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Enhance flexible definition in config files / defaults.yaml #969
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Overall great improvements in the readability of the default parameter file.
- Defining the chain to be flexible is probably more intuitive for the user.
- There was an already implemented check that all 3
fle_sta_Y
,fle_end_Y
andfle_seg_Y
are defined, so that's cool.
Nevertheless, I do have some comments related to this new implementation:
- I feel it weird that only the
nfle
parameter is modified but notnseg
, which, from what I understand for now, follows the same semantic. - Also, the new parameter
fle_seg_X
is strange, because on one sideseg
is used to defined a segment ID, and innseg
to define number of semi-flexible segments. Can't we usefle_chain_X
instead ? - Do we really need to keep the
nfle
parameter while we could also count the number offle_sta_X
that should also match the same number ? - There is no error when
nfle
value no not match the number offle_sta_X
definitions. e.g.:
nfle = 1
fle_sta_1 = 1
fle_end_1 = 5
fle_seg_1 = "B"
fle_sta_2 = 6
fle_end_2 = 11
fle_seg_2 = "B"
so I guess computing nfle
on-the-fly could be an interesting solution.
- In some part of the haddock3 parameters, we use
moleculesID
and some otherchainID
/segmentID
. I believe this might get very confusing to some extend. I don't know what is best. Do we still want to use molecule IDs or do we want to talk about chain IDs ? Uniforming this could also help the users.
There is a reason why only
About computing nlfe on the fly, this should be then implemented at the python level in the module and the corresponding parameters passed to CNS. You are welcome to try :-) As for the |
And we are speaking here about full flexibility of defined segment, which means flexible from the start of the simulated annealing process. This is different than the semi-flexible segments that are only treated as flexible in the last two cooling phases, first only side-chains and then side-chains and backbone. |
I've added the missing integrations tests to account for this parameters, |
Changes/additions made by Rodrigo will be in a seperate branch/pull request
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From now on it will be much easier to define a fully flexible segment, amazing!
I’ve added some suggestions for extra clarity, but they are rather minor
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
Co-authored-by: Arha <kravchenko.anna.d@gmail.com>
You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and that you comply with the following criteria:
tox
tests pass. Runtox
command inside the repository folder-test.cfg
examples execute without errors. Insideexamples/
runpython run_tests.py -b
Simplified the fully flexible segments definitions, removing the per-molecule definition.
This removes a lot of parameters from the defaults.yaml files.
Also cleaned up the related CNS scripts, removing unused parameters.
Closes #919