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De-lint iterative.py

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See https://github.com/jensengroup/propka-3.1/issues/43.
This commit is contained in:
Nathan Baker
2020-05-25 18:55:02 -07:00
parent 919305d8a3
commit e5dedc1786
1 changed files with 20 additions and 11 deletions
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31
propka/iterative.py
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@@ -10,12 +10,14 @@ from propka.lib import info, debug
UNK_MIN_VALUE = 0.005 UNK_MIN_VALUE = 0.005
def add_to_determinant_list(group1, group2, distance, iterative_interactions, version): def add_to_determinant_list(group1, group2, distance, iterative_interactions,
version):
"""Add iterative determinantes to the list. """Add iterative determinantes to the list.
[[R1, R2], [side-chain, coulomb], [A1, A2]], ... [[R1, R2], [side-chain, coulomb], [A1, A2]], ...
NOTE - the sign is determined when the interaction is added to the iterative object! NOTE - sign is determined when the interaction is added to the iterative
object!
NOTE - distance < coulomb_cutoff here NOTE - distance < coulomb_cutoff here
Args: Args:
@@ -141,14 +143,18 @@ def add_iterative_ion_pair(object1, object2, interaction, version):
q2 = object2.q q2 = object2.q
comp1 = object1.pka_old + annihilation[0] + q1*coulomb_value comp1 = object1.pka_old + annihilation[0] + q1*coulomb_value
comp2 = object2.pka_old + annihilation[1] + q2*coulomb_value comp2 = object2.pka_old + annihilation[1] + q2*coulomb_value
if object1.res_name not in version.parameters.exclude_sidechain_interactions: if (object1.res_name
not in version.parameters.exclude_sidechain_interactions):
comp1 += q1*hbond_value comp1 += q1*hbond_value
if object2.res_name not in version.parameters.exclude_sidechain_interactions: if (object2.res_name
not in version.parameters.exclude_sidechain_interactions):
comp2 += q2*hbond_value comp2 += q2*hbond_value
if q1 == -1.0 and comp1 < comp2: if q1 == -1.0 and comp1 < comp2:
add_term = True # pKa(acid) < pKa(base) # pKa(acid) < pKa(base)
add_term = True
elif q1 == 1.0 and comp1 > comp2: elif q1 == 1.0 and comp1 > comp2:
add_term = True # pKa(base) > pKa(acid) # pKa(base) > pKa(acid)
add_term = True
else: else:
add_term = False add_term = False
annihilation[0] = 0.00 annihilation[0] = 0.00
@@ -167,12 +173,14 @@ def add_iterative_ion_pair(object1, object2, interaction, version):
# Side-chain # Side-chain
if hbond_value > UNK_MIN_VALUE: if hbond_value > UNK_MIN_VALUE:
# residue1 # residue1
if object1.res_name not in version.parameters.exclude_sidechain_interactions: if (object1.res_name
not in version.parameters.exclude_sidechain_interactions):
interaction = [object2, q1*hbond_value] interaction = [object2, q1*hbond_value]
annihilation[0] += -q1*hbond_value annihilation[0] += -q1*hbond_value
object1.determinants['sidechain'].append(interaction) object1.determinants['sidechain'].append(interaction)
# residue2 # residue2
if object2.res_name not in version.parameters.exclude_sidechain_interactions: if (object2.res_name
not in version.parameters.exclude_sidechain_interactions):
interaction = [object1, q2*hbond_value] interaction = [object1, q2*hbond_value]
annihilation[1] += -q2*hbond_value annihilation[1] += -q2*hbond_value
object2.determinants['sidechain'].append(interaction) object2.determinants['sidechain'].append(interaction)
@@ -191,7 +199,7 @@ def add_determinants(iterative_interactions, version, _=None):
# --- setup --- # --- setup ---
iteratives = [] iteratives = []
done_group = [] done_group = []
# creating iterative objects with references to their real group counterparts # create iterative objects with references to their real group counterparts
for interaction in iterative_interactions: for interaction in iterative_interactions:
pair = interaction[0] pair = interaction[0]
for group in pair: for group in pair:
@@ -354,8 +362,9 @@ class Iterative:
return self.label == other.label return self.label == other.label
else: else:
# For heterogene atoms we also need to check the residue number # For heterogene atoms we also need to check the residue number
return self.label == other.label \ return (
and self.atom.res_num == other.atom.res_num self.label == other.label
and self.atom.res_num == other.atom.res_num)
def __hash__(self): def __hash__(self):
"""Needed to use objects in sets.""" """Needed to use objects in sets."""