De-lint coupled_groups.py
Some methods/attributes were changed but were checked in Google to make sure other codes were not affected.
This commit is contained in:
Nathan Baker
@@ -3,7 +3,7 @@ import functools
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import propka.ligand
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import propka.ligand
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from propka.output import make_interaction_map
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from propka.output import make_interaction_map
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from propka.determinant import Determinant
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from propka.determinant import Determinant
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from propka.coupled_groups import nccg
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from propka.coupled_groups import NCCG
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from propka.determinants import setBackBoneDeterminants, setIonDeterminants
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from propka.determinants import setBackBoneDeterminants, setIonDeterminants
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from propka.determinants import setDeterminants
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from propka.determinants import setDeterminants
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from propka.group import Group, is_group
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from propka.group import Group, is_group
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@@ -112,7 +112,7 @@ class ConformationContainer:
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if len(list(filter(lambda g: len(g.non_covalently_coupled_groups) > 0,
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if len(list(filter(lambda g: len(g.non_covalently_coupled_groups) > 0,
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self.get_titratable_groups()))) > 0:
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self.get_titratable_groups()))) > 0:
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self.non_covalently_coupled_groups = True
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self.non_covalently_coupled_groups = True
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nccg.identify_non_covalently_coupled_groups(self, verbose=verbose)
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NCCG.identify_non_covalently_coupled_groups(self, verbose=verbose)
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# re-do the check
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# re-do the check
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if len(list(filter(lambda g: len(g.non_covalently_coupled_groups) > 0,
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if len(list(filter(lambda g: len(g.non_covalently_coupled_groups) > 0,
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self.get_titratable_groups()))) > 0:
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self.get_titratable_groups()))) > 0:
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@@ -1,113 +1,113 @@
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"""Describe coupling between groups."""
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from __future__ import division
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import itertools
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from __future__ import print_function
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import propka.lib
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from propka.group import Group
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import math, propka.output, propka.group, propka.lib, itertools
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from propka.output import make_interaction_map
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from propka.lib import info, warning
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from propka.lib import info
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class non_covalently_couple_groups:
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class NonCovalentlyCoupledGroups:
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"""Groups that are coupled without covalent bonding."""
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def __init__(self):
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def __init__(self):
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self.parameters = None
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self.parameters = None
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# self.do_intrinsic = False
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# self.do_pair_wise = False
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self.do_prot_stat = True
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self.do_prot_stat = True
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return
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def is_coupled_protonation_state_probability(self, group1, group2,
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energy_method,
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return_on_fail=True):
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#
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"""Check whether two groups are energetically coupled.
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# Methods for finding coupled groups
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#
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def is_coupled_protonation_state_probability(self, group1, group2, energy_method, return_on_fail=True):
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Args:
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group1: first group for interaction
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group2: second group for interaction
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energy_method: function for calculating energy
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return_on_fail: return if part of the calculation fails
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Returns:
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dictionary describing coupling
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"""
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# check if the interaction energy is high enough
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# check if the interaction energy is high enough
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interaction_energy = max(self.get_interaction(group1,group2), self.get_interaction(group2,group1))
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interaction_energy = max(self.get_interaction(group1, group2),
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self.get_interaction(group2, group1))
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if interaction_energy<=self.parameters.min_interaction_energy and return_on_fail:
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if interaction_energy <= self.parameters.min_interaction_energy \
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return {'coupling_factor':-1.0}
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and return_on_fail:
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return {'coupling_factor': -1.0}
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# calculate intrinsic pKa's, if not already done
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# calculate intrinsic pKa's, if not already done
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for group in [group1, group2]:
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for group in [group1, group2]:
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if not hasattr(group, 'intrinsic_pKa'):
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if not hasattr(group, 'intrinsic_pKa'):
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group.calculate_intrinsic_pka()
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group.calculate_intrinsic_pka()
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use_ph = self.parameters.pH
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use_pH = self.parameters.pH
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if self.parameters.pH == 'variable':
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if self.parameters.pH == 'variable':
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use_pH = min(group1.pka_value, group2.pka_value)
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use_ph = min(group1.pka_value, group2.pka_value)
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default_energy = energy_method(ph=use_ph,
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default_energy = energy_method(ph=use_pH, reference=self.parameters.reference)
