atomMap.list[num1].element;
let element2 = comp.object.atomMap.list[num2].element;
let a1c = element1 === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element1];
let a2c = element2 === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element2];
let alternativeColor = ELEMENT_COLORS.ALTERNATIVE;
let bond_label = 'bond: '.concat(atom_info_array[num1], '-', atom_info_array[num2]);

let bond_size = 0.05 / (0.5 * bondorder);
if (bondorder === 1) {
drawStripyBond(acoord, bcoord, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
} else if (bondorder === 2) {
let acoord1 = [acoord[0] - vShift.x, acoord[1] - vShift.y, acoord[2] - vShift.z];
let bcoord1 = [bcoord[0] - vShift.x, bcoord[1] - vShift.y, bcoord[2] - vShift.z];
let acoord2 = [acoord[0] + vShift.x, acoord[1] + vShift.y, acoord[2] + vShift.z];
let bcoord2 = [bcoord[0] + vShift.x, bcoord[1] + vShift.y, bcoord[2] + vShift.z];
// draw bonds
drawStripyBond(acoord1, bcoord1, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord2, bcoord2, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
} else if (bondorder === 3) {
let acoord1 = [acoord[0] - vShift.x, acoord[1] - vShift.y, acoord[2] - vShift.z];
let bcoord1 = [bcoord[0] - vShift.x, bcoord[1] - vShift.y, bcoord[2] - vShift.z];
let acoord2 = [acoord[0] + vShift.x, acoord[1] + vShift.y, acoord[2] + vShift.z];
let bcoord2 = [bcoord[0] + vShift.x, bcoord[1] + vShift.y, bcoord[2] + vShift.z];
// draw bonds
drawStripyBond(acoord, bcoord, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord1, bcoord1, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord2, bcoord2, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
if (element1 && element2) {
let a1c = element1 === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element1];
let a2c = element2 === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element2];
let alternativeColor = ELEMENT_COLORS.ALTERNATIVE;
let bond_label = 'bond: '.concat(atom_info_array[num1], '-', atom_info_array[num2]);

let bond_size = 0.05 / (0.5 * bondorder);
if (bondorder === 1) {
drawStripyBond(acoord, bcoord, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
} else if (bondorder === 2) {
let acoord1 = [acoord[0] - vShift.x, acoord[1] - vShift.y, acoord[2] - vShift.z];
let bcoord1 = [bcoord[0] - vShift.x, bcoord[1] - vShift.y, bcoord[2] - vShift.z];
let acoord2 = [acoord[0] + vShift.x, acoord[1] + vShift.y, acoord[2] + vShift.z];
let bcoord2 = [bcoord[0] + vShift.x, bcoord[1] + vShift.y, bcoord[2] + vShift.z];
// draw bonds
drawStripyBond(acoord1, bcoord1, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord2, bcoord2, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
} else if (bondorder === 3) {
let acoord1 = [acoord[0] - vShift.x, acoord[1] - vShift.y, acoord[2] - vShift.z];
let bcoord1 = [bcoord[0] - vShift.x, bcoord[1] - vShift.y, bcoord[2] - vShift.z];
let acoord2 = [acoord[0] + vShift.x, acoord[1] + vShift.y, acoord[2] + vShift.z];
let bcoord2 = [bcoord[0] + vShift.x, bcoord[1] + vShift.y, bcoord[2] + vShift.z];
// draw bonds
drawStripyBond(acoord, bcoord, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord1, bcoord1, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
drawStripyBond(acoord2, bcoord2, a1c, a2c, bond_label, bond_size, shape, alternativeColor);
}
}
}
});
Expand All @@ -119,26 +121,28 @@ export function loadQualityFromFile(stage, file, quality, object_name, orientati
});

let element = comp.object.atomMap.list[id]?.element;
let eleC = element === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element];
if (element) {
let eleC = element === 'C' ? [rgbColor.r, rgbColor.g, rgbColor.b] : ELEMENT_COLORS[element];

let col2 = Array(m.length)
.fill(1)
.map(function(v, i) {
return eleC[i % 3] / 255;
});
let col2 = Array(m.length)
.fill(1)
.map(function(v, i) {
return eleC[i % 3] / 255;
});

let col = new Float32Array(col2);
let col = new Float32Array(col2);

shape.addSphere(origin, [eleC[0] / 255, eleC[1] / 255, eleC[2] / 255], 0.2, atom_label);
shape.addSphere(origin, [eleC[0] / 255, eleC[1] / 255, eleC[2] / 255], 0.2, atom_label);

var meshBuffer = new MeshBuffer({
position: new Float32Array(m),
color: col
});
var meshBuffer = new MeshBuffer({
position: new Float32Array(m),
color: col
});

shape.addBuffer(meshBuffer);
var shapeComp = stage.addComponentFromObject(shape);
shapeComp.addRepresentation(MOL_REPRESENTATION_BUFFER, { isShape: true });
shape.addBuffer(meshBuffer);
var shapeComp = stage.addComponentFromObject(shape);
shapeComp.addRepresentation(MOL_REPRESENTATION_BUFFER, { isShape: true });
}
}

if (orientationMatrix && orientationMatrix.elements) {
Expand Down
2 changes: 1 addition & 1 deletion package.json
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "fragalysis-frontend",
"version": "0.10.27",
"version": "0.10.28",
"description": "Frontend for fragalysis",
"main": "webpack.config.js",
"scripts": {
Expand Down

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