list of bobgr's minor bugfix and feature requests

User 870ab5b546

12-01-2015 15:53:28

I thought it would be worthwhile to make a list of my outstanding minor bug alerts and feature requests so that they are all in one place. Alerts of more important bugs are in separate threads.

Minor bugs:

When I draw a coordinate bond from atom P with a lone pair to another atom M, and lone pairs are visible, either the lone pair of P should not be displayed (preferred, and the current behavior in MarvinSketch), or it should be displayed at the starting point of the coordinate bond.

Using an iPad, for toolbar buttons with submenus (bond, arrow, electron-flow arrow, and rectangle/ellipse), is very difficult to find just the right spot on the lower right corner of the toolbar button to press and hold so that the submenus will appear.

Using an iPad, even when I can get the submenus to appear, I am unable to select any of the options. For example, I cannot select the bold bond or the two-electron electron-flow arrow. Dragging my finger over to the desired option has no effect, and the submenus simply disappear when I lift my finger.

Currently, I am unable to draw a graphical arrow from one rectangle corner/midpoint to another rectangle corner/midpoint if they are within a certain distance.

I can change the arc of an electron-flow arrow, but the arc parameters are evidently not stored in the MRV, because if I export the structure and then import it back, the arc changes back to its original appearance.

Higher priority feature requests (in my priority order):

Add a color property to graphical reaction and resonance arrows, just as rectangles have already.

Make the two-electron arrow the default option in the toolbar.

Add a radical toggle button to the default toolbar.

Implement divalent radicals.

Add the capability to draw a multicenter S-group.

Add textboxes, even if they don't initially permit formatting.

Lower priority feature requests (no particular order):

If I choose to look at R/S configurations in Marvin4JS, there doesn't seem to be any way to get rid of the stereochemical descriptors other than by modifying the structure. If the View R/S button has just been pressed, then pressing it again should get rid of all the stereochemical descriptors.

In a 3D structure, the ends of the bonds don't quite touch, making the structure a little hard to read. The fading is nice, but the ends of the bonds should touch.

In aliases, numbers should be subscripted only when they follow letters.

Adjust the positions of the shortcut groups' names so that the bonds point to their left, not their center. (Unless you implement lefthand and righthand names, like MarvinSketch has, in which case the bonds might point to the right in certain cases.)

Make the focus automatically shift to the text field in the popup window that appears when I click on the pseudoatom button.

If I choose a stereobond from the Bond button group, then click on an atom button, and then I draw the atom and an associated bond by click-holding on an existing atom and dragging, the new bond should be the type that I have chosen from the Bond button group.

In the various dialog boxes (View settings, Atom properties, Bond properties), enable the OK button even if I haven't changed a value.

Recognize molecule properties (of any name) in an imported MRV, and add setProperty() and getProperty() methods to the API.

Add an option to hide valence flags.

Add an option to hide absolute stereo flags.

ChemAxon f052bdfe3c

12-01-2015 16:18:31

Hi Bob,

Thank you for the list version, it is really useful, we try to fix/implement them as soon as I find the capacity.

I am missing an item: to have line breaks in MRV in the import/export dialog, which unfortunately seems to be harder than we thought before.

However, I do not really understand the last two item on your list. You can set `absolute flag` and `valance error` visibility through API (and via GUI as well) already. Please check our API doc: https://marvinjs-demo.chemaxon.com/latest/jsdoc.html Please set `valenceErrorVisible` and `chiralFlagVisible` as false.

Best regards,

Efi

User 870ab5b546

12-01-2015 16:58:28

ehoffmann wrote:

I am missing an item: to have line breaks in MRV in the import/export dialog, which unfortunately seems to be harder than we thought before.

Yes, that is one that I missed. Thanks!

Can't you just do a global replace of > with >[return] in the returned string?

ehoffmann wrote:

However, I do not really understand the last two item on your list. You can set `absolute flag` and `valence error` visibility through API (and via GUI as well) already. Please check our API doc: https://marvinjs-demo.chemaxon.com/latest/jsdoc.html Please set `valenceErrorVisible` and `chiralFlagVisible` as false.

Re valence flag (lower priority feature request 9): this MRV:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.9.8.0">

<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4" elementType="H C O C" formalCharge="-1 0 2 0" mrvValence="- - 2 -" x2="0.0 4.18 5.513679121828035 6.847358243656071" y2="0.0 0.2566666666666666 -0.5133333333333334 0.25666666666666704"></atomArray><bondArray><bond id="b1" atomRefs2="a2 a3" order="1"></bond><bond id="b2" atomRefs2="a3 a4" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>

</cml>

when loaded into MarvinJS shows (v2) in blue next to the O atom. I would like the option to hide that flag.

