De-lint groups.py

I did my best (via Google) to make sure that renamed public members and
methods had minimal impact on others' code.

propka.cfg

@@ -342,7 +342,7 @@ common_charge_centre             0
 remove_penalised_group	         1
 
 # non-covalent coupling
-max_intrinsic_pKa_diff         2.0
+max_intrinsic_pka_diff         2.0
 min_interaction_energy         0.5
 max_free_energy_diff           1.0
 min_swap_pka_shift             1.0

propka/calculations.py

@@ -89,8 +89,8 @@ def setup_bonding_and_protonation(parameters, molecular_container):
     my_bond_maker.add_pi_electron_information(molecular_container)
     # Protonate atoms
     if molecular_container.options.protonate_all:
-        my_protonator = propka.protonate.Protonate(verbose=False)
+        PROTONATOR = propka.protonate.Protonate(verbose=False)
-        my_protonator.protonate(molecular_container)
+        PROTONATOR.protonate(molecular_container)
 
 
 def setup_bonding(molecular_container):
@@ -386,10 +386,10 @@ def radial_volume_desolvation(parameters, group):
     """
     all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
     volume = 0.0
-    # TODO - Nathan really wants to rename the Nmass variable.
+    # TODO - Nathan really wants to rename the num_volume variable.
     # He had to re-read the original paper to figure out what it was.
     # A better name would be num_volume.
-    group.Nmass = 0
+    group.num_volume = 0
     min_dist_4th = MIN_DISTANCE_4TH
     for atom in all_atoms:
         # ignore atoms in the same residue
@@ -410,11 +410,11 @@ def radial_volume_desolvation(parameters, group):
             volume += dv_inc
         # buried
         if sq_dist < parameters.buried_cutoff_squared:
-            group.Nmass += 1
+            group.num_volume += 1
-    group.buried = calculate_weight(parameters, group.Nmass)
+    group.buried = calculate_weight(parameters, group.num_volume)
     scale_factor = calculate_scale_factor(parameters, group.buried)
     volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance)
-    group.Emass = group.charge * parameters.desolvationPrefactor \
+    group.energy_volume = group.charge * parameters.desolvationPrefactor \
         * volume_after_allowance * scale_factor
 
 
@@ -589,7 +589,7 @@ def hydrogen_bond_interaction(group1, group2, version):
             # is closer to the titratable atom than the hydrogen. In either
             # case, we set the angle factor to 0
             f_angle = 0.0
-    weight = version.calculate_pair_weight(group1.Nmass, group2.Nmass)
+    weight = version.calculate_pair_weight(group1.num_volume, group2.num_volume)
     exception, value = version.check_exceptions(group1, group2)
     if exception:
         # Do nothing, value should have been assigned.
@@ -614,7 +614,7 @@ def electrostatic_interaction(group1, group2, dist, version):
     # check if we should do coulomb interaction at all
     if not version.check_coulomb_pair(group1, group2, dist):
         return None
-    weight = version.calculate_pair_weight(group1.Nmass, group2.Nmass)
+    weight = version.calculate_pair_weight(group1.num_volume, group2.num_volume)
     value = version.calculate_coulomb_energy(dist, weight)
     return value
 
@@ -633,7 +633,7 @@ def check_coulomb_pair(parameters, group1, group2, dist):
     Returns:
         Boolean
     """
-    num_volume = group1.Nmass + group2.Nmass
+    num_volume = group1.num_volume + group2.num_volume
     do_coulomb = True
     # check if both groups are titratable (ions are taken care of in
     # determinants::set_ion_determinants)
@@ -695,7 +695,7 @@ def backbone_reorganization(parameters, conformation):
                 value = 1.0 - (dist-UNK_BACKBONE_DISTANCE2) \
                     / (UNK_BACKBONE_DISTANCE1-UNK_BACKBONE_DISTANCE2)
                 dpka += UNK_PKA_SCALING2*min(1.0, value)
-        titratable_group.Elocl = dpka*weight
+        titratable_group.energy_local = dpka*weight
 
 
 def check_exceptions(version, group1, group2):
@@ -799,7 +799,7 @@ def check_coo_coo_exception(group1, group2, version):
                                                               closest_atom2)
     f_angle = 1.00
     value = hydrogen_bond_energy(dist, dpka_max, cutoff, f_angle)
-    weight = calculate_pair_weight(version.parameters, group1.Nmass, group2.Nmass)
+    weight = calculate_pair_weight(version.parameters, group1.num_volume, group2.num_volume)
     value = value * (1.0 + weight)
     return exception, value
 
