Bio.PDB.HSExposure module¶
Half-sphere exposure and coordination number calculation.
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class
Bio.PDB.HSExposure.
HSExposureCA
(model, radius=12, offset=0)¶ Bases:
Bio.PDB.HSExposure._AbstractHSExposure
Class to calculate HSE based on the approximate CA-CB vectors.
Uses three consecutive CA positions.
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__init__
(self, model, radius=12, offset=0)¶ Initialse class.
- Parameters
model (L{Model}) – the model that contains the residues
radius (float) – radius of the sphere (centred at the CA atom)
offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors
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pcb_vectors_pymol
(self, filename='hs_exp.py')¶ Write PyMol script for visualization.
Write a PyMol script that visualizes the pseudo CB-CA directions at the CA coordinates.
- Parameters
filename (string) – the name of the pymol script file
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class
Bio.PDB.HSExposure.
HSExposureCB
(model, radius=12, offset=0)¶ Bases:
Bio.PDB.HSExposure._AbstractHSExposure
Class to calculate HSE based on the real CA-CB vectors.
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__init__
(self, model, radius=12, offset=0)¶ Initialize class.
- Parameters
model (L{Model}) – the model that contains the residues
radius (float) – radius of the sphere (centred at the CA atom)
offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors
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class
Bio.PDB.HSExposure.
ExposureCN
(model, radius=12.0, offset=0)¶ Bases:
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap
Residue exposure as number of CA atoms around its CA atom.
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__init__
(self, model, radius=12.0, offset=0)¶ Initialize.
A residue’s exposure is defined as the number of CA atoms around that residues CA atom. A dictionary is returned that uses a L{Residue} object as key, and the residue exposure as corresponding value.
- Parameters
model (L{Model}) – the model that contains the residues
radius (float) – radius of the sphere (centred at the CA atom)
offset (int) – number of flanking residues that are ignored in the calculation of the number of neighbors
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