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reference=self.parameters.reference)
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default_pka1 = group1.pka_value
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default_pka1 = group1.pka_value
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default_pka2 = group2.pka_value
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default_pka2 = group2.pka_value
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# check that pka values are within relevant limits
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# check that pka values are within relevant limits
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if max(default_pka1, default_pka2) < self.parameters.min_pka or \
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if max(default_pka1, default_pka2) < self.parameters.min_pka or \
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min(default_pka1, default_pka2) > self.parameters.max_pka:
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min(default_pka1, default_pka2) > self.parameters.max_pka:
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if return_on_fail:
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if return_on_fail:
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return {'coupling_factor':-1.0}
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return {'coupling_factor': -1.0}
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# Swap interactions and re-calculate pKa values
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# Swap interactions and re-calculate pKa values
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self.swap_interactions([group1], [group2])
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self.swap_interactions([group1], [group2])
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group1.calculate_total_pka()
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group1.calculate_total_pka()
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group2.calculate_total_pka()
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group2.calculate_total_pka()
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# store swapped energy and pka's
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# store swapped energy and pka's
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swapped_energy = energy_method(ph=use_pH, reference=self.parameters.reference)
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swapped_energy = energy_method(ph=use_ph, reference=self.parameters.reference)
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swapped_pka1 = group1.pka_value
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swapped_pka1 = group1.pka_value
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swapped_pka2 = group2.pka_value
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swapped_pka2 = group2.pka_value
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pka_shift1 = swapped_pka1 - default_pka1
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pka_shift1 = swapped_pka1 - default_pka1
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pka_shift2 = swapped_pka2 - default_pka2
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pka_shift2 = swapped_pka2 - default_pka2
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# Swap back to original protonation state
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# Swap back to original protonation state
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self.swap_interactions([group1], [group2])
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self.swap_interactions([group1], [group2])
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group1.calculate_total_pka()
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group1.calculate_total_pka()
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group2.calculate_total_pka()
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group2.calculate_total_pka()
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# check difference in free energy
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# check difference in free energy
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if abs(default_energy - swapped_energy) > self.parameters.max_free_energy_diff and return_on_fail:
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if abs(default_energy - swapped_energy) > self.parameters.max_free_energy_diff \
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return {'coupling_factor':-1.0}
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and return_on_fail:
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return {'coupling_factor': -1.0}
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# check pka shift
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# check pka shift
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if max(abs(pka_shift1), abs(pka_shift2)) < self.parameters.min_swap_pka_shift and return_on_fail:
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if max(abs(pka_shift1), abs(pka_shift2)) < self.parameters.min_swap_pka_shift \
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return {'coupling_factor':-1.0}
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and return_on_fail:
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return {'coupling_factor': -1.0}
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# check intrinsic pka diff
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# check intrinsic pka diff
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if abs(group1.intrinsic_pKa - group2.intrinsic_pKa) > self.parameters.max_intrinsic_pKa_diff and return_on_fail:
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if abs(group1.intrinsic_pKa - group2.intrinsic_pKa) \
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return {'coupling_factor':-1.0}
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> self.parameters.max_intrinsic_pKa_diff and return_on_fail:
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return {'coupling_factor': -1.0}
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# if everything is OK, calculate the coupling factor and return all info
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# if everything is OK, calculate the coupling factor and return all info
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factor = self.get_free_energy_diff_factor(default_energy, swapped_energy)*\
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factor = self.get_free_energy_diff_factor(default_energy, swapped_energy) \
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self.get_pka_diff_factor(group1.intrinsic_pKa, group2.intrinsic_pKa)*\
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* self.get_pka_diff_factor(group1.intrinsic_pKa, group2.intrinsic_pKa) \
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self.get_interaction_factor(interaction_energy)
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* self.get_interaction_factor(interaction_energy)
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return {'coupling_factor': factor, 'default_energy': default_energy,
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return {'coupling_factor':factor,
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'swapped_energy': swapped_energy,
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'default_energy':default_energy,
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'interaction_energy': interaction_energy,
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'swapped_energy':swapped_energy,
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'swapped_pka1': swapped_pka1, 'swapped_pka2': swapped_pka2,
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'interaction_energy':interaction_energy,
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'pka_shift1': pka_shift1, 'pka_shift2': pka_shift2,
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'swapped_pka1':swapped_pka1,
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'pH': use_ph}
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'swapped_pka2':swapped_pka2,
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'pka_shift1':pka_shift1,
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'pka_shift2':pka_shift2,
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'pH':use_pH}
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#
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# Methods for calculating the coupling factor
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#
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def get_pka_diff_factor(self, pka1, pka2):
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def get_pka_diff_factor(self, pka1, pka2):
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"""Get scaling factor for difference between intrinsic pKa values.