@@ -816,7 +816,7 @@ def check_coo_his_exception(group1, group2, version):
         2. value associated with atypical interaction (None if Boolean is False)
     """
     exception = False
-    if check_buried(group1.Nmass, group2.Nmass):
+    if check_buried(group1.num_volume, group2.num_volume):
         exception = True
     return exception, version.parameters.COO_HIS_exception
 
@@ -833,7 +833,7 @@ def check_oco_his_exception(group1, group2, version):
         2. value associated with atypical interaction (None if Boolean is False)
     """
     exception = False
-    if check_buried(group1.Nmass, group2.Nmass):
+    if check_buried(group1.num_volume, group2.num_volume):
         exception = True
     return exception, version.parameters.OCO_HIS_exception
 
@@ -850,7 +850,7 @@ def check_cys_his_exception(group1, group2, version):
         2. value associated with atypical interaction (None if Boolean is False)
     """
     exception = False
-    if check_buried(group1.Nmass, group2.Nmass):
+    if check_buried(group1.num_volume, group2.num_volume):
         exception = True
     return exception, version.parameters.CYS_HIS_exception
 
@@ -867,7 +867,7 @@ def check_cys_cys_exception(group1, group2, version):
         2. value associated with atypical interaction (None if Boolean is False)
     """
     exception = False
-    if check_buried(group1.Nmass, group2.Nmass):
+    if check_buried(group1.num_volume, group2.num_volume):
         exception = True
     return exception, version.parameters.CYS_CYS_exception
 

propka/coupled_groups.py

@@ -33,7 +33,7 @@ class NonCovalentlyCoupledGroups:
             return {'coupling_factor': -1.0}
          # calculate intrinsic pKa's, if not already done
         for group in [group1, group2]:
-            if not hasattr(group, 'intrinsic_pKa'):
+            if group.intrinsic_pka is None:
                 group.calculate_intrinsic_pka()
         use_ph = self.parameters.pH
         if self.parameters.pH == 'variable':
@@ -70,12 +70,12 @@ class NonCovalentlyCoupledGroups:
             and return_on_fail:
             return {'coupling_factor': -1.0}
         # check intrinsic pka diff
-        if abs(group1.intrinsic_pKa - group2.intrinsic_pKa) \
+        if abs(group1.intrinsic_pka - group2.intrinsic_pka) \
-            > self.parameters.max_intrinsic_pKa_diff and return_on_fail:
+            > self.parameters.max_intrinsic_pka_diff and return_on_fail:
             return {'coupling_factor': -1.0}
         # if everything is OK, calculate the coupling factor and return all info
         factor = self.get_free_energy_diff_factor(default_energy, swapped_energy) \
-            * self.get_pka_diff_factor(group1.intrinsic_pKa, group2.intrinsic_pKa) \
+            * self.get_pka_diff_factor(group1.intrinsic_pka, group2.intrinsic_pka) \
             * self.get_interaction_factor(interaction_energy)
         return {'coupling_factor': factor, 'default_energy': default_energy,
                 'swapped_energy': swapped_energy,
@@ -95,8 +95,8 @@ class NonCovalentlyCoupledGroups:
         """
         intrinsic_pka_diff = abs(pka1-pka2)
         res = 0.0
-        if intrinsic_pka_diff <= self.parameters.max_intrinsic_pKa_diff:
+        if intrinsic_pka_diff <= self.parameters.max_intrinsic_pka_diff:
-            res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pKa_diff)**2
+            res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pka_diff)**2
         return res
 
     def get_free_energy_diff_factor(self, energy1, energy2):
@@ -147,7 +147,7 @@ class NonCovalentlyCoupledGroups:
             info(' Detecting non-covalently coupled residues')
             info('-' * 103)
             info('   Maximum pKa difference:     %4.2f pKa units' \
-                % self.parameters.max_intrinsic_pKa_diff)
+                % self.parameters.max_intrinsic_pka_diff)
             info('   Minimum interaction energy: %4.2f pKa units' \
                 % self.parameters.min_interaction_energy)
             info('   Maximum free energy diff.:  %4.2f pKa units' \
@@ -263,7 +263,7 @@ class NonCovalentlyCoupledGroups:
         str_ = ' ' + '-' * 113 + '\n'
         for group in system:
             str_ += self.tagged_format(' %-8s|' % tag,
-                                       group.getDeterminantString(),
+                                       group.get_determinant_string(),
                                        all_labels)
         return str_ + '\n'
 