You're right, it is already possible to hide the absolute stereochemistry flag. I was confusing the MarvinJS chiralFlagVisible flag with the MarvinSketch chiralitySupport flag. So you can cross lower priority feature request 10 off the list already! So we now have:

Minor bugs:

When I draw a coordinate bond from atom P with a lone pair to another atom M, and lone pairs are visible, either the lone pair of P should not be displayed (preferred, and the current behavior in MarvinSketch), or it should be displayed at the starting point of the coordinate bond.

Using an iPad, for toolbar buttons with submenus (bond, arrow, electron-flow arrow, and rectangle/ellipse), is very difficult to find just the right spot on the lower right corner of the toolbar button to press and hold so that the submenus will appear.

Using an iPad, even when I can get the submenus to appear, I am unable to select any of the options. For example, I cannot select the bold bond or the two-electron electron-flow arrow. Dragging my finger over to the desired option has no effect, and the submenus simply disappear when I lift my finger.

Currently, I am unable to draw a graphical arrow from one rectangle corner/midpoint to another rectangle corner/midpoint if they are within a certain distance.

I can change the arc of an electron-flow arrow, but the arc parameters are evidently not stored in the MRV, because if I export the structure and then import it back, the arc changes back to its original appearance.

Higher priority feature requests (in my priority order):

Add a color property to graphical reaction and resonance arrows, just as rectangles have already.

Make the two-electron arrow the default option in the toolbar.

Add a radical toggle button to the default toolbar.

Implement divalent radicals.

Add the capability to draw a multicenter S-group.

Add textboxes, even if they don't initially permit formatting.

Lower priority feature requests (no particular order):

If I choose to look at R/S configurations in Marvin4JS, there doesn't seem to be any way to get rid of the stereochemical descriptors other than by modifying the structure. If the View R/S button has just been pressed, then pressing it again should get rid of all the stereochemical descriptors.

In a 3D structure, the ends of the bonds don't quite touch, making the structure a little hard to read. The fading is nice, but the ends of the bonds should touch.

In aliases, numbers should be subscripted only when they follow letters.

Adjust the positions of the shortcut groups' names so that the bonds point to their left, not their center. (Unless you implement lefthand and righthand names, like MarvinSketch has, in which case the bonds might point to the right in certain cases.)

Make the focus automatically shift to the text field in the popup window that appears when I click on the pseudoatom button.

If I choose a stereobond from the Bond button group, then click on an atom button, and then I draw the atom and an associated bond by click-holding on an existing atom and dragging, the new bond should be the type that I have chosen from the Bond button group.

In the various dialog boxes (View settings, Atom properties, Bond properties), enable the OK button even if I haven't changed a value.

Recognize molecule properties (of any name) in an imported MRV, and add setProperty() and getProperty() methods to the API.

Add an option to hide valence number (mrvValence) flags.

Add line breaks to exported MRVs.

ChemAxon f052bdfe3c

14-01-2015 12:39:13

Thank you,

Efi

User 870ab5b546

20-04-2015 16:25:51

Minor bugs:

When I draw a coordinate bond from atom P with a lone pair to another atom M, and lone pairs are visible, either the lone pair of P should not be displayed (preferred, and the current behavior in MarvinSketch), or it should be displayed at the starting point of the coordinate bond.

Using an iPad, for toolbar buttons with submenus (bond, arrow, electron-flow arrow, and rectangle/ellipse), is very difficult to find just the right spot on the lower right corner of the toolbar button to press and hold so that the submenus will appear.

Using an iPad, even when I can get the submenus to appear, I am unable to select any of the options. For example, I cannot select the bold bond or the two-electron electron-flow arrow. Dragging my finger over to the desired option has no effect, and the submenus simply disappear when I lift my finger.

Currently, I am unable to draw a graphical arrow from one rectangle corner/midpoint to another rectangle corner/midpoint if they are within a certain distance.

I can change the arc of an electron-flow arrow, but the arc parameters are evidently not stored in the MRV, because if I export the structure and then import it back, the arc changes back to its original appearance.

Charge symbols are too small. Even worse, if the view is shrunk, + symbols start to look like – symbols. See the attached screen shot.

Charges and electrons around atoms sometimes overlap with bonds; they should not.

