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expand matrix energy docs
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jamesmkrieger committed Nov 19, 2024
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11 changes: 11 additions & 0 deletions prody/proteins/interactions.py
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Expand Up @@ -3460,6 +3460,17 @@ def buildInteractionMatrixEnergy(self, **kwargs):
:arg energy_list_type: name of the list with energies
default is 'IB_solv'
:type energy_list_type: 'IB_nosolv', 'IB_solv', 'CS'
'IB_solv' and 'IB_nosolv' are derived from empirical potentials from
O Keskin, I Bahar and colleagues from [OK98]_.
'CS' is from MD simulations of amino acid pairs from Carlos Simmerling
and Gary Wu.
.. [OK98] Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL,
Empirical solvent-mediated potentials hold for both intra-molecular
and inter-molecular inter-residue interactions
*Protein Sci* **1998** 7(12):2578-2586.
"""

import numpy as np
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