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Fix: modernise HBA to use AG as objects internally instead of selection strings - code only PR (Issue #3933) #4533

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Fix: modernise HBA to use AG as objects internally instead of selection strings - code only PR (Issue #3933) #4533

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6d8b947
changed hbonds
lunamorrow Mar 27, 2024
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gsoc-1
lunamorrow Mar 27, 2024
670781e
gsoc-1
lunamorrow Mar 27, 2024
24b5371
updated-hbond-analysis-with-atomgroups
lunamorrow Apr 16, 2024
29aa86e
revised changes, still needs some adjustments and docstring example u…
lunamorrow Apr 25, 2024
466d6c0
changed hbonds
lunamorrow Mar 27, 2024
7a514dc
gsoc-1
lunamorrow Mar 27, 2024
4f8d1c1
gsoc-1
lunamorrow Mar 27, 2024
f0bd521
updated-hbond-analysis-with-atomgroups
lunamorrow Apr 16, 2024
2996d0d
revised changes, still needs some adjustments and docstring example u…
lunamorrow Apr 25, 2024
39e77c9
rebasing and fixing
lunamorrow Apr 26, 2024
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1 change: 1 addition & 0 deletions package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -236,6 +236,7 @@ Chronological list of authors
2024
- Aditya Keshari
- Philipp Stärk
- Luna Morrow

External code
-------------
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21 changes: 21 additions & 0 deletions package/CHANGELOG
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Expand Up @@ -14,6 +14,27 @@ The rules for this file:


-------------------------------------------------------------------------------
03/27/23 lunamorrow

* 2.8.1

Fixes

Enhancements
* modernise `HydrogenBondAnalysis` to use `AtomGroups` as objects internally
instead of selection strings

Changes
* `guess_acceptors`, `guess_hydrogens` and `guess_donators` no longer return
selection strings (return `AtomGroups`instead)
* `_prepare` and `_single_frame` no longer pass selection strings to other
class methods (pass `AtomGroups` instead)

Deprecations
* Selection string return of `guess_acceptors`, `guess_hydrogens` and
`guess_donators` has been deprecated in favour of return of `AtomGroups`
and will removed in removed in version 3.0.0 (PR #4533)

??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
tyler.je.reddy
Expand Down
90 changes: 56 additions & 34 deletions package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py
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Expand Up @@ -406,9 +406,9 @@ def guess_hydrogens(self,

Returns
-------
potential_hydrogens: str
String containing the :attr:`resname` and :attr:`name` of all
hydrogen atoms potentially capable of forming hydrogen bonds.
potential_hydrogens: AtomGroup
AtomGroup corresponding to all hydrogen atoms potentially capable
of forming hydrogen bonds.

Notes
-----
Expand All @@ -425,9 +425,9 @@ def guess_hydrogens(self,
the selection.

Alternatively, this function may be used to quickly generate a
:class:`str` of potential hydrogen atoms involved in hydrogen bonding.
This str may then be modified before being used to set the attribute
:attr:`hydrogens_sel`.
:class:`AtomGroup` of potential hydrogen atoms involved in hydrogen
bonding. This :class:`AtomGroup` may then be modified before being used
to set the attribute :attr:`hydrogens_sel`.


.. versionchanged:: 2.4.0
Expand All @@ -447,7 +447,7 @@ def guess_hydrogens(self,
))
]

return self._group_categories(hydrogens_ag)
return hydrogens_ag

def guess_donors(self, select='all', max_charge=-0.5):
"""Guesses which atoms could be considered donors in the analysis. Only
Expand All @@ -465,9 +465,9 @@ def guess_donors(self, select='all', max_charge=-0.5):

Returns
-------
potential_donors: str
String containing the :attr:`resname` and :attr:`name` of all atoms
that are potentially capable of forming hydrogen bonds.
potential_donors: AtomGroup
AtomGroup corresponding to all atoms potentially capable of forming
hydrogen bonds.

Notes
-----
Expand All @@ -485,9 +485,9 @@ def guess_donors(self, select='all', max_charge=-0.5):
selection.

Alternatively, this function may be used to quickly generate a
:class:`str` of potential donor atoms involved in hydrogen bonding.
This :class:`str` may then be modified before being used to set the
attribute :attr:`donors_sel`.
:class:`AtomGroup` of potential donor atoms involved in hydrogen
bonding. This :class:`AtomGroup` may then be modified before being used
to set the attribute :attr:`donors_sel`.


