Closed ClairePA closed 6 years ago
Could you paste the HELM notation here? I guess the missing information is not specified. Thanks.
The HELM is:
PEPTIDE1{A.C.D.D.P.P}|PEPTIDE2{A.C.D.D.P.P}$PEPTIDE1,PEPTIDE2,1:?-?:?$G3(PEPTIDE1+PEPTIDE2:2)$$V2.0
and the bond attributes are;
So the display is correct, but confusing. It should show which attributes are not specified. Please note that the HELM notation says that if the ratio is not specified the proportion of that component is unknown and you cannot assume a value (e.g. 1).
Fixed in 2018-01-08 update. It is able to set the default ratio value by changing the value of this variable:
org.helm.webeditor.defaultbondratio = null; // or ?, 1
Good start but there is some work to do before this is fully functioning. The main issues are;
Action | Value | Display | Preferred Display | |
---|---|---|---|---|
1 | Draw bond | Position = ? | null | |
R# = ? | null | |||
Ratio = 1 | Null | |||
1 | Position = ? | null | ||
R# = ? | null | |||
Ratio = 1 | Null | |||
HELM is invalid - see screenshots below. | ||||
2 | Go into ‘set attributes' and make no changes. Exit 'set attributes' | Position = ? | null | |
R# = ? | null | |||
Ratio = 1 | Ratio =1 | should be as action1 i.e. the ratio should not be displayed. | ||
2 | Position = ? | null | ||
R# = ? | null | |||
Ratio = 1 | Ratio =1 | |||
3 | Go into ‘set attributes' and remove the 1 from the ratio. Save and then go back into the 'set attributes' box. The ratio boxes have 1 in them again, this is incorrect - it must be possible to specify an unknown ratio, either by removing the 1 or by adding ?. | |||
4 | Change the value of R# for the first group to 1. | Position = ? | Pos:? | |
R# = 1 | R#: R1 | |||
Ratio = 1 | Ratio =1 | |||
4 | Position = ? | null | Pos:? Should be displayed | |
R# = ? | null | R# should be displayed | ||
Ratio = 1 | Ratio =1 |
Could you write down the steps on how to generate this help?
I can't reproduce the nulls, so please take this off the list of issues.
fixed in 2018-01-10 update
The behaviour still looks the same to me. the issues identified in the comment above are still there. Please implement the changes described in the table and the list below:
Fixed
Perfect! Many thanks.
If an ambiguous bond between groups has only some of the attributes defined, only the defined attributes are displayed. This is confusing.
All attributes should be shown.