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InSty - typos and TypeError fixed [James comments]
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karolamik13 committed Sep 11, 2024
1 parent cf86d94 commit 11738ad
Showing 1 changed file with 5 additions and 4 deletions.
9 changes: 5 additions & 4 deletions prody/proteins/interactions.py
Original file line number Diff line number Diff line change
Expand Up @@ -231,8 +231,8 @@ def get_energy(pair, source):

try:
data_results = data[np.where(np.array(aa_pairs)==lookup)[0]][0][2:][np.where(np.array(sources)==source)][0]
except ImportError:
raise ImportError('Please replace non-standard names of residues with standard names.')
except TypeError:
raise TypeError('Please replace non-standard names of residues with standard names.')

return data_results

Expand Down Expand Up @@ -277,7 +277,7 @@ def showPairEnergy(data, **kwargs):
at the last position in the list. Energy is based on the residue types and not on the distances.
The unit of energy is kcal/mol. The energies defined as 'IB_nosolv' (non-solvent-mediated), 'IB_solv' (solvent-mediated)
are taken from [OK98]_ and 'CS' from InSty paper (under preparation).
Protonation of resiudues is not distinguished. The protonation of residues is not distinguished.
Protonation of residues is not distinguished. The protonation of residues is not distinguished.
Known residues such as HSD, HSE, HIE, and HID (used in MD simulations) are treated as HIS.
:arg data: list with interactions from calcHydrogenBonds() or other types
Expand Down Expand Up @@ -2047,7 +2047,8 @@ def calcStatisticsInteractions(data, **kwargs):
"""Return the statistics of interactions from PDB Ensemble or trajectory including:
(1) the weight for each residue pair: corresponds to the number of counts divided by the
number of frames (values >1 are obtained when the residue pair creates multiple contacts);
(2) average distance of interactions for each pair [in Ang], (3) standard deviation [Ang.],
(2) average distance of interactions for each pair [in Ang],
(3) standard deviation [Ang.],
(4) Energy [in kcal/mol] that is not distance dependent. Energy by default is solvent-mediated
from [OK98]_ ('IB_solv'). To use non-solvent-mediated entries ('IB_nosolv') from [OK98]_ or
solvent-mediated values obtained for InSty paper ('CS', under preparation) change
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