From 11738ad78d64e84ba1e7b9b2bb14bda6a59e66ba Mon Sep 17 00:00:00 2001 From: karolamik13 Date: Wed, 11 Sep 2024 22:46:55 +0200 Subject: [PATCH] InSty - typos and TypeError fixed [James comments] --- prody/proteins/interactions.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py index e996427da..cbe700d87 100644 --- a/prody/proteins/interactions.py +++ b/prody/proteins/interactions.py @@ -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 @@ -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 @@ -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