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graph generation file for formats without occupancy information #2

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pegerto opened this issue Sep 20, 2023 · 0 comments
Open

graph generation file for formats without occupancy information #2

pegerto opened this issue Sep 20, 2023 · 0 comments
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@pegerto
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pegerto commented Sep 20, 2023

Using main branch:

when a trajectory file do not contain occupancy,
and a developer try to generate graph
then graph generation file due expected occupancy information.

src/graphpro/graphgen.py:32: in generate
    G = rep.generate(self.ag, self.name)
src/graphpro/graphgen.py:20: in generate
    ca_position = ag.c_alphas_positions(self.chain)
src/graphpro/model.py:39: in c_alphas_positions
    return self._c_alphas(chain).positions
src/graphpro/model.py:29: in _c_alphas
    atoms_filtered = [ag[ag.occupancies.tolist().index(
src/graphpro/model.py:29: in <listcomp>
    atoms_filtered = [ag[ag.occupancies.tolist().index(
../ml/lib/python3.10/site-packages/MDAnalysis/core/groups.py:2537: in __getattr__
    return super(AtomGroup, self).__getattr__(attr)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <AtomGroup with 1 atom>, attr = 'occupancies'

    def __getattr__(self, attr):
        selfcls = type(self).__name__
        if attr in _TOPOLOGY_ATTRS:
            cls = _TOPOLOGY_ATTRS[attr]
            if attr == cls.singular and attr != cls.attrname:
                err = ('{selfcls} has no attribute {attr}. '
                       'Do you mean {plural}?')
                raise AttributeError(err.format(selfcls=selfcls, attr=attr,
                                                plural=cls.attrname))
            else:
                err = 'This Universe does not contain {singular} information'
>               raise NoDataError(err.format(singular=cls.singular))
E               MDAnalysis.exceptions.NoDataError: This Universe does not contain occupancy information


@pegerto pegerto changed the title graph generation file for formats without occupancy information. graph generation file for formats without occupancy information Sep 20, 2023
@pegerto pegerto added the bug Something isn't working label Sep 20, 2023
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