Support agents information in SMILES format

[dariasviridova]

As a Ketcher User
I want to have reagent/condition information in "Daylight SMILES'/'Extended SMILES' formats
So that I have information how does reaction go and use this reaction information further (e.g. for analysis)

Business need:

Reagent - substance that can be added to mixture of reactants to trigger a chain of chemical reactions. Reagent is not consumed during chemical reaction.
Chemical condition specifies the condition under which the reaction shall go (temperature, UV etc.).
Reagent and condition are defined above or under the arrow and are considered as separate reaction participants. In SMILES format specification reagent and conditions are united with entity agent.

Context:

There were several requests (#1523, #1404) from the End Users for supporting reagents in reaction in different file formats.
For now User can add reagents and conditions simply by adding molecule/text above or below an arrow. However, system will not identify them as agent. To have full information about reaction to analyze and export it, system shall be able to identify agents as a separate entity.

Assumptions:

• Users do not have a limited and standardized list of reagents.
• User can specify reagents and conditions both as molecules and as text.

In scope
Support reagent(s) only for "Daylight SMILES' and 'SMILES Extended' formats

Out of the scope
Validation of reagent(s) and warning messages for text-based agents.

Acceptance criteria:

No	User	GIVEN	WHEN	THEN
1	Ketcher User	User added arrow (any reagent arrow type) on canvas AND User added molecule/text on canvas above/below an arrow (in the area bounded by perpendiculars passing through the end of the arrow)	User clicks on saving icon or uses a shortcut Ctr+C AND User chooses "Daylight SMILES'/'Extended SMILES' format from the 'File format' dropdown	System shall detect molecule/text as agent and write agent information in according to format specification* in "Preview" tab
	Ketcher User	User opened 'Open structure' tab AND clicked on 'Paste from clipboard'	User pastes "Daylight SMILES'/'Extended SMILES' that contains agents information AND clicks 'Add to Canvas' or 'Display as a New Project'	System shall display agents information on canvas according to "Daylight SMILES'/'Extended SMILES' format specification
	Ketcher user	User opened 'Open structure' tab AND clicked on 'Open from file'	User chooses "Daylight SMILES'/'SMILES Extended' that contains agents information AND clicks 'Add to Canvas' or 'Display as a New Project'	System shall display agents information on canvas according to format specification

SMILES agents specification

Reactions are indicated in SMILES by specifying reactant, agent and product molecule(s) separated by the "greater-than" symbol ('>').
'Daylight SMILES' example:

'Extended SMILES' example:

• "Daylight SMILES'/'SMILES Extended' do not support text elements and test-based agents in particular. Text-based agents are lost when converted to "Daylight SMILES'/'SMILES Extended' formats.
• "Daylight SMILES'/'SMILES Extended' do not support multistep reactions.