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Resolve cyclic import problem.

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Fixes https://github.com/jensengroup/propka-3.1/issues/49

Moved I/O into higher level of of code; should make
issue https://github.com/jensengroup/propka-3.1/issues/51
easier to resolve
This commit is contained in:
Nathan Baker
2020-05-30 12:01:30 -07:00
parent b597a6f257
commit 84846aad8c
11 changed files with 107 additions and 92 deletions
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6
propka/__init__.py
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@@ -15,6 +15,6 @@ predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-53
"""
__all__ = ["atom", "bonds", "calculations", "conformation_container",
"coupled_groups", "determinant", "determinants", "group",
"hybrid36", "iterative", "lib", "ligand_pka_values", "ligand",
"molecular_container", "output", "parameters", "pdb", "protonate",
"run", "vector_algebra", "version"]
"hybrid36", "iterative", "input", "lib", "ligand_pka_values",
"ligand", "molecular_container", "output", "parameters",
"protonate", "run", "vector_algebra", "version"]

4
propka/atom.py
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@@ -1,7 +1,7 @@
"""Atom class - contains all atom information found in the PDB file"""
import string
from . import hybrid36
from propka.lib import make_tidy_atom_label
from . import hybrid36
# Format strings that get used in multiple places (or are very complex)
@@ -25,7 +25,7 @@ STR_FMT = (
"({r.chain_id:1s}) [{r.x:>8.3f} {r.y:>8.3f} {r.z:>8.3f}] {r.element:s}")
class Atom(object):
class Atom:
"""Atom class - contains all atom information found in the PDB file"""
def __init__(self, line=None):

1
propka/conformation_container.py
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@@ -36,7 +36,6 @@ class ConformationContainer:
self.groups = []
self.chains = []
self.current_iter_item = 0
# TODO - what is marvin_pkas_calculated?
self.marvin_pkas_calculated = False
self.non_covalently_coupled_groups = False

69
propka/input.py
View File

@@ -1,5 +1,8 @@
"""Input routines."""
from pathlib import Path
from pkg_resources import resource_filename
from propka.lib import protein_precheck
from propka.output import write_propka
from propka.atom import Atom
from propka.conformation_container import ConformationContainer
from propka.group import initialize_atom_group
@@ -27,6 +30,67 @@ def open_file_for_reading(input_file):
return file_
def read_molecule_file(input_file, mol_container):
"""Read input file (PDB or PROPKA) for a molecular container
Args
input_file: input file to read
mol_container: MolecularContainer object
Returns
updated MolecularContainer object
Raises
ValuError if invalid input given
"""
input_path = Path(input_file)
mol_container.name = input_path.stem
input_file_extension = input_path.suffix
if input_file_extension.lower() == '.pdb':
# input is a pdb file. read in atoms and top up containers to make
# sure that all atoms are present in all conformations
conformations, conformation_names = read_pdb(
input_path, mol_container.version.parameters, mol_container)
if len(conformations) == 0:
str_ = ('Error: The pdb file does not seems to contain any '
'molecular conformations')
raise ValueError(str_)
mol_container.conformations = conformations
mol_container.conformation_names = conformation_names
mol_container.top_up_conformations()
# make a structure precheck
protein_precheck(
mol_container.conformations, mol_container.conformation_names)
# set up atom bonding and protonation
mol_container.version.setup_bonding_and_protonation(mol_container)
# Extract groups
mol_container.extract_groups()
# sort atoms
for name in mol_container.conformation_names:
mol_container.conformations[name].sort_atoms()
# find coupled groups
mol_container.find_covalently_coupled_groups()
# write out the input file
# TODO - figure out why this I/O has to happen here
output_path = Path(input_path.name.replace(
input_file_extension, '.propka_input'))
write_propka(mol_container, output_path)
elif input_file_extension.lower() == '.propka_input':
# input is a propka_input file
conformations, conformation_names = read_propka(
input_file, mol_container.version.parameters, mol_container)
mol_container.conformations = conformations
mol_container.conformation_names = conformation_names
# Extract groups - this merely sets up the groups found in the
# input file
mol_container.extract_groups()
# do some additional set up
mol_container.additional_setup_when_reading_input_file()
else:
str_ = "Unknown input file type {0!s} for file {1!s}".format(
input_file_extension, input_path)
raise ValueError(str_)
return mol_container
def read_parameter_file(input_file, parameters):
"""Read a parameter file.
@@ -47,7 +111,6 @@ def read_parameter_file(input_file, parameters):
return parameters
def conformation_sorter(conf):
"""TODO - figure out what this function does."""
model = int(conf[:-1])
@@ -121,7 +184,7 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
terminal = None
def read_input(input_file, parameters, molecule):
def read_propka(input_file, parameters, molecule):
"""Read PROPKA input file for molecular container.
Args:
@@ -235,5 +298,3 @@ def read_pdb(pdb_file, parameters, molecule):
# make a sorted list of conformation names
names = sorted(conformations.keys(), key=conformation_sorter)
return [conformations, names]

