I want to get the RMSD for each pair of poses generated by an autodock docking via the align function:
align pose1, pose2, cycles=0, transform=0
Instead of using the names of the poses as input, I want to access a list that contains all poses.
This list is successfully obtained via:
allobjects = cmd.get_object_list('all')
and
print(allobjects[x])
successfully prints the pose at position x in this list.
However, the following method did not work:
align allobjects[1], allobjects[2], cycles=0, transform=0
yields error: Invalid selection name "allobjects[1]"
What would be the correct way to feed the align function with the list indices?
Thank you in advance!
As far as I know, you can not pass values from python variables to the built-in functions of PyMOL. But there is almost always an equivalent python function that does the same and can receive regular pythonic arguments. In the case of align it would be cmd.align().
The result of cmd.align() is not printed as nice as the align function, but instead a list of 7 elements is returned, being the first element the calculated RMSD. The meaning of the rest of the values can be found in the source code of the function.
I also assume that you intent to calculate the RMSD for every possible pair of docked structures. For that purpose you have to use all the unique combinations of all structures and manually do a python loop over them. Be aware that the calculation time will increase exponentially with the number of structures you have.
allobjects = cmd.get_object_list('all')
from itertools import combinations
for pair in combinations(allobjects, 2): print(pair[0], pair[1], cmd.align(pair[0], pair[1], cycles=0, transform=0)[0])
I know that you can use model.wv.most_similar(...) to get words by cosine similarity in gensim.
I also know gensim gives you input and output vectors in e.g. model.syn0 and model.syn1neg.
Is there a simple way to calculate cosine similarity and create a list of most similar using only the input or output vectors, one or the other? E.g. I want to try doing it using just output vectors.
There's no built-in facility, but I believe you could achieve it by creating a separate KeyedVectors instance where you replace the usual ('input projection'/'syn0') vector-array with the same-sized output array (as exists in negative-sampling models).
Roughly the following may work:
full_w2v_model = ... # whatever training/loading is necessary
full_w2v_model.wv.save_word2vec_format(PATH) # saves just the word-vectors
out_vecs = KeyedVectors.load_word2vec_format(PATH) # reloads as separate object
out_vecs.vectors = full_w2v_model.syn1neg # clobber raw vecs with model's output layer
(Let me know if this works as-is or neds some further touch-up to work!)
I have a list that should display 7 items that each look like this:
Date Weekday Distance Time
Long text that may span many lines
two column text Distance Time
two column text Distance Time
two column text Distance Time
The last lines repeat in a number depending on the data, i e there may be different amounts of such lines for each list item.
I have tried implementing this with a ListCellRenderer that creates a table according to the requirements above, but I have a few problems with it:
The long text that may span many lines is implemented in a SpanLabel. But this text will not display more than one line anyway
Each item in the list will get space for the same number of lines below the first two..
So it seems that items in a list must be of the same size.
Later I also want to be able to detect selection on the entire list item, not just individual fields of it.
Is there a better way to do this?
How do I ensure that the SpanLabel actually gets as much space as it needs?
How do I ensure that the unknown number of lines gets the space they need, depending on how many they are?
Don't use a list: https://www.codenameone.com/blog/deeper-in-the-renderer.html
Lists in Codename One assume every entry is exactly the same height and provide no flexibility here.
I suggest doing something like the property cross demo: https://www.udemy.com/learn-mobile-programming-by-example-with-codename-one/
Where we use a Container with components within to provide a list like behavior with the full flexibility that arbitrary components allow.
I am running a NetLogo model in BehaviorSpace each time varying number of runs. I have turtle-breed pigs, and they accumulate a table with patch-types as keys and number of visits to each patch-type as values.
In the end I calculate a list of mean number of visits from all pigs. The list has the same length as long as the original table has the same number of keys (number of patch-types). I would like to export this mean number of visits to each patch-type with BehaviorSpace.
Perhaps I could write a separate csv file (tried - creates many files, so lots of work later on putting them together). But I would rather have everything in the same file output after a run.
I could make a global variable for each patch-type but this seems crude and wrong. Especially if I upload a different patch configuration.
I tried just exporting the list, but then in Excel I see it with brackets e.g. [49 0 31.5 76 7 0].
So my question Q1: is there a proper way to export a list of values so that in BehaviorSpace table output csv there is a column for each value?
Q2: Or perhaps there is an example of how to output a single csv that looks exactly as I want it from BehaviorSpace?
PS: In my case the patch types are costs. And I might change those in the future and rerun everything. Ideally I would like to have as output: a graph of costs vs frequency of visits.
Thanks
If the lists are a fixed length that doesn't vary from run to run, you can get the items into separate columns by using one metric for each item. So in your BehaviorSpace experiment definition, instead of putting mylist, put item 0 mylist and item 1 mylist and so on.
If the lists aren't always the same length, you're out of luck. BehaviorSpace isn't flexible that way. You would have to write a separate program (in the programming language of your choice, perhaps NetLogo itself, perhaps an Excel macro, perhaps something else) to postprocess the BehaviorSpace output and make it look how you want.
I am new to prolog and I am trying to create a predicate and am having some trouble.
I have a list of cities that are connected via train. They are connected via my links/2 clause.
links(toronto, ajax).
links(toronto, markham).
links(toronto, brampton).
links(brampton, markham).
links(markham, ajax).
links(brampton, mississauga).
links(mississauga, toronto).
links(mississuaga, oakville).
links(oakville, st.catharines).
links(oakville, hamilton).
links(hamilton, st.catharines).
I am writing a predicate called addnewcities which will take a list of cities and then return a new list containing the original list, plus all the cities that are directly connected to each of the cities in the original list.
Here is a (rough looking) visual representation of the links.
If my input list was [toronto] I want my output to be (order doesnt matter) [ajax,markham,brampton,mississauga,toronto].
If input was [oakville,hamilton] I want the output to be [mississauga,st.catharines,oakville,hamilton].
Here is my predicate so far.
addnewcities([],_).
addnewcities([CitiesH|Tail],Ans):- directer(CitiesH,Ans2), merger(Ans2,[CitiesH],Ans), addnewcities(Tail,Ans).
directer/2 takes a city and saves a list containing all the directly connected cities in the second arg.
merger/3 just merges two lists making sure there are no duplicates in the final list.
When my input is a list with one element ie [toronto] it works!
But when I have a list with multiple elements [toronto,ajax] it says "false" every time.
I'm pretty sure my issue is that when it recurses for the second time, merge is what says its false. I just don't know how to get around this so that my list can keep being updated instead of being checked if true or false.
Any help is appreciated!
this query uses library support to solve the problem:
addcities(Cs, L) :-
setof(D, C^(member(C,Cs), (C=D;link(C,D);link(D,C))), L).
This should work for what you want:
addcities(A,B):-
addcitiesaux(A,[],B).
addcitiesaux([],X,X).
addcitiesaux([X|Xs],L,R):-
link(X,A),
\+ member(A,L),
!,
addcitiesaux([X|Xs],[A|L],R).
addcitiesaux([X|Xs],L,R):-
link(A,X),
\+ member(A,L),
!,
addcitiesaux([X|Xs],[A|L],R).
addcitiesaux([X|Xs],L,R):-
addcitiesaux(Xs,[X|L],R).