omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Clean up line breaks in calculations.py

Browse Source 
See https://github.com/jensengroup/propka-3.1/issues/43.
This commit is contained in:
Nathan Baker
2020-05-25 17:33:16 -07:00
parent 142fa5a004
commit 1ce44b77bf
1 changed files with 34 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

62
propka/calculations.py
View File

@@ -259,14 +259,14 @@ def add_amd_hydrogen(residue):
o_atom = None o_atom = None
n_atom = None n_atom = None
for atom in residue: for atom in residue:
if (atom.res_name == "GLN" and atom.name == "CD") \ if ((atom.res_name == "GLN" and atom.name == "CD")
or (atom.res_name == "ASN" and atom.name == "CG"): or (atom.res_name == "ASN" and atom.name == "CG")):
c_atom = atom c_atom = atom
elif (atom.res_name == "GLN" and atom.name == "OE1") \ elif ((atom.res_name == "GLN" and atom.name == "OE1")
or (atom.res_name == "ASN" and atom.name == "OD1"): or (atom.res_name == "ASN" and atom.name == "OD1")):
o_atom = atom o_atom = atom
elif (atom.res_name == "GLN" and atom.name == "NE2") \ elif ((atom.res_name == "GLN" and atom.name == "NE2")
or (atom.res_name == "ASN" and atom.name == "ND2"): or (atom.res_name == "ASN" and atom.name == "ND2")):
n_atom = atom n_atom = atom
if (c_atom is None) or (o_atom is None) or (n_atom is None): if (c_atom is None) or (o_atom is None) or (n_atom is None):
errstr = "Unable to find all atoms for %s %s" % (residue[0].res_name, errstr = "Unable to find all atoms for %s %s" % (residue[0].res_name,
@@ -445,8 +445,8 @@ def radial_volume_desolvation(parameters, group):
min_dist_4th = MIN_DISTANCE_4TH min_dist_4th = MIN_DISTANCE_4TH
for atom in all_atoms: for atom in all_atoms:
# ignore atoms in the same residue # ignore atoms in the same residue
if atom.res_num == group.atom.res_num \ if (atom.res_num == group.atom.res_num
and atom.chain_id == group.atom.chain_id: and atom.chain_id == group.atom.chain_id):
continue continue
sq_dist = squared_distance(group, atom) sq_dist = squared_distance(group, atom)
# desolvation # desolvation
@@ -466,8 +466,9 @@ def radial_volume_desolvation(parameters, group):
group.buried = calculate_weight(parameters, group.num_volume) group.buried = calculate_weight(parameters, group.num_volume)
scale_factor = calculate_scale_factor(parameters, group.buried) scale_factor = calculate_scale_factor(parameters, group.buried)
volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance) volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance)
group.energy_volume = group.charge * parameters.desolvationPrefactor \ group.energy_volume = (
* volume_after_allowance * scale_factor group.charge * parameters.desolvationPrefactor
* volume_after_allowance * scale_factor)
def calculate_scale_factor(parameters, weight): def calculate_scale_factor(parameters, weight):
@@ -494,8 +495,9 @@ def calculate_weight(parameters, num_volume):
Returns: Returns:
desolvation weight desolvation weight
""" """
weight = float(num_volume - parameters.Nmin) \ weight = (
/ float(parameters.Nmax - parameters.Nmin) float(num_volume - parameters.Nmin)
/ float(parameters.Nmax - parameters.Nmin))
weight = min(1.0, weight) weight = min(1.0, weight)
weight = max(0.0, weight) weight = max(0.0, weight)
return weight return weight
@@ -647,8 +649,8 @@ def hydrogen_bond_interaction(group1, group2, version):
# Do nothing, value should have been assigned. # Do nothing, value should have been assigned.
pass pass
else: else:
value = version.calculate_side_chain_energy(dist, dpka_max, cutoff, weight, value = version.calculate_side_chain_energy(
f_angle) dist, dpka_max, cutoff, weight, f_angle)
return value return value
@@ -712,15 +714,16 @@ def coulomb_energy(dist, weight, parameters):
""" """
diel = UNK_DIELECTRIC1 - (UNK_DIELECTRIC1 - UNK_DIELECTRIC2)*weight diel = UNK_DIELECTRIC1 - (UNK_DIELECTRIC1 - UNK_DIELECTRIC2)*weight
dist = max(dist, parameters.coulomb_cutoff1) dist = max(dist, parameters.coulomb_cutoff1)