14
propka/ligand_pka_values.py
View File

@@ -2,11 +2,8 @@
import os
import subprocess
import sys
import propka.molecular_container
import propka.calculations
import propka.parameters
from propka.output import write_mol2_for_atoms
from propka.lib import info, warning
from propka.lib import info, warning, split_atoms_into_molecules
class LigandPkaValues:
@@ -47,17 +44,17 @@ class LigandPkaValues:
sys.exit(-1)
return locs[0]
def get_marvin_pkas_for_pdb_file(self, pdbfile, num_pkas=10, min_ph=-10,
max_ph=20):
def get_marvin_pkas_for_pdb_file(
self, molecule, parameters, num_pkas=10, min_ph=-10, max_ph=20):
"""Use Marvin executables to get pKas for a PDB file.
Args:
pdbfile: PDB file
molecule: MolecularContainer object
num_pkas: number of pKas to get
min_ph: minimum pH value
max_ph: maximum pH value
"""
molecule = propka.molecular_container.Molecular_container(pdbfile)
self.get_marvin_pkas_for_molecular_container(
molecule, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
@@ -110,7 +107,7 @@ class LigandPkaValues:
max_ph: maximum pH value
"""
# do one molecule at the time so we don't confuse marvin
molecules = propka.lib.split_atoms_into_molecules(atoms)
molecules = split_atoms_into_molecules(atoms)
for i, molecule in enumerate(molecules):
filename = '{0:s}_{1:d}.mol2'.format(name, i+1)
self.get_marvin_pkas_for_molecule(
@@ -196,4 +193,3 @@ class LigandPkaValues:
if len(indices) != len(values) != len(types):
raise Exception('Lengths of atoms and pka values mismatch')
return indices, values, types

66
propka/molecular_container.py
View File

@@ -1,12 +1,8 @@
"""Molecular container for storing all contents of PDB files."""
import os
import sys
import propka.version
from propka.input import read_pdb, read_input, read_parameter_file
from propka.parameters import Parameters
from propka.output import write_input
from propka.conformation_container import ConformationContainer
from propka.lib import info, warning, protein_precheck, make_grid
from propka.lib import info, warning, make_grid
# TODO - these are constants whose origins are a little murky
@@ -15,36 +11,26 @@ UNK_PI_CUTOFF = 0.01
MAX_ITERATION = 4
class Molecular_container:
class MolecularContainer:
"""Container for storing molecular contents of PDB files.
TODO - this class name does not conform to PEP8 but has external use.
We should deprecate and change eventually.
"""
def __init__(self, input_file, options=None):
def __init__(self, parameters, options=None):
"""Initialize molecular container.
Args:
input_file: molecular input file
parameters: Parameters() object
options: options object
"""
# printing out header before parsing input
propka.output.print_header()
# set up some values
self.conformation_names = []
self.conformations = {}
self.options = options
self.input_file = input_file
# TODO - replace this indelicate os.path code with pathlib
self.dir = os.path.split(input_file)[0]
self.file = os.path.split(input_file)[1]
self.name = self.file[0:self.file.rfind('.')]
input_file_extension = input_file[input_file.rfind('.'):]
parameters = Parameters()
if options:
parameters = read_parameter_file(
self.options.parameters, parameters)
else:
parameters = read_parameter_file('propka.cfg', parameters)
self.name = None
try:
version_class = getattr(propka.version, parameters.version)
self.version = version_class(parameters)
@@ -53,44 +39,6 @@ class Molecular_container:
errstr = 'Error: Version {0:s} does not exist'.format(
parameters.version)
raise Exception(errstr)
# read the input file
if input_file_extension[0:4] == '.pdb':
# input is a pdb file. read in atoms and top up containers to make
# sure that all atoms are present in all conformations
[self.conformations, self.conformation_names] = (
read_pdb(input_file, self.version.parameters, self))
if len(self.conformations) == 0:
info('Error: The pdb file does not seems to contain any '
'molecular conformations')
sys.exit(-1)
self.top_up_conformations()
# make a structure precheck
protein_precheck(
self.conformations, self.conformation_names)
# set up atom bonding and protonation
self.version.setup_bonding_and_protonation(self)
# Extract groups
self.extract_groups()
# sort atoms
for name in self.conformation_names:
self.conformations[name].sort_atoms()
# find coupled groups
self.find_covalently_coupled_groups()
# write out the input file
filename = self.file.replace(input_file_extension, '.propka_input')
write_input(self, filename)
elif input_file_extension == '.propka_input':
#input is a propka_input file
[self.conformations, self.conformation_names] = read_input(
input_file, self.version.parameters, self)
# Extract groups - this merely sets up the groups found in the
# input file
self.extract_groups()
# do some additional set up
self.additional_setup_when_reading_input_file()
else:
info('Unrecognized input file:{0:s}'.format(input_file))
sys.exit(-1)
def top_up_conformations(self):
"""Makes sure that all atoms are present in all conformations."""

2
propka/output.py
View File

@@ -582,7 +582,7 @@ def write_mol2_for_atoms(atoms, filename):
out.write(substructure_section)
out.close()
def write_input(molecular_container, filename):
def write_propka(molecular_container, filename):
"""Write PROPKA input file for molecular container.
Args:

4
propka/parameters.py
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@@ -1,6 +1,4 @@
"""Holds parameters and settings."""
import pkg_resources
import propka.lib as lib
from propka.lib import info, warning
@@ -346,7 +344,7 @@ O2
'N1', 'O2', 'OP', 'SH']
lines = [
"",
"\\begin{longtable}{{{0:s}}}".format('l'*len(agroups)),
"\\begin{{longtable}}{{{0:s}}}".format('l'*len(agroups)),
("\\caption{{Ligand interaction parameters. For interactions not "
"listed, the default value of {0:s} is applied.}}").format(
str(self.sidechain_cutoffs.default)),

12
propka/run.py
View File

@@ -1,7 +1,9 @@
"""Entry point for PROPKA script."