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schwede
openstructure
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12189444
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12189444
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2 years ago
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Xavier Robin
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doc: attempt to clarify issues.
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modules/io/doc/profile.rst
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@@ -151,14 +151,15 @@ The IOProfile Class
:type: bool
Only relevant when reading PDB format. When set to true, reads CONECT
statements and applies them in the pdb reader. This can result in
hydrogen bonds salt bridges etc. to be connected. Check the PDB format
definition for more info. This may cause issues in subsequent processing
with the processor as we suddenly have two places where connectivity is
built. For the use case of valid CONECT statements for all hetatms, you
may want to disable processing of bonds between them in
:attr:`ost.conop.Processor.connect_hetatm`
Only relevant when reading files in PDB format. When set to true, reads CONECT
statements and applies them in the PDB reader. This can result in
hydrogen bonds, salt bridges etc. to be connected. Check the PDB format
definition for more info. This may cause issues in subsequent processing,
such as bonds being overriden, or extra, inconsistent bonds, as the
processor suddenly has two separate sources of connectivity.
For the use case where the input PDB file contains valid CONECT
statements for all hetatms, you may want to disable processing of bonds
between them in :attr:`ost.conop.Processor.connect_hetatm`
.. attribute:: processor
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