scale = (dist - parameters.coulomb_cutoff2)/(parameters.coulomb_cutoff1 \ scale = (
- parameters.coulomb_cutoff2) (dist - parameters.coulomb_cutoff2)
/ (parameters.coulomb_cutoff1 - parameters.coulomb_cutoff2))
scale = max(0.0, scale) scale = max(0.0, scale)
scale = min(1.0, scale) scale = min(1.0, scale)
dpka = UNK_PKA_SCALING1/(diel*dist)*scale dpka = UNK_PKA_SCALING1/(diel*dist)*scale
return abs(dpka) return abs(dpka)
def backbone_reorganization(parameters, conformation): def backbone_reorganization(_, conformation):
"""Perform calculations related to backbone reorganizations. """Perform calculations related to backbone reorganizations.
NOTE - this was described in the code as "adding test stuff" NOTE - this was described in the code as "adding test stuff"
@@ -728,7 +731,7 @@ def backbone_reorganization(parameters, conformation):
TODO - figure out why a similar function exists in version.py TODO - figure out why a similar function exists in version.py
Args: Args:
parameters: not used _: not used
conformation: specific molecule conformation conformation: specific molecule conformation
""" """
titratable_groups = conformation.get_backbone_reorganisation_groups() titratable_groups = conformation.get_backbone_reorganisation_groups()
@@ -744,8 +747,9 @@ def backbone_reorganization(parameters, conformation):
atom3=bbc_group.atom, atom3=bbc_group.atom,
center=center) center=center)
if dist < UNK_BACKBONE_DISTANCE1 and f_angle > UNK_FANGLE_MIN: if dist < UNK_BACKBONE_DISTANCE1 and f_angle > UNK_FANGLE_MIN:
value = 1.0 - (dist-UNK_BACKBONE_DISTANCE2) \ value = (
/ (UNK_BACKBONE_DISTANCE1-UNK_BACKBONE_DISTANCE2) 1.0 - (dist-UNK_BACKBONE_DISTANCE2)
/ (UNK_BACKBONE_DISTANCE1-UNK_BACKBONE_DISTANCE2))
dpka += UNK_PKA_SCALING2 * min(1.0, value) dpka += UNK_PKA_SCALING2 * min(1.0, value)
titratable_group.energy_local = dpka*weight titratable_group.energy_local = dpka*weight
@@ -774,14 +778,14 @@ def check_exceptions(version, group1, group2):
exception, value = check_coo_coo_exception(group1, group2, version) exception, value = check_coo_coo_exception(group1, group2, version)
elif (res_type1 == "CYS") and (res_type2 == "CYS"): elif (res_type1 == "CYS") and (res_type2 == "CYS"):
exception, value = check_cys_cys_exception(group1, group2, version) exception, value = check_cys_cys_exception(group1, group2, version)
elif (res_type1 == "COO") and (res_type2 == "HIS") or \ elif ((res_type1 == "COO") and (res_type2 == "HIS")
(res_type1 == "HIS") and (res_type2 == "COO"): or (res_type1 == "HIS") and (res_type2 == "COO")):
exception, value = check_coo_his_exception(group1, group2, version) exception, value = check_coo_his_exception(group1, group2, version)
elif (res_type1 == "OCO") and (res_type2 == "HIS") or \ elif ((res_type1 == "OCO") and (res_type2 == "HIS")
(res_type1 == "HIS") and (res_type2 == "OCO"): or (res_type1 == "HIS") and (res_type2 == "OCO")):
exception, value = check_oco_his_exception(group1, group2, version) exception, value = check_oco_his_exception(group1, group2, version)
elif (res_type1 == "CYS") and (res_type2 == "HIS") or \ elif ((res_type1 == "CYS") and (res_type2 == "HIS")
(res_type1 == "HIS") and (res_type2 == "CYS"): or (res_type1 == "HIS") and (res_type2 == "CYS")):
exception, value = check_cys_his_exception(group1, group2, version) exception, value = check_cys_his_exception(group1, group2, version)
else: else:
# do nothing, no exception for this pair # do nothing, no exception for this pair
@@ -933,8 +937,8 @@ def check_buried(num_volume1, num_volume2):
Returns: Returns:
True if interaction is buried, False otherwise True if interaction is buried, False otherwise
""" """
if (num_volume1 + num_volume2 <= COMBINED_NUM_BURIED_MAX) \ if ((num_volume1 + num_volume2 <= COMBINED_NUM_BURIED_MAX)
and (num_volume1 <= SEPARATE_NUM_BURIED_MAX \ and (num_volume1 <= SEPARATE_NUM_BURIED_MAX
or num_volume2 <= SEPARATE_NUM_BURIED_MAX): or num_volume2 <= SEPARATE_NUM_BURIED_MAX)):
return False return False
return True return True