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Args:
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pka1: first pKa to compare
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pka2: second pKa to compare
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Returns:
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float value of scaling factor
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"""
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intrinsic_pka_diff = abs(pka1-pka2)
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intrinsic_pka_diff = abs(pka1-pka2)
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res = 0.0
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res = 0.0
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if intrinsic_pka_diff <= self.parameters.max_intrinsic_pKa_diff:
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if intrinsic_pka_diff <= self.parameters.max_intrinsic_pKa_diff:
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res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pKa_diff)**2
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res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pKa_diff)**2
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return res
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return res
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def get_free_energy_diff_factor(self, energy1, energy2):
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def get_free_energy_diff_factor(self, energy1, energy2):
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"""Get scaling factor for difference between free energies.
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Args:
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energy1: first energy to compare
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energy2: second energy to compare
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Returns:
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float value of scaling factor
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"""
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free_energy_diff = abs(energy1-energy2)
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free_energy_diff = abs(energy1-energy2)
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res = 0.0
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res = 0.0
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if free_energy_diff <= self.parameters.max_free_energy_diff:
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if free_energy_diff <= self.parameters.max_free_energy_diff:
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@@ -115,19 +115,28 @@ class non_covalently_couple_groups:
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return res
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return res
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def get_interaction_factor(self, interaction_energy):
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def get_interaction_factor(self, interaction_energy):
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"""Get scaling factor related to interaction energy.
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Args:
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interaction_energy: interaction energy
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Returns:
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float value of scaling factor
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"""
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res = 0.0
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res = 0.0
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interaction_energy = abs(interaction_energy)
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interaction_energy = abs(interaction_energy)
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if interaction_energy >= self.parameters.min_interaction_energy:
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if interaction_energy >= self.parameters.min_interaction_energy:
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res = (interaction_energy-self.parameters.min_interaction_energy)/(1.0+interaction_energy-self.parameters.min_interaction_energy)
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res = (interaction_energy-self.parameters.min_interaction_energy) \
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/ (1.0+interaction_energy-self.parameters.min_interaction_energy)
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return res
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return res
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def identify_non_covalently_coupled_groups(self, conformation,
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verbose=True):
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"""Find coupled residues in protein.