@@ -355,8 +355,8 @@ class NonCovalentlyCoupledGroups:
      (group1.label, group2.label, data['coupling_factor'],
       data['default_energy'], data['swapped_energy'],
       data['default_energy'] - data['swapped_energy'], data['pH'],
-      data['interaction_energy'], group1.intrinsic_pKa, group2.intrinsic_pKa,
+      data['interaction_energy'], group1.intrinsic_pka, group2.intrinsic_pka,
-      group1.intrinsic_pKa-group2.intrinsic_pKa, data['swapped_pka1'],
+      group1.intrinsic_pka-group2.intrinsic_pka, data['swapped_pka1'],
       data['swapped_pka2'], data['pka_shift1'], data['pka_shift2'])
 
         return str_

propka/determinants.py

@@ -188,8 +188,8 @@ def set_ion_determinants(conformation_container, version):
         for ion_group in conformation_container.get_ions():
             dist_sq = squared_distance(titratable_group, ion_group)
             if dist_sq < version.parameters.coulomb_cutoff2_squared:
-                weight = version.calculate_pair_weight(titratable_group.Nmass,
+                weight = version.calculate_pair_weight(titratable_group.num_volume,
-                                                       ion_group.Nmass)
+                                                       ion_group.num_volume)
                 # the pKa of both acids and bases are shifted up by negative
                 # ions (and vice versa)
                 value = (-ion_group.charge) \

propka/iterative.py

@@ -339,8 +339,8 @@ class Iterative:
             coulomb    += value
 
         self.pKa_NonIterative  = group.model_pka
-        self.pKa_NonIterative += group.Emass
+        self.pKa_NonIterative += group.energy_volume
-        self.pKa_NonIterative += group.Elocl
+        self.pKa_NonIterative += group.energy_local
         self.pKa_NonIterative += side_chain
         self.pKa_NonIterative += back_bone
         self.pKa_NonIterative += coulomb

propka/output.py

@@ -133,7 +133,7 @@ def getDeterminantSection(protein, conformation, parameters):
             groups = [g for g in protein.conformations[conformation].groups if g.atom.chain_id == chain]
             for group in groups:
                 if group.residue_type == residue_type:
-                    str += "%s" % ( group.getDeterminantString(parameters.remove_penalised_group) )
+                    str += "%s" % ( group.get_determinant_string(parameters.remove_penalised_group) )
 
     # Add a warning in case of coupled residues
     if protein.conformations[conformation].non_covalently_coupled_groups and not protein.options.display_coupled_residues:
@@ -151,7 +151,7 @@ def getSummarySection(protein, conformation, parameters):
     for residue_type in parameters.write_out_order:
         for group in protein.conformations[conformation].groups:
           if group.residue_type == residue_type:
-            str += "%s" % ( group.getSummaryString(parameters.remove_penalised_group) )
+            str += "%s" % ( group.get_summary_string(parameters.remove_penalised_group) )
 
     return str
 

propka/parameters.py

@@ -33,7 +33,7 @@ parameters =          ['Nmin','Nmax','desolvationSurfaceScalingFactor','desolvat
                        'include_H_in_interactions','coupling_max_number_of_bonds',
                        'min_bond_distance_for_hydrogen_bonds','coupling_penalty',
                        'shared_determinants','common_charge_centre','hide_penalised_group', 'remove_penalised_group',
-                       'max_intrinsic_pKa_diff','min_interaction_energy','max_free_energy_diff','min_swap_pka_shift',
+                       'max_intrinsic_pka_diff','min_interaction_energy','max_free_energy_diff','min_swap_pka_shift',
                        'min_pka','max_pka','sidechain_interaction']
 
 strings =             ['version','output_file_tag','ligand_typing','pH','reference']

propka/propka.cfg

@@ -342,7 +342,7 @@ common_charge_centre             0
 remove_penalised_group	         1
 
 # non-covalent coupling
-max_intrinsic_pKa_diff         2.0
+max_intrinsic_pka_diff         2.0
 min_interaction_energy         0.5
 max_free_energy_diff           1.0
 min_swap_pka_shift             1.0

propka/version.py

@@ -18,8 +18,8 @@ class version:
     def calculate_desolvation(self, group):
         return self.desolvation_model(self.parameters, group)
 
-    def calculate_pair_weight(self, Nmass1, Nmass2):
+    def calculate_pair_weight(self, num_volume1, num_volume2):
-        return self.weight_pair_method(self.parameters, Nmass1, Nmass2)
+        return self.weight_pair_method(self.parameters, num_volume1, num_volume2)
 
     # side chains
     def hydrogen_bond_interaction(self, group1, group2):