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Partial de-lint of calculations.py.

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Pausing here since I just deleted contactDesolvation().  However, there
was no way that anyone was using this function since it was very badly
broken and could not run.
This commit is contained in:
Nathan Baker
2020-05-23 13:24:05 -07:00
parent 02ca72d91d
commit 1611e9d6ea
1 changed files with 14 additions and 72 deletions
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86
propka/calculations.py
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@@ -352,26 +352,32 @@ def make_new_h(atom, x,y,z):
return new_H
# TODO - the remaining functions form a dist
# TODO - the remaining functions form a distinct "module" for desolvation
#
# Desolvation methods
#
MYSTERY_MIN_DISTANCE = 2.75
MIN_DISTANCE_4TH = math.pow(MYSTERY_MIN_DISTANCE, 4)
def radial_volume_desolvation(parameters, group):
"""Calculate desolvation terms for group.
Args:
parameters: parameters for desolvation calculation
group: group of atoms for calculation
"""
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
volume = 0.0
# TODO - Nathan really wants to rename the Nmass 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
min_distance_4th = 57.1914 # pow(2.75, 4)
min_distance_4th = MIN_DISTANCE_4TH
for atom in all_atoms:
# ignore atoms in the same residue
if atom.res_num == group.atom.res_num and atom.chain_id == group.atom.chain_id:
continue
sq_dist = squared_distance(group, atom)
# desolvation
if sq_dist < parameters.desolv_cutoff_squared:
# use a default relative volume of 1.0 if the volume of the element is not found in parameters
@@ -380,79 +386,15 @@ def radial_volume_desolvation(parameters, group):
dv = parameters.VanDerWaalsVolume['C4']
else:
dv = parameters.VanDerWaalsVolume.get(atom.element, 1.0)
dv_inc = dv/max(min_distance_4th, sq_dist*sq_dist)
# dv_inc = dv/(sq_dist*sq_dist) - dv/(parameters.desolv_cutoff_squared*parameters.desolv_cutoff_squared)
volume += dv_inc
# buried
if sq_dist < parameters.buried_cutoff_squared:
group.Nmass += 1
group.buried = calculate_weight(parameters, group.Nmass)
scale_factor = calculate_scale_factor(parameters, group.buried)
volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance)
group.Emass = group.charge * parameters.desolvationPrefactor * volume_after_allowance * scale_factor
# Emass, Nmass
# Elocl, Nlocl -> reorganisation energy (count backbone hydorgen bond acceptors, C=O)
#info('%s %5.2f %5.2f %4d'%(group, group.buried, group.Emass, group.Nmass))
return
def contactDesolvation(parameters, group):
"""
calculates the desolvation according to the Contact Model, the old default
"""
local_radius = {'ASP': 4.5,
'GLU': 4.5,
'HIS': 4.5,
'CYS': 3.5,
'TYR': 3.5,
'LYS': 4.5,
'ARG': 5.0,
'C-': 4.5,
'N+': 4.5}
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
if residue.res_name in version.desolvationRadii:
local_cutoff = version.desolvationRadii[residue.res_name]
else:
local_cutoff = 0.00
residue.Nmass = 0
residue.Nlocl = 0
for atom in all_atoms:
if atom.res_num != group.atom.res_num or atom.chain_id != group.atom.chain_id:
dX = atom.x - residue.x
dY = atom.y - residue.y
dZ = atom.z - residue.z
distance = math.sqrt(dX*dX + dY*dY + dZ*dZ)
if distance < local_cutoff:
group.Nlocl += 1
if distance < parameters.buried_cutoff:
group.Nmass += 1
if residue.Nmass > 400:
group.location = "BURIED "
else:
group.location = "SURFACE"
group.Emass = group.charge * parameters.desolvationPrefactor * max(0.00, group.Nmass-parameters.desolvationAllowance)
group.Elocl = group.charge * parameters.desolvationLocal * group.Nlocl
# Buried ratio - new feature in propka3.0
# Note, there will be an unforseen problem: e.g. if one residue has Nmass > Nmax and
# the other Nmass < Nmax, the Npair will not be Nmass1 + Nmass2!
residue.buried = calculateWeight(residue.Nmass)
return 0.00, 0.00, 0.00, 0.00
def calculate_scale_factor(parameters, weight):