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Args:
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conformation: protein conformation to test
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def identify_non_covalently_coupled_groups(self, conformation, verbose=True):
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verbose: verbose output (boolean)
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""" Finds coupled residues in protein """
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"""
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self.parameters = conformation.parameters
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self.parameters = conformation.parameters
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if verbose:
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if verbose:
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info('')
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info('')
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@@ -137,186 +146,220 @@ class non_covalently_couple_groups:
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info('-' * 103)
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info('-' * 103)
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info(' Detecting non-covalently coupled residues')
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info(' Detecting non-covalently coupled residues')
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info('-' * 103)
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info('-' * 103)
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info(' Maximum pKa difference: %4.2f pKa units' % self.parameters.max_intrinsic_pKa_diff)
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info(' Maximum pKa difference: %4.2f pKa units' \
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info(' Minimum interaction energy: %4.2f pKa units' % self.parameters.min_interaction_energy)
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% self.parameters.max_intrinsic_pKa_diff)
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info(' Maximum free energy diff.: %4.2f pKa units' % self.parameters.max_free_energy_diff)
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info(' Minimum interaction energy: %4.2f pKa units' \
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info(' Minimum swap pKa shift: %4.2f pKa units' % self.parameters.min_swap_pka_shift)
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% self.parameters.min_interaction_energy)
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info(' Maximum free energy diff.: %4.2f pKa units' \
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% self.parameters.max_free_energy_diff)
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info(' Minimum swap pKa shift: %4.2f pKa units' \
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% self.parameters.min_swap_pka_shift)
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info(' pH: %6s ' % str(self.parameters.pH))
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info(' pH: %6s ' % str(self.parameters.pH))
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info(' Reference: %s' % self.parameters.reference)
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info(' Reference: %s' % self.parameters.reference)
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info(' Min pKa: %4.2f' % self.parameters.min_pka)
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info(' Min pKa: %4.2f' % self.parameters.min_pka)
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info(' Max pKa: %4.2f' % self.parameters.max_pka)
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info(' Max pKa: %4.2f' % self.parameters.max_pka)
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info('')
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info('')
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# find coupled residues
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# find coupled residues
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titratable_groups = conformation.get_titratable_groups()
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titratable_groups = conformation.get_titratable_groups()
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if not conformation.non_covalently_coupled_groups:
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if not conformation.non_covalently_coupled_groups:
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for g1 in titratable_groups:
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for group1 in titratable_groups:
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for g2 in titratable_groups:
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for group2 in titratable_groups:
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if g1==g2:
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if group1 == group2:
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break
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break
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if not group1 in group2.non_covalently_coupled_groups \
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if not g1 in g2.non_covalently_coupled_groups and self.do_prot_stat:
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and self.do_prot_stat:
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data = self.is_coupled_protonation_state_probability(g1, g2,conformation.calculate_folding_energy)
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data = self.\
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if data['coupling_factor'] >0.0:
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is_coupled_protonation_state_probability(group1,
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g1.couple_non_covalently(g2)
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group2,
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conformation.\
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calculate_folding_energy)
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if data['coupling_factor'] > 0.0:
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group1.couple_non_covalently(group2)
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if verbose:
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if verbose:
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self.print_out_swaps(conformation)
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self.print_out_swaps(conformation)
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return
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def print_out_swaps(self, conformation):
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"""Print out something having to do with coupling interactions.
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def print_out_swaps(self, conformation, verbose=True):
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Args:
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map = propka.output.make_interaction_map('Non-covalent coupling map for %s'%conformation,
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conformation: conformation to print
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"""
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map_ = make_interaction_map('Non-covalent coupling map for %s' % conformation,
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conformation.get_non_covalently_coupled_groups(),
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conformation.get_non_covalently_coupled_groups(),
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lambda g1,g2: g1 in g2.non_covalently_coupled_groups)
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lambda g1, g2: g1 in g2.non_covalently_coupled_groups)
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info(map)
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info(map_)
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for system in conformation.get_coupled_systems(conformation.\
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for system in conformation.get_coupled_systems(conformation.get_non_covalently_coupled_groups(),propka.group.Group.get_non_covalently_coupled_groups):
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get_non_covalently_coupled_groups(), \
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Group.get_non_covalently_coupled_groups):
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self.print_system(conformation, list(system))
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self.print_system(conformation, list(system))
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return
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def print_system(self, conformation, system):
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def print_system(self, conformation, system):
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"""Print out something about the system.
