updates for chain-wise calculations and fixes multichain processing#14
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ftclark3 wants to merge 31 commits intocabb99:mainfrom
Open
updates for chain-wise calculations and fixes multichain processing#14ftclark3 wants to merge 31 commits intocabb99:mainfrom
ftclark3 wants to merge 31 commits intocabb99:mainfrom
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…ing openmm to keepIds when writing it
…ask attribute of the AWSEM class
…ration tests in the future
…o, watch out for the changes made to the constraints on the pairs for which configurational frustration is evaluated. Now, a pair must be more than 3.5 angstroms apart to be evaluated. This was done to match the default requirement in the write_tcl_script function
…strated contacts (in addition to minimally frustrated contacts, which was already implemented)
…airs in sequence to be calculated if the residues are on different chains. should do a better fix in the future. this current fix could be useful for testing going forward
…meter into amyloid_atlas new edits
fetching latest commits
…irs (i,j) engaging in direct, water-mediated, and protein-mediated contacts
… who don't fall into the short range (4.5-6.5) or long range (6.5-9.5) distance wells
…) but needs to be refactored
…we can now almost completely remove the prody dependency from write_tcl_script
…ce_matrix to Structure and AWSEM classes
… chain in amyloid
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will revisit this soon |
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Description
Improves functionality for multichain processing.
Structure(...,chain="A C")aa_freqandrhovalues to different segments of the chain(s)Todos
Notable points that this PR has either accomplished or will accomplish.
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