If a C atom is charged or has one or more electrons displayed around it, the atom should be labeled with C and implicit H atoms, e.g., CH or CH₂.

Higher priority feature requests (in my priority order):

Add a color property to graphical reaction and resonance arrows, just as rectangles have already.

Make the two-electron arrow the default option in the toolbar.

Add a radical toggle button to the default toolbar.

Implement divalent radicals.

Add the capability to draw a multicenter S-group.

Add textboxes, even if they don't initially permit formatting.

Lower priority feature requests (no particular order):

If I choose to look at R/S configurations in Marvin JS, there doesn't seem to be any way to get rid of the stereochemical descriptors other than by modifying the structure. If the View R/S button has just been pressed, then pressing it again should get rid of all the stereochemical descriptors.

In a 3D structure, the ends of the bonds don't quite touch, making the structure a little hard to read. The fading is nice, but the ends of the bonds should touch.

In aliases, numbers should be subscripted only when they follow letters.

Adjust the positions of the shortcut groups' names so that the bonds point to their left, not their center. (Unless you implement lefthand and righthand names, like MarvinSketch has, in which case the bonds might point to the right in certain cases.)

Make the focus automatically shift to the text field in the popup window that appears when I click on the pseudoatom button.

If I choose a stereobond from the Bond button group, then click on an atom button, and then I draw the atom and an associated bond by click-holding on an existing atom and dragging, the new bond should be the type that I have chosen from the Bond button group.

In the various dialog boxes (View settings, Atom properties, Bond properties), enable the OK button even if I haven't changed a value.

Recognize molecule properties (of any name) in an imported MRV, and add setProperty() and getProperty() methods to the API.

Add an option to hide valence number (mrvValence) flags.

Add line breaks to exported MRVs.

Add a function that creates a popup Marvin JS window that the user can expand to fill the entire screen (analogous to "Sketcher window" option in MarvinSketch).

ChemAxon f052bdfe3c

21-04-2015 14:54:35

Thank you for updating this list. I have a question: Divalent triplet radical is enough or do you want to use divalent singlet as well?

Best regards,

Efi

User 870ab5b546

21-04-2015 14:56:25

Actually, if I have to make a choice, I'd much prefer divalent singlet. It's much more common than divalent triplet.

ChemAxon f052bdfe3c

22-04-2015 08:05:23

Thank you for your prompt reply.

Efi

User 870ab5b546

08-07-2015 19:10:55

You've taken care of some of the items on this list, so here's an updated one.

Minor bugs:

When I draw a coordinate bond from atom P with a lone pair to another atom M, and lone pairs are visible, either the lone pair of P should not be displayed (preferred, and the current behavior in MarvinSketch), or it should be displayed at the starting point of the coordinate bond.

Using an iPad, for toolbar buttons with submenus (bond, arrow, electron-flow arrow, and rectangle/ellipse), is very difficult to find just the right spot on the lower right corner of the toolbar button to press and hold so that the submenus will appear.

Using an iPad, even when I can get the submenus to appear, I am unable to select any of the options. For example, I cannot select the bold bond or the two-electron electron-flow arrow. Dragging my finger over to the desired option has no effect, and the submenus simply disappear when I lift my finger.

Currently, I am unable to draw a graphical arrow from one rectangle corner/midpoint to another rectangle corner/midpoint if they are within a certain distance.

I can change the arc of an electron-flow arrow, but the arc parameters are evidently not stored in the MRV, because if I export the structure and then import it back, the arc changes back to its original appearance.

Use an en dash for a minus sign; the currently used hyphen is very hard to see.

Higher priority feature requests (in my priority order):

Add a color property to graphical reaction and resonance arrows, just as rectangles have already.

Add the capability to draw a multicenter S-group.

Lower priority feature requests (no particular order):

If I choose to look at R/S configurations in Marvin4JS, there doesn't seem to be any way to get rid of the stereochemical descriptors other than by modifying the structure. If the View R/S button has just been pressed, then pressing it again should get rid of all the stereochemical descriptors.

In a 3D structure, the ends of the bonds don't quite touch, making the structure a little hard to read. The fading is nice, but the ends of the bonds should touch.

In aliases, numbers should be subscripted only when they follow letters.

Adjust the positions of the shortcut groups' names so that the bonds point to their left, not their center. (Unless you implement lefthand and righthand names, like MarvinSketch has, in which case the bonds might point to the right in certain cases.)

