Polymer Editor Open file

As	I want	so that
Ketcher polymer editor user	to open *.mol file containing peptide structure	I can see the structure in Ketcher and be able to modify it using Ketcher
Ketcher polymer editor user	to open *.helm file containing peptide structure	I can see the structure in Ketcher and be able to modify it using Ketcher

1. Context

Supported formats are: *.mol (v3000), .HELM and text files with MOL or HELM notation inside (.txt , .*doc, .docx, .rtf). Explore the *.mol information here:

Peptide structures are supported only by the v3000 format of the *.mol file. The v2000 format is not presents structured view of polymers and couldn't be recognized by peptide editor. The problem for future development is to recognize polymer structure in v2000 format from the chemical libraries.

There are 2 possible ways to capture the peptides in the v3000 mol file, explore them here http://help.accelrysonline.com/insight/2018/content/pdf_files/bioviachemicalrepresentation.pdf:

Glossary: Peptide Glossary - check it for information on HELM format

3. Assumptions

ID	Assumption
1	HELM notation will most like be opened as text pasted from the clipboard. Opening from files of .helm, .txt format would be more rare scenario.
2	*.MOL notation of v3000 will be opened mostly from files with *.mol, *.txt format. Opening from clipboard will be more rare scenario, but we should support it just like we do in general Ketcher.
3

4. Additional information (optional)

The window will have the same appearance as in the standard Ketcher, except the image opening icon

8. Acceptance Criteria

№	User Group	GIVEN	WHEN	THEN
1	Ketcher polymer editor User	Polymer editor mode of the Ketcher enabled	viewing on the tool panel	I see the Open icon with tooltip "Open... (Ctrl + O) " when hovering on it
2			clicking on the Open icon OR using the shortcut Ctrl + O	Ketcher provides the ability to select file from the workstation OR drag file OR paste the text from the clipboard AND Ketcher Polymer Editor allows to select *.mol, *.helm files by default with the ability to select all files
3			clicking on the Open icon OR using the shortcut Ctrl + O AND way of adding file is selected	Ketcher Polymer Editor checks that structure opened is a polymer one AND Ketcher provides the ability to add structure to Canvas OR Open structure as a new project
3.1			conditions from the no3 are fulfilled AND 'Add to Canvas' option was selected	Canvas in the same state as it was before adding new structure AND Ketcher creates the new structure which is moved on canvas by the user's cursor. The first cursor click determines the location of the structure on the canvas
3.2			conditions from the no3 are fulfilled AND 'Open as New project' option was selected	New canvas is opening and Ketcher creates the structure in the upper left corner.
4			selecting the *.HELM or *txt file with HELM format content or HELM format text was copied from the clipboard AND the opening was confirmed	Ketcher creates the structure for the canvas in accordance with HELM mapping rules AND positions it on the canvas in accordance with the open mode selected and in accordance with the alignment rules AND Ketcher enumerates chains and monomers in it in accordance with Peptide business rules
5			selecting the *.mol or *txt file with *mol format content or *mol format text was copied from the clipboard AND the opening was confirmed AND Ketcher recognize that the format of *.mol file is v2000	Pop-up window with 2 options is showing: Open the file in the regular Ketcher OR Stay in Polimer editor mode
5.1			conditions from the no5 are fulfilled AND " Open the file in the regular Ketcher '' option is selected	Ketcher switched to standard mode Ketcher creates the structure for the canvas in accordance with existing *.MOL mapping rules AND positions it on the canvas in accordance with the open mode selected and in accordance with the alignment rules
5.2			conditions from the no5 are fulfilled AND "Stay in Polimer editor moder '' option is selected	Pop-up window is closed AND Ketcher stay in Polymer editor mod AND Canvas in the same state as it was before Conditions from the no5 are started
6			selecting the *.mol or *txt file with *mol format content or *mol format text was copied from the clipboard AND the opening was confirmed AND Ketcher recognize that the format of *.mol file is v3000	Ketcher creates the structure for the canvas in accordance with *.MOL mapping rules AND positions it on the canvas in accordance with the open mode selected and in accordance with the alignment rules AND Ketcher enumerates chains and monomers in it in accordance with Peptide business rules
7			selecting the supported format, which includes names of monomers not from Ketcher's library AND the opening was confirmed	Ketcher creates the structure for the canvas for known monomers AND messege shown "Part of monomers was not recognized and was not added"
8			**selecting unsupported format. AND the opening was confirmed **	**Error message is shown "Given file could not be loaded. Please select a file in supported format: *.mol, .HELM, .txt"
9			empty file or file without HELM/mol notation selected AND the opening was confirmed	'OPEN STRUCTURE' window is shown (the same window as shown after "paste the text from the clipboard" option is selected) AND Ketcher provides the ability to paste the text from the clipboard
10			option 'paste the text from the clipboard ' is selected AND information pasted not in helm/mol format AND the opening was confirmed	Error message is shown "Convert error! Given string could not be loaded as (query or plain) molecule or reaction, see the error messages: 'scanner: BufferScanner::read() error', 'scanner: BufferScanner::read() error', 'molecule auto loader: SMILES loader: unexpected end of input', 'molecule auto loader: SMILES loader: unexpected end of input'"