Ndx2resttop fix #25
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Ndx2resttop fix #25
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The user is able to overwrite these values. However the user will probably use the "define" keyword. Thus the mdp_dict will contain "define" and "Define" keywords. As mdp is case insensitive - it will complaint about the "define" keyword being assigned twice. Setting Define to define for consistency and to avoid this situation
- label should be updated after the previous group is closed - Catch the last group of the file (do not expect another '[' character - Catch groups with just one line increasing the second index by one, otherwise the start and close indices are equal and it returns an empty rest and ref group later on
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Hi!
I leave here some changes that I have found necessary. Let me know what you think.
The modifications in common.py are due to the fact that the user can provide mdp keywords in a different format as the preset dictionary (e.g. using upper instead of lower case or using '_' instead of '-'). The mdp dictionary will have a keyword defined twice in those cases. And gromp will complain as it is not sensitive to those changes - not sure if there are more changes that should be taken into account. Cleaning the keywords before building the mdp dict solves the issue.
Changes in ndx2resttop are done to extend its use to topologies of a single chain. With a single chain pdb2gmx just writes the .top file instead of a .itp for each chain. I have also noticed different issues with how the index_dict was built that now should be corrected. Finally I added a custom posres keyword, so the user has more control over which position restraints are being activated.
I'm available to discuss these changes in detail if needed, hope this helps :)