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The following lines from the manual are giving me problems.

>>> params_list = Vector1('ATP.params')
>>> res_set=generate_nonstandard_residue_set(params_list)

This results in an error
ERROR: Cannot find file 'A'
ERROR:: Exit from: src/core/chemical/ line: 147
RuntimeError: unidentifiable C++ exception

If I rename ATP.params to A, and put it in my home directory it finds it.
It looks like a miscommunication passing the string.

Post Situation: 
Tue, 2013-07-09 07:19

This is just a syntax thing. You need to pass a list to Vector1(), so it should be:
>>> params_list = Vector1(['ATP.params'])

with brackets.

Since you didn't use brackets, it interprets the whole string as a list of characters; hence it looking for a file called "A".

Let us know if this still does not work.

Tue, 2013-07-09 07:56

Try using an explicit Vector1_string and making sure you are passing it a list:

params_paths = utility.vector1_string()
residuetypeset = generate_nonstandard_residue_set(params_paths)

Tue, 2013-07-09 07:58


That did it, thanks.

Wed, 2013-07-10 08:54