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fix filterInteractions to be more general #2014

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merged 3 commits into from
Dec 13, 2024
Merged

fix filterInteractions to be more general #2014

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1013f4e
fix filterInteractions single selection to include chain
jamesmkrieger Dec 10, 2024
532dba1
complete general filterInteractions
jamesmkrieger Dec 13, 2024
eadb59c
Merge branch 'main' of github.com:prody/ProDy into filter_ints
jamesmkrieger Dec 13, 2024
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56 changes: 37 additions & 19 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,33 +127,51 @@ def get_permutation_from_dic(dictionary, key):


def filterInteractions(list_of_interactions, atoms, **kwargs):
"""Return interactions based on selection."""
"""Return interactions based on *selection* and *selection2*."""

if 'selection1' in kwargs:
kwargs['selection'] = kwargs['selection1']

if 'selection' in kwargs:
if 'selection2' in kwargs:
if not 'chid' in kwargs['selection'] and not 'chain' in kwargs['selection']:
LOGGER.warn('selection does not include chid or chain, so no filtering is performed')
return list_of_interactions
selection = atoms.select(kwargs['selection'])
if selection is None:
LOGGER.warn('selection did not work, so no filtering is performed')
return list_of_interactions

ch1 = selection.getChids()
x1 = selection.getResnames()
y1 = selection.getResnums()
listOfselection = np.unique(list(map(lambda x1, y1, ch1: (ch1, x1 + str(y1)),
x1, y1, ch1)),
axis=0)
listOfselection = [list(i) for i in listOfselection] # needed for in check to work

if not 'chid' in kwargs['selection2'] and not 'chain' in kwargs['selection2']:
LOGGER.warn('selection2 does not include chid or chain, so no filtering is performed')
if 'selection2' in kwargs:
selection2 = atoms.select(kwargs['selection2'])
if selection2 is None:
LOGGER.warn('selection2 did not work, so no filtering is performed')
return list_of_interactions

ch1 = kwargs['selection'].split()[-1]
ch2 = kwargs['selection2'].split()[-1]
final = [i for i in list_of_interactions if (i[2] == ch1 and i[5] == ch2) or (i[5] == ch1 and i[2] == ch2)]

ch2 = selection2.getChids()
x2 = selection2.getResnames()
y2 = selection2.getResnums()
listOfselection2 = np.unique(list(map(lambda x2, y2, ch2: (ch2, x2 + str(y2)),
x2, y2, ch2)),
axis=0)
listOfselection2 = [list(i) for i in listOfselection2] # needed for in check to work

final = [i for i in list_of_interactions if (([i[2], i[0]] in listOfselection)
and ([i[5], i[3]] in listOfselection2)
or ([i[2], i[0]] in listOfselection2)
and ([i[5], i[3]] in listOfselection))]
else:
p = atoms.select('same residue as protein within 10 of ('+kwargs['selection']+')')
if p is None:
LOGGER.warn('selection did not work, so no filtering is performed')
return list_of_interactions
final = [i for i in list_of_interactions
if (([i[2], i[0]] in listOfselection)
or ([i[5], i[3]] in listOfselection))]

x = p.select(kwargs['selection']).getResnames()
y = p.select(kwargs['selection']).getResnums()
listOfselection = np.unique(list(map(lambda x, y: x + str(y), x, y)))
final = [i for i in list_of_interactions if i[0] in listOfselection or i[3] in listOfselection]
elif 'selection2' in kwargs:
LOGGER.warn('selection2 by itself is ignored')
final = list_of_interactions
else:
final = list_of_interactions
return final
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