Make the focus automatically shift to the text field in the popup window that appears when I click on the pseudoatom button.

If I choose a stereobond from the Bond button group, then click on an atom button, and then I draw the atom and an associated bond by click-holding on an existing atom and dragging, the new bond should be the type that I have chosen from the Bond button group.

In the various dialog boxes (View settings, Atom properties, Bond properties), enable the OK button even if I haven't changed a value.

Recognize molecule properties (of any name) in an imported MRV, and add setProperty() and getProperty() methods to the API.

Add an option to hide valence number (mrvValence) flags.

Add line breaks to exported MRVs.

ChemAxon f052bdfe3c

10-07-2015 09:48:59

Thank you for the update.

Best regards,

Efi

User 870ab5b546

28-07-2015 16:19:35

I just noticed that electron-flow arrows also lack a coloring property in Marvin JS. We need it.

Major bugs:

Hypervalent heavy atoms, for example, a nine-electron Br atom, should not trigger a valence error.

There is a problem with cross-compatibility of rectangle sides/midpoints between MarvinSketch and Marvin JS. If I draw a rectangle in one editor, then draw a reaction arrow that starts at the midpoint of its bottom edge, then display the structure in the other editor, the arrow starts at the top instead.

If in MarvinSketch, I draw a rectangle A, then I draw an arrow B that begins at the midpoint of the bottom edge of A, then I draw an arrow C that begins at the midpoint of arrow B, then, when I import the structure into Marvin JS, arrow C disappears. Evidently, MarvinJS doesn't understand the concept of one arrow beginning at the midpoint of another arrow, so it just ignores it.

If I replace an atom in a 3D structure with a shortcut group, the z-coordinate of the original atom is not transferred to the shortcut group.

Minor bugs:

When I draw a coordinate bond from atom P with a lone pair to another atom M, and lone pairs are visible, either the lone pair of P should not be displayed (preferred, and the current behavior in MarvinSketch), or it should be displayed at the starting point of the coordinate bond.

Using an iPad, for toolbar buttons with submenus (bond, arrow, electron-flow arrow, and rectangle/ellipse), is very difficult to find just the right spot on the lower right corner of the toolbar button to press and hold so that the submenus will appear.

Using an iPad, even when I can get the submenus to appear, I am unable to select any of the options. For example, I cannot select the bold bond or the two-electron electron-flow arrow. Dragging my finger over to the desired option has no effect, and the submenus simply disappear when I lift my finger.

Currently, I am unable to draw a graphical arrow from one rectangle corner/midpoint to another rectangle corner/midpoint if they are within a certain distance.

I can change the arc of an electron-flow arrow, but the arc parameters are evidently not stored in the MRV, because if I export the structure and then import it back, the arc changes back to its original appearance.

Use an en dash for a minus sign; the currently used hyphen is very hard to see.

When a structure shrinks, the + and – signs should not shrink into invisibility.

Boundaries of textboxes drawn in MarvinSketch should be respected by Marvin JS, so that the text wraps properly and doesn't overlap with a structure to the right.

Higher priority feature requests (in my priority order):

Add a color property to reaction arrows and electron-flow arrows, just as rectangles have already.

Add the capability to draw a multicenter S-group.

Lower priority feature requests (no particular order):

If I choose to look at R/S configurations in Marvin4JS, there doesn't seem to be any way to get rid of the stereochemical descriptors other than by modifying the structure. If the View R/S button has just been pressed, then pressing it again should get rid of all the stereochemical descriptors.

In a 3D structure, the ends of the bonds don't quite touch, making the structure a little hard to read. The fading is nice, but the ends of the bonds should touch.

In aliases, numbers should be subscripted only when they follow letters.

Adjust the positions of the shortcut groups' names so that the bonds point to their left, not their center. (Unless you implement lefthand and righthand names, like MarvinSketch has, in which case the bonds might point to the right in certain cases.)

Make the focus automatically shift to the text field in the popup window that appears when I click on the pseudoatom button.

If I choose a stereobond from the Bond button group, then click on an atom button, and then I draw the atom and an associated bond by click-holding on an existing atom and dragging, the new bond should be the type that I have chosen from the Bond button group.

In the various dialog boxes (View settings, Atom properties, Bond properties), enable the OK button even if I haven't changed a value.

Recognize molecule properties (of any name) in an imported MRV, and add setProperty() and getProperty() methods to the API.

Add an option to hide valence number (mrvValence) flags.

Add line breaks to exported MRVs.