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De-lint calculations.py up to difficult decision.

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Do we drop 3.0 support?  I vote "yes" but will leave that for the next
commit.
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Nathan Baker
2020-05-21 20:45:47 -07:00
parent 013167026f
commit 76418a1a15
1 changed files with 23 additions and 23 deletions
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propka/calculations.py
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@@ -1,53 +1,53 @@
"""PROPKA calculations."""
from __future__ import division import math
from __future__ import print_function import copy
import sys
import math, propka.protonate, propka.bonds,copy, sys import propka.protonate
import propka.bonds
from propka.lib import info, warning from propka.lib import info, warning
#
# methods for setting up atom naming, bonding, and protonation
#
def setup_bonding_and_protonation(parameters, molecular_container): def setup_bonding_and_protonation(parameters, molecular_container):
"""Set up bonding and protonation for a molecule.
Args:
molecular_container: molecule container.
"""
# make bonds # make bonds
my_bond_maker = setup_bonding(parameters, molecular_container) my_bond_maker = setup_bonding(parameters, molecular_container)
# set up ligand atom names # set up ligand atom names
set_ligand_atom_names(molecular_container) set_ligand_atom_names(molecular_container)
# apply information on pi electrons # apply information on pi electrons
my_bond_maker.add_pi_electron_information(molecular_container) my_bond_maker.add_pi_electron_information(molecular_container)
# Protonate atoms # Protonate atoms
if molecular_container.options.protonate_all: if molecular_container.options.protonate_all:
my_protonator = propka.protonate.Protonate(verbose=False) my_protonator = propka.protonate.Protonate(verbose=False)
my_protonator.protonate(molecular_container) my_protonator.protonate(molecular_container)
return
def setup_bonding(parameters, molecular_container): def setup_bonding(parameters, molecular_container):
# make bonds """Set up bonding for a molecular container.
Args:
molecular_container: the molecular container in question
Returns:
BondMaker object
"""
my_bond_maker = propka.bonds.BondMaker() my_bond_maker = propka.bonds.BondMaker()
my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container) my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
return my_bond_maker return my_bond_maker
def set_ligand_atom_names(molecular_container): def set_ligand_atom_names(molecular_container):
"""Set names for ligands in molecular container.
Args:
molecular_container: molecular container for ligand names
"""
for name in molecular_container.conformation_names: for name in molecular_container.conformation_names:
molecular_container.conformations[name].set_ligand_atom_names() molecular_container.conformations[name].set_ligand_atom_names()
return
#
# The following methods imitates propka3.0 protonation!
#
def setup_bonding_and_protonation_30_style(parameters, molecular_container): def setup_bonding_and_protonation_30_style(parameters, molecular_container):
# Protonate atoms # Protonate atoms
protonate_30_style(molecular_container) protonate_30_style(molecular_container)