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Incorrect bond length and angle for some natural monomers #6563

Closed
Tracked by #6600
ljubica-milovic opened this issue Feb 24, 2025 · 0 comments · Fixed by #6566, #6574, #6578 or #6580
Closed
Tracked by #6600

Incorrect bond length and angle for some natural monomers #6563

ljubica-milovic opened this issue Feb 24, 2025 · 0 comments · Fixed by #6566, #6574, #6578 or #6580
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@rrodionov91
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Monomer Library User`s Feedback
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Ketcher 3.0.3

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@ljubica-milovic
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ljubica-milovic commented Feb 24, 2025 •
edited
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  1. Go to Ketcher Macromolecules mode
  2. Add base A to the canvas
  3. Go to small molecules mode
  4. Expand the structure
  5. Draw a cyclohexane
  6. Compare bond lengths

Actual behavior
Bond length is significantly bigger than standard:
Image

Expected behavior
All natural monomers should have standard bond lengths and angles.

Natural monomers are bases: Adenine, Cytosine, Guanine, Thymine, Uracil, and Inosine; sugars: Ribose and Deoxy-Ribose; phosphate: Phosphate; and amino-acids: Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Pyrrolysine, Selenocysteine, Serine, Threonine, Tryptophan, Tyrosine and Valine.
@rrodionov91 rrodionov91 added this to the Ketcher 3.0.2 milestone Feb 24, 2025
@rrodionov91 rrodionov91 self-assigned this Feb 25, 2025
@ljubica-milovic ljubica-milovic changed the title Incorrect bond length and angle for some monomers Incorrect bond length and angle for some natural monomers Feb 25, 2025
@rrodionov91 rrodionov91 linked a pull request Feb 25, 2025 that will close this issue
#6563 - Incorrect bond length and angle for some monomers #6566
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Feb 25, 2025
@rrodionov91
#6563 - Incorrect bond length and angle for some monomers (#6566)
531f3d8 
* - updated monomers library
* - changed font size for monomer preview
* - updated screenshots
* - updated ketcher to 3.0.2
@ljubica-milovic ljubica-milovic mentioned this issue Feb 26, 2025
Closed
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
#6563 - Incorrect bond length and angle for some natural monomers
a61b250
@rrodionov91 rrodionov91 linked a pull request Feb 26, 2025 that will close this issue
#6563 - Incorrect bond length and angle for some natural monomers #6574
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
#6563 - Incorrect bond length and angle for some natural monomers (#6574
3a65ce7 
)
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
#6563 - Incorrect bond length and angle for some monomers (#6566)
1a9234f 
* - updated monomers library
* - changed font size for monomer preview
* - updated screenshots
* - updated ketcher to 3.0.2

(cherry picked from commit 531f3d8)
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
#6563 - Incorrect bond length and angle for some natural monomers (#6574
533e6d0 
)

(cherry picked from commit 3a65ce7)
@rrodionov91 rrodionov91 linked a pull request Feb 26, 2025 that will close this issue
Backmerge: #6563 - Incorrect bond length and angle for some natural monomers #6578
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
Backmerge: #6563 - Incorrect bond length and angle for some natural m…
9452406 
…onomers (#6578)

* #6563 - Incorrect bond length and angle for some monomers (#6566)

* - updated monomers library
* - changed font size for monomer preview
* - updated screenshots
* - updated ketcher to 3.0.2

(cherry picked from commit 531f3d8)

* #6563 - Incorrect bond length and angle for some natural monomers (#6574)

(cherry picked from commit 3a65ce7)

* - updated ketcher to 3.1.0-rc.6
* - updated screenshots
rrodionov91 added a commit that referenced this issue Feb 26, 2025
@rrodionov91
Backmerge: #6563 - Incorrect bond length and angle for some natural m…
f4fa37b 
…onomers (#6578)

* #6563 - Incorrect bond length and angle for some monomers (#6566)

* - updated monomers library
* - changed font size for monomer preview
* - updated screenshots
* - updated ketcher to 3.0.2

(cherry picked from commit 531f3d8)

* #6563 - Incorrect bond length and angle for some natural monomers (#6574)

(cherry picked from commit 3a65ce7)

* - updated ketcher to 3.1.0-rc.6
* - updated screenshots

(cherry picked from commit 9452406)
@rrodionov91 rrodionov91 linked a pull request Feb 26, 2025 that will close this issue
Backmerge: #6563 - Incorrect bond length and angle for some natural monomers #6580
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Feb 27, 2025
@rrodionov91
Backmerge: #6563 - Incorrect bond length and angle for some natural m…
5b3ca32 
…onomers (#6580)

* Backmerge: #6563 - Incorrect bond length and angle for some natural monomers (#6578)

* #6563 - Incorrect bond length and angle for some monomers (#6566)

* - updated monomers library
* - changed font size for monomer preview
* - updated screenshots

(cherry picked from commit 531f3d8)

* #6563 - Incorrect bond length and angle for some natural monomers (#6574)

(cherry picked from commit 3a65ce7)

* - updated ketcher to 3.1.0-rc.6
* - updated screenshots

(cherry picked from commit 9452406)

* - updated screenshots
@AlexeyGirin AlexeyGirin mentioned this issue Mar 4, 2025
Open
38 tasks
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