Matlab: Building a molecular library through permutation [duplicate] - matlab

Question

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Generate a matrix containing all combinations of elements taken from n vectors
(4 answers)
Closed 8 years ago.
I am trying to make an index all possible molecules with 0-46 Hydrogen, 0-20 carbon, 0-13 oxygen, etc. I have 7 atoms in which I am interested: H, C, O, N, Cl, F, and S. I have written the following for loop to show what I am trying to achieve:
MassListIndex = []
%MassIndex = [h,c,o,n,cl,f,s]
for h = 0:46;
for c = 0:20;
for o = 0:13;
for n = 0:15;
for cl=0:5;
for f=0:5;
for s=0:5;
MassListIndex = [MassListIndex;[h,c,o,n,cl,f,s]];
end;
end;
end;
end;
end;
end;
end;
This strikes me as terribly inefficient; I don't want to wait around for 2 months for this to run. I have tried using the combinator.m script, but the problem is that there is only one input for the length of the set that is 'permutated' ie if I want to have up to 46 hydrogens, I need to also have 46 of each of the other 6 atoms. This is computationally...heavy (46^7 ~= 436 billion).
Is there any way to make this sort of computation more efficient? Or do I need to think more about shrinking my list by riding it of 'nonsense permutations' (As far as I know, the molecule H40C2 has never been observed!)
Thanks

Answer 1

The first problem is not that hard. At least not if you remember to preallocate!
I changed you the code into this:
mxidx = 47*21*14*16*6*6*6;
MassListIndex = zeros(mxidx,7);
idx = 1;
for h = 0:46;
for c = 0:20;
for o = 0:13;
for n = 0:15;
for cl=0:5;
for f=0:5;
for s=0:5;
MassListIndex(idx,:) = [h,c,o,n,cl,f,s];
idx = idx + 1;
end;
end;
end;
end;
end;
end;
end;
And it ran in less than a minute on my computer.
Usually Matlab will warn you if you forget to preallocate; and whenever you (like in this case) know in advance the size of you matrix, you should preallocate!
The other problem on the other hand, 47^7 = 506623120463 (more than 500 billions - it is 47^7 instead of 46^7 since the list 0:46 has 47 elements). So even if you only use one byte pr. row in you matrix (which you certainly don't) it will still take up more that a half terabyte! And the calculation times will likewise be humongous!
But really when would you ever need this list. The way you have constructed your list you can easily calculate an entry just by the index eg.:
function m = MassListIndex(a,b)
a = a - 1;
lst = zeros(1,7);
for i = 1:7
lst(8-i) = mod(a,47);
a = floor(a /47);
end
if nargin < 2
m = lst;
else
m = lst(b);
end
end
Edit:
If you want it to also calculate the mass, you may do something like:
function mass = getMassFromPermutationNumber(a)
a = a - 1;
lst = zeros(1,7);
for i = 1:7
lst(8-i) = mod(a,47);
a = floor(a /47);
end
mass = lst*[1.00794;12.011;15.9994;20.1797;35.4527;18.9984;32.066];
end
Source for masses: http://environmentalchemistry.com/yogi/periodic/mass.html
Disclaimer: I'm not that good at chemistry, so please apply reasonable amounts of skepticism!