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Import of standard IDT monomers #1588

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olganaz opened this issue Jan 18, 2024 · 1 comment · Fixed by #1904
Closed

Import of standard IDT monomers #1588

olganaz opened this issue Jan 18, 2024 · 1 comment · Fixed by #1904

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@olganaz
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olganaz commented Jan 18, 2024

Background
In IDT notation modified sequences represented as a plain strings with a combination of standard and modified monomers.
Standard monomer [s]<Base>[*] is nucleotides with the same configurations as supported in Ketcher.
Modified monomer /<pos><Identifier>/[*] could be nucleotide or CHEM or their combination.
This task covers only import of standard IDT monomers.

Requirements

The system should interpret standard monomers [s]<Base>[*] as nucleotides with a structure (defined by the name components):

Base - standard unmodified nucleotide base symbol (see table below)
s - optional symbol of the sugar that makes the nucleotide (see table below). If not specified, standard sugar deoxy-ribose (dR) is implied.
* - optional indicator of modified phosphate. If specified, indicates that Phosphorothioate (sP) is included into nucleotide, otherwise standard phosphate (P) is implied.
The last monomer in the chain is considered to be nucleoside (nucleotide, which lacks phosphate), so * couldn't be the last symbol in the sequence.

Solution
A clear and concise description of what you want to happen.

Alternatives
For base symbols R , Y, M, K, S, W, H, B, V, D, N and Modified IDT monomers Error message should be displayed.
Modified IDT monomers /<pos><Identifier>/[*] will be supported as described in #1899

Additional context
Examples:
ACG

rArC*rG

A*C*G

+C*+G*A

mA*mGC

@olganaz olganaz changed the title Import IDT format Import modified sequences in IDT format Jan 19, 2024
@olganaz olganaz changed the title Import modified sequences in IDT format Import modified sequences from IDT format Jan 19, 2024
@even1024 even1024 self-assigned this Jan 22, 2024
@even1024 even1024 added this to the Indigo-1.19.0-rc.1 milestone Jan 22, 2024
@olganaz olganaz changed the title Import modified sequences from IDT format Import standard IDT monomers Apr 3, 2024
@olganaz olganaz changed the title Import standard IDT monomers Import of standard IDT monomers Apr 3, 2024
AliaksandrDziarkach added a commit that referenced this issue Apr 5, 2024
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Apr 5, 2024 that will close this issue
7 tasks
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Apr 9, 2024 that will close this issue
4 tasks
AliaksandrDziarkach added a commit that referenced this issue Apr 9, 2024
Co-authored-by: even1024 <roman.porozhnetov@gmail.com>
Co-authored-by: Aliakasndr Dziarkach <Aliakasndr.Dziarkach@gmail.com>
@AlexeyGirin
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Will be tested in the context of epam/ketcher#4495

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