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Args:
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conformation: conformation to print
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system: system to print
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"""
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info('System containing %d groups:' % len(system))
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info('System containing %d groups:' % len(system))
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# make list of interactions within this system
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# make list of interactions withi this system
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interactions = list(itertools.combinations(system, 2))
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interactions = list(itertools.combinations(system,2))
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# print out coupling info for each interaction
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# print out coupling info for each interaction
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coup_info = ''
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coup_info = ''
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for interaction in interactions:
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for interaction in interactions:
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data = self.is_coupled_protonation_state_probability(interaction[0], interaction[1],conformation.calculate_folding_energy, return_on_fail=False)
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data = self.is_coupled_protonation_state_probability(interaction[0], \
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coup_info += self.make_data_to_string(data,interaction[0],interaction[1])+'\n\n'
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interaction[1], conformation.calculate_folding_energy, \
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return_on_fail=False)
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coup_info += self.make_data_to_string(data, interaction[0], \
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interaction[1]) + '\n\n'
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info(coup_info)
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info(coup_info)
|
||||||
|
|
||||||
# make list of possible combinations of swap to try out
|
# make list of possible combinations of swap to try out
|
||||||
combinations = propka.lib.generate_combinations(interactions)
|
combinations = propka.lib.generate_combinations(interactions)
|
||||||
|
|
||||||
# Make possible swap combinations
|
# Make possible swap combinations
|
||||||
swap_info = ''
|
swap_info = ''
|
||||||
swap_info += self.print_determinants_section(system,'Original')
|
swap_info += self.print_determinants_section(system, 'Original')
|
||||||
|
|
||||||
for combination in combinations:
|
for combination in combinations:
|
||||||
# Tell the user what is swap in this combination
|
# Tell the user what is swap in this combination
|
||||||
swap_info += 'Swapping the following interactions:\n'
|
swap_info += 'Swapping the following interactions:\n'
|
||||||
for interaction in combination:
|
for interaction in combination:
|
||||||
swap_info += ' %s %s\n'%(interaction[0].label, interaction[1].label)
|
swap_info += ' %s %s\n' % (interaction[0].label,
|
||||||
|
interaction[1].label)
|
||||||
# swap...
|
# swap...
|
||||||
for interaction in combination:
|
for interaction in combination:
|
||||||
self.swap_interactions([interaction[0]],[interaction[1]])
|
self.swap_interactions([interaction[0]], [interaction[1]])
|
||||||
|
swap_info += self.print_determinants_section(system, 'Swapped')
|
||||||
swap_info += self.print_determinants_section(system,'Swapped')
|
|
||||||
# ...and swap back
|
|
||||||
#for interaction in combination:
|
|
||||||
# self.swap_interactions([interaction[0]], [interaction[1]])
|
|
||||||
|
|
||||||
info(swap_info)
|
info(swap_info)
|
||||||
|
|
||||||
return
|
@staticmethod
|
||||||
#
|
def get_interaction(group1, group2, include_side_chain_hbs=True):
|
||||||
# Interaction and swapping methods
|
"""Get interaction energy between two groups.
|
||||||
#
|
|
||||||
|
|
||||||
def get_interaction(self, group1, group2, include_side_chain_hbs = True):
|
Args:
|
||||||
|
group1: first group for interaction
|
||||||
|
group2: second group for interaction
|
||||||
|
include_side_chain_hbs: include side-chain hydrogen bonds in energy
|
||||||
|
Returns:
|
||||||
|
interaction energy (float)
|
||||||
|
"""
|
||||||
determinants = group1.determinants['coulomb']
|
determinants = group1.determinants['coulomb']
|
||||||
if include_side_chain_hbs:
|
if include_side_chain_hbs:
|
||||||
determinants = group1.determinants['sidechain'] + group1.determinants['coulomb']
|
determinants = group1.determinants['sidechain'] \
|
||||||
|
+ group1.determinants['coulomb']
|
||||||
interaction_energy = 0.0
|
interaction_energy = 0.0
|
||||||
for det in determinants:
|
for det in determinants:
|
||||||
if group2 == det.group:
|
if group2 == det.group:
|
||||||
interaction_energy += det.value
|
interaction_energy += det.value
|
||||||
|
|
||||||
return interaction_energy
|
return interaction_energy
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def print_determinants_section(self, system, tag):
|
def print_determinants_section(self, system, tag):
|
||||||
|
"""Print determinants of system.
