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bfactor metric #149

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Merged
TecnomaLaser merged 1 commit into from
Jul 31, 2026
Merged

bfactor metric #149

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18 changes: 16 additions & 2 deletions protflow/metrics/biopython_metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -775,12 +775,13 @@ def calc(
return float(np.sum(sequence_separations[contact_mask]) / (protein_length * contact_count))

class Sasa(BiopythonMetric):

"Calculate solvent accessible surface area (SASA) for input atoms"
def __init__(self, name: str | None = None, target: AtomSelectionInput|str = None, probe_radius: float = 1.4, n_points: int = 100, radii_dict: dict = None) -> None:
'''Initialize a Clash detection metric.'''
'''Initialize SASA metric.'''
super().__init__(name=name, target=target, probe_radius=probe_radius, n_points=n_points, radii_dict=radii_dict)

def calc(self, biomolecule: Entity, target: AtomSelectionInput|str = None, probe_radius: float = 1.4, n_points: int = 100, radii_dict: dict = None) -> float: #pylint: disable=W0221
"Run solvent accessible surface area (SASA) calculation for input atoms"

sasa_calc = SASA.ShrakeRupley(probe_radius=probe_radius, n_points=n_points, radii_dict=radii_dict)

Expand All @@ -789,3 +790,16 @@ def calc(self, biomolecule: Entity, target: AtomSelectionInput|str = None, probe
target_atoms = self._parse_atoms(biomolecule, target)

return sum([atom.sasa for atom in target_atoms])

class Bfactor(BiopythonMetric):
"Calculate mean B-factors for selected atoms"
def __init__(self, name: str | None = None, target: AtomSelectionInput|str = None) -> None:
'''Initialize Bfactor metric.'''
super().__init__(name=name, target=target)

def calc(self, biomolecule: Entity, target: AtomSelectionInput|str = None) -> float: #pylint: disable=W0221
"Run calculation of mean B-factors for selected atoms"

target_atoms = self._parse_atoms(biomolecule, target)

return sum([atom.bfactor for atom in target_atoms]) / len(target_atoms)
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