.. versionchanged:: 2.4.0
Expand All @@ -498,11 +498,11 @@ def guess_donors(self, select='all', max_charge=-0.5):
# We need to know `hydrogens_sel` before we can find donors
# Use a new variable `hydrogens_sel` so that we do not set
# `self.hydrogens_sel` if it is currently `None`
hydrogens_ag = self.guess_hydrogens()
if self.hydrogens_sel is None:
hydrogens_sel = self.guess_hydrogens()
hydrogens_sel = self._group_categories(hydrogens_ag)
else:
hydrogens_sel = self.hydrogens_sel
hydrogens_ag = self.u.select_atoms(hydrogens_sel)

# We're using u._topology.bonds rather than u.bonds as it is a million
# times faster to access. This is because u.bonds also calculates
Expand All @@ -521,9 +521,7 @@ def guess_donors(self, select='all', max_charge=-0.5):
)
)

donors_ag = donors_ag[donors_ag.charges < max_charge]

return self._group_categories(donors_ag)
return donors_ag[donors_ag.charges < max_charge]

def guess_acceptors(self, select='all', max_charge=-0.5):
"""Guesses which atoms could be considered acceptors in the analysis.
Expand All @@ -542,9 +540,9 @@ def guess_acceptors(self, select='all', max_charge=-0.5):

Returns
-------
potential_acceptors: str
String containing the :attr:`resname` and :attr:`name` of all atoms
that potentially capable of forming hydrogen bonds.
potential_acceptors: AtomGroup
AtomGroup corresponding to all atoms potentially capable of forming
hydrogen bonds.

Notes
-----
Expand All @@ -560,20 +558,19 @@ def guess_acceptors(self, select='all', max_charge=-0.5):
the selection.

Alternatively, this function may be used to quickly generate a
:class:`str` of potential acceptor atoms involved in hydrogen bonding.
This :class:`str` may then be modified before being used to set the
attribute :attr:`acceptors_sel`.
:class:`AtomGroup` of potential acceptor atoms involved in hydrogen
bonding. This :class:`AtomGroup` may then be modified before being used
to set the attribute :attr:`acceptors_sel`.


.. versionchanged:: 2.4.0
Added ability to use atom types

"""

ag = self.u.select_atoms(select)
acceptors_ag = ag[ag.charges < max_charge]
ag = self.u.select_atoms(select, updating=self.update_selections)

return self._group_categories(acceptors_ag)
return ag[ag.charges < max_charge]

@staticmethod
def _group_categories(group):
Expand Down Expand Up @@ -633,15 +630,17 @@ def _get_dh_pairs(self):
'topology guesser; or set HydrogenBondAnalysis.donors_sel so that a distance cutoff '
'can be used.')

hydrogens = self.u.select_atoms(self.hydrogens_sel)
hydrogens = self.hydrogens_ag
donors = sum(h.bonded_atoms[0] for h in hydrogens) if hydrogens \
else AtomGroup([], self.u)

# Otherwise, use d_h_cutoff as a cutoff distance
else:

hydrogens = self.u.select_atoms(self.hydrogens_sel)
donors = self.u.select_atoms(self.donors_sel)
# hydrogens = self.guess_hydrogens()
# donors = self.guess_donors()
hydrogens = self.hydrogens_ag #NOTE: do I need this?
donors = self.donors_ag #NOTE: do I need this?
donors_indices, hydrogen_indices = capped_distance(
donors.positions,
hydrogens.positions,
Expand All @@ -653,6 +652,19 @@ def _get_dh_pairs(self):
donors = donors[donors_indices]
hydrogens = hydrogens[hydrogen_indices]

# hydrogens = self.hydrogens_ag #NOTE: do I need this?
# donors = self.donors_ag #NOTE: do I need this?
# donors_indices, hydrogen_indices = capped_distance(
# donors.positions,
# hydrogens.positions,
# max_cutoff=self.d_h_cutoff,
# box=self.u.dimensions,
# return_distances=False
# ).T

# donors = donors[donors_indices]
# hydrogens = hydrogens[hydrogen_indices]

return donors, hydrogens

def _filter_atoms(self, donors, acceptors):
Expand Down Expand Up @@ -699,15 +711,25 @@ def _filter_atoms(self, donors, acceptors):
def _prepare(self):
self.results.hbonds = [[], [], [], [], [], []]

# Set unpaired acceptor and hydrogen AtomGroups
# self.acceptors_ag = self.guess_acceptors() #NOTE: do I need this?
# self.hydrogens_ag = self.guess_hydrogens()
# self.donors_ag = self.guess_donors()

# Set atom selections if they have not been provided
if self.acceptors_sel is None:
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You need to make sure acceptors_ag, hydrogens_ag, etc. always exist.

else:
    self.acceptors_ag = self.u.select_atoms(self.acceptors_sel)

self.acceptors_sel = self.guess_acceptors()
self.acceptors_ag = self.guess_acceptors()
self.acceptors_sel = self._group_categories(self.acceptors_ag) #NOTE: do I need this?
if self.hydrogens_sel is None:
self.hydrogens_sel = self.guess_hydrogens()
self.hydrogens_ag = self.guess_hydrogens()
self.hydrogens_sel = self._group_categories(self.hydrogens_ag)
#NOTE: add in self.donors_sel? Is this not done for a reason?
if self.donors_sel is None:
self.donors_ag = self.guess_donors()
self.donors_sel = self._group_categories(self.donors_ag)

# Select atom groups
self._acceptors = self.u.select_atoms(self.acceptors_sel,
updating=self.update_selections)
self._acceptors = self.guess_acceptors()
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You already have self.acceptors_ag above so you don't need to guess it again. Simply parse self._acceptors = self.acceptors_ag

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Oops I missed this one, thank you for picking it up :)

self._donors, self._hydrogens = self._get_dh_pairs()

def _single_frame(self):
Expand Down
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