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Less ambiguous selection when building biomolecule #1758

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merged 5 commits into from
Oct 12, 2023

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dkoes
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@dkoes dkoes commented Oct 4, 2023

If a protein has a chain 'x' and a chain '2' and the x happens to be
next to the 2 in the selection string (chain a b c x 2) the parser fails
to realize that x and 2 are chain identifiers. This makes sure there is
no ambiguity.

There is still a problem with PDBs that have a chain 'bb' (e.g. 2VVJ),
but I'm not up for diving into the parser to fix that.

dkoes added 5 commits October 4, 2023 11:26
If a protein has a chain 'x' and a chain '2' and the x happens to be
next to the 2 in the selection string (chain a b c x 2) the parser fails
to realize that x and 2 are chain identifiers.  This makes sure there is
no ambiguity.

There is still a problem with PDBs that have a chain 'bb' (e.g. 2VVJ),
but I'm not up for diving into the parser to fix that.
Correctly parse biotransform header and include mutiple assemblies if
present.  Some tweaks to the atom parser for efficiency.
@dkoes
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dkoes commented Oct 12, 2023

Any chance of a merge @jamesmkrieger ?

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ok. I'm not sure why it works, but I've made a pdb file with a chain x and it works, so yes.

@jamesmkrieger jamesmkrieger merged commit cd3e513 into prody:master Oct 12, 2023
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2 participants