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De-lint propka/atom.py

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Other changes are a result of Atom use in other files.
This commit is contained in:
Nathan Baker
2020-05-17 17:08:38 -07:00
parent 303aaae25a
commit 10efc3c7f9
10 changed files with 178 additions and 177 deletions
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12
propka/iterative.py
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@@ -124,9 +124,9 @@ def addIterativeIonPair(object1, object2, interaction, version):
Q2 = object2.Q
comp1 = object1.pKa_old + annihilation[0] + Q1*coulomb_value
comp2 = object2.pKa_old + annihilation[1] + Q2*coulomb_value
if object1.resName not in version.parameters.exclude_sidechain_interactions:
if object1.res_name not in version.parameters.exclude_sidechain_interactions:
comp1 += Q1*hbond_value
if object2.resName not in version.parameters.exclude_sidechain_interactions:
if object2.res_name not in version.parameters.exclude_sidechain_interactions:
comp2 += Q2*hbond_value
if Q1 == -1.0 and comp1 < comp2:
@@ -155,12 +155,12 @@ def addIterativeIonPair(object1, object2, interaction, version):
# Side-chain
if hbond_value > 0.005:
# residue1
if object1.resName not in version.parameters.exclude_sidechain_interactions:
if object1.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object2, Q1*hbond_value]
annihilation[0] += -Q1*hbond_value
object1.determinants['sidechain'].append(interaction)
# residue2
if object2.resName not in version.parameters.exclude_sidechain_interactions:
if object2.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object1, Q2*hbond_value]
annihilation[1] += -Q2*hbond_value
object2.determinants['sidechain'].append(interaction)
@@ -309,7 +309,7 @@ class Iterative:
self.label = group.label
self.atom = group.atom
self.resName = group.residue_type
self.res_name = group.residue_type
self.Q = group.charge
self.pKa_old = None
self.pKa_new = None
@@ -357,7 +357,7 @@ class Iterative:
return self.label==other.label
else:
# For heterogene atoms we also need to check the residue number
return self.label==other.label and self.atom.resNumb == other.atom.resNumb
return self.label==other.label and self.atom.res_num == other.atom.res_num
def __hash__(self):
""" Needed together with __eq__ - otherwise we can't make sets of groups """