|
||||||
|
|
||||||
|
Args:
|
||||||
|
system: set of groups
|
||||||
|
tag: something to add to output
|
||||||
|
Returns:
|
||||||
|
string with summary
|
||||||
|
"""
|
||||||
all_labels = [g.label for g in system]
|
all_labels = [g.label for g in system]
|
||||||
s = ' '+'-'*113+'\n'
|
str_ = ' ' + '-' * 113 + '\n'
|
||||||
for group in system:
|
for group in system:
|
||||||
s += self.tagged_format(' %-8s|' % tag, group.getDeterminantString(), all_labels)
|
str_ += self.tagged_format(' %-8s|' % tag,
|
||||||
|
group.getDeterminantString(),
|
||||||
|
all_labels)
|
||||||
|
return str_ + '\n'
|
||||||
|
|
||||||
return s+'\n'
|
def swap_interactions(self, groups1, groups2, include_side_chain_hbs=True):
|
||||||
|
"""Swap interactions between two groups.
|
||||||
|
|
||||||
def swap_interactions(self, groups1, groups2, include_side_chain_hbs = True):
|
Args:
|
||||||
|
group1: first group to swap
|
||||||
for i in range(len(groups1)):
|
group2: second group to swap
|
||||||
group1 = groups1[i]
|
"""
|
||||||
|
for i, group1 in enumerate(groups1):
|
||||||
group2 = groups2[i]
|
group2 = groups2[i]
|
||||||
|
|
||||||
# swap the interactions!
|
# swap the interactions!
|
||||||
self.transfer_determinant(group1.determinants['coulomb'], group2.determinants['coulomb'], group1.label, group2.label)
|
self.transfer_determinant(group1.determinants['coulomb'],
|
||||||
|
group2.determinants['coulomb'],
|
||||||
|
group1.label, group2.label)
|
||||||
if include_side_chain_hbs:
|
if include_side_chain_hbs:
|
||||||
self.transfer_determinant(group1.determinants['sidechain'], group2.determinants['sidechain'], group1.label, group2.label)
|
self.transfer_determinant(group1.determinants['sidechain'],
|
||||||
|
group2.determinants['sidechain'],
|
||||||
|
group1.label, group2.label)
|
||||||
# re-calculate pKa values
|
# re-calculate pKa values
|
||||||
group1.calculate_total_pka()
|
group1.calculate_total_pka()
|
||||||
group2.calculate_total_pka()
|
group2.calculate_total_pka()
|
||||||
|
|
||||||
return
|
@staticmethod
|
||||||
|
def transfer_determinant(determinants1, determinants2,
|
||||||
|
label1, label2):
|
||||||
|
"""Transfer information between two sets of determinants.
|
||||||
|
|
||||||
|
Args:
|
||||||
def transfer_determinant(self, determinants1, determinants2, label1, label2):
|
determinants1: determinant list
|
||||||
|
determinants2: determinant list
|
||||||
|
label1: label for list 1
|
||||||
|
label2: label for list 2
|
||||||
|
"""
|
||||||
# find out what to transfer...
|
# find out what to transfer...
|
||||||
from1to2 = []
|
from1to2 = []
|
||||||
from2to1 = []
|
from2to1 = []
|
||||||
for det in determinants1:
|
for det in determinants1:
|
||||||
if det.label == label2:
|
if det.label == label2:
|
||||||
from1to2.append(det)
|
from1to2.append(det)
|
||||||
|
|
||||||
for det in determinants2:
|
for det in determinants2:
|
||||||
if det.label == label1:
|
if det.label == label1:
|
||||||
from2to1.append(det)
|
from2to1.append(det)
|
||||||
|
|
||||||
# ...and transfer it!
|
# ...and transfer it!
|
||||||
for det in from1to2:
|
for det in from1to2:
|
||||||
det.label = label1
|
det.label = label1
|
||||||
determinants2.append(det)
|
determinants2.append(det)
|
||||||
determinants1.remove(det)
|
determinants1.remove(det)
|
||||||
|
|
||||||
for det in from2to1:
|
for det in from2to1:
|
||||||
det.label = label2
|
det.label = label2
|
||||||
determinants1.append(det)
|
determinants1.append(det)
|
||||||
determinants2.remove(det)
|
determinants2.remove(det)
|
||||||
|
|
||||||
return
|
@staticmethod
|
||||||
|
def tagged_format(tag, str_, labels):
|
||||||
|
"""Tag a string.
|
||||||
|
|
||||||
#
|
Args:
|
||||||
# Output methods
|
tag: tag to add
|
||||||
#
|
str_: string to tag
|
||||||
|
labels: labels to replace
|
||||||
def tagged_format(self, tag, s, labels):
|
Returns:
|
||||||
s = "%s %s"%(tag,s)
|
tagged string
|
||||||
s = s.replace('\n','\n%s '%tag)
|
"""
|
||||||
|
str_ = "%s %s" % (tag, str_)
|
||||||
|
str_ = str_.replace('\n', '\n%s ' % tag)
|
||||||
for label in labels:
|
for label in labels:
|
||||||
s = s.replace(label, '\033[31m%s\033[30m'%label)
|
str_ = str_.replace(label, '\033[31m%s\033[30m' % label)
|
||||||
return s+'\n'
|
return str_ + '\n'
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def make_data_to_string(data, group1, group2):
|
||||||
|
"""Describe interaction between groups.
|
||||||
|
|
||||||
def make_data_to_string(self, data, group1, group2):
|
Args:
|
||||||
s = """ %s and %s coupled (prot.state): %5.2f
|
data: data about interactions
|
||||||
|
group1: first group
|
||||||
|
group2: second group
|
||||||
|
Returns:
|
||||||
|
formatted string with information.
|
||||||
|
"""
|
||||||
|
str_ = \
|
||||||
|
""" %s and %s coupled (prot.state): %5.2f
|
||||||
Energy levels: %6.2f, %6.2f (difference: %6.2f) at pH %6.2f
|
Energy levels: %6.2f, %6.2f (difference: %6.2f) at pH %6.2f
|
||||||
Interaction energy: %6.2f
|
Interaction energy: %6.2f
|
||||||
Intrinsic pka's: %6.2f, %6.2f (difference: %6.2f)
|
Intrinsic pka's: %6.2f, %6.2f (difference: %6.2f)
|
||||||
Swapped pKa's: %6.2f, %6.2f (difference: %6.2f, %6.2f)"""%(group1.label,
|
Swapped pKa's: %6.2f, %6.2f (difference: %6.2f, %6.2f)""" % \
|
||||||
group2.label,
|
(group1.label, group2.label, data['coupling_factor'],
|
||||||
data['coupling_factor'],
|
|
||||||
data['default_energy'], data['swapped_energy'],
|
data['default_energy'], data['swapped_energy'],
|
||||||
data['default_energy'] - data['swapped_energy'],
|
data['default_energy'] - data['swapped_energy'], data['pH'],
|
||||||
data['pH'],
|
data['interaction_energy'], group1.intrinsic_pKa, group2.intrinsic_pKa,
|
||||||
data['interaction_energy'],
|
group1.intrinsic_pKa-group2.intrinsic_pKa, data['swapped_pka1'],
|
||||||
group1.intrinsic_pKa,
|
data['swapped_pka2'], data['pka_shift1'], data['pka_shift2'])
|
||||||
group2.intrinsic_pKa,
|
|
||||||
group1.intrinsic_pKa-group2.intrinsic_pKa,
|
|
||||||
data['swapped_pka1'],
|
|
||||||
data['swapped_pka2'],
|
|
||||||
data['pka_shift1'],
|
|
||||||
data['pka_shift2'])
|
|
||||||
|
|
||||||
return s
|
return str_
|
||||||
|
|
||||||
|
|
||||||
nccg = non_covalently_couple_groups()
|
NCCG = NonCovalentlyCoupledGroups()
|
||||||
|
|||||||
Reference in New Issue
Block a user