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add other dali filter arguments to runDali #2020

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add other dali filter arguments to runDali #2020

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23 changes: 21 additions & 2 deletions prody/proteins/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3832,7 +3832,8 @@ def runDali(pdb, chain, **kwargs):
:arg chain: chain identifier
:type chain: str

:arg cutoff_len: Length of aligned residues < cutoff_len (must be an integer or a float between 0 and 1)
:arg cutoff_len: Length of aligned residues < cutoff_len
(must be an integer or a float between 0 and 1)
See searchDali for more details
Default is 0.5
:type cutoff_len: float
Expand All @@ -3841,6 +3842,18 @@ def runDali(pdb, chain, **kwargs):
Default is 1.0
:type cutoff_rmsd: float

:arg cutoff_Z: Z score cutoff (see searchDali)
Default is None
:type cutoff_Z: float

:arg cutoff_identity: RMSD cutoff (see searchDali)
Default is None
:type cutoff_identity: float

:arg stringency: stringency for Dali cutoffs (see searchDali)
Default is False
:type stringency: bool

:arg subset_Dali: fullPDB, PDB25, PDB50, PDB90
Default is 'fullPDB'
:type subset_Dali: str
Expand Down Expand Up @@ -3871,6 +3884,10 @@ def runDali(pdb, chain, **kwargs):

cutoff_len = kwargs.pop('cutoff_len', 0.5)
cutoff_rmsd = kwargs.pop('cutoff_rmsd', 1.0)
cutoff_Z = kwargs.pop('cutoff_Z', None)
cutoff_identity = kwargs.pop('cutoff_identity', None)
stringency = kwargs.pop('stringency', False)

fixer = kwargs.pop('fixer', 'pdbfixer')
subset_Dali = kwargs.pop('subset_Dali', 'fullPDB')
subset = kwargs.pop('subset', 'ca')
Expand All @@ -3883,7 +3900,9 @@ def runDali(pdb, chain, **kwargs):
while not dali_rec.isSuccess:
dali_rec.fetch()

pdb_ids = dali_rec.filter(cutoff_len=cutoff_len, cutoff_rmsd=cutoff_rmsd)
pdb_ids = dali_rec.filter(cutoff_len=cutoff_len, cutoff_rmsd=cutoff_rmsd,
cutoff_Z=cutoff_Z, cutoff_identity=cutoff_identity,
stringency=stringency)
pdb_hits = [ (i[:4], i[4:]) for i in pdb_ids ]

list_pdbs = []
Expand Down
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