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Link any residues #29

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Link any residues #29

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@js1710 js1710 commented Feb 25, 2019

Added more general support for multi-residue molecules. Currently only works for one molecule and cannot use itps as input.

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first commit. The linking of residues is not fully implemented.
ee67c5d
@js1710
first commit. The linking of residues is not fully implemented.
655c6d7
@js1710
Now can connect residues using the [ global ] section. Will only work…
26ce80d 
… for one molecule in water at the moment
@js1710
Updated documentation
a9d67ad
@js1710
Fixed multiple bugs in the output of multi-residue information. At th…
a67d29e 
…e moment only one multi-residue molecule is supported.
@js1710
updated tests
2dfa5cd
@js1710
Global section removed. Now can enter inter residue connections under…
e51667c 
… a molecule section [< mol >] and the name used for mol will apper in the itp file.
@js1710
updated inter residue test files
4ad9e90
@js1710
updated all bonset workflow to go via Molecule objects. Added test fo…
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…r multi residue molecule itp output
@js1710
fixed bug in previous commit
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@js1710
refactored output to make more streamlined for molecules with any num…
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…ber of residues
@js1710
removed any overlap between Molecule instances and Bead instances
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@js1710
updated documentation
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@js1710 js1710 requested a review from jag1g13 February 25, 2019 12:28
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jag1g13 reviewed Feb 25, 2019
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There's a couple of places I'd like to do a little bit of rearrangement before this gets merged, but generally happy. The tests will make it much easier to do the rearrangements without having to worry too much about whether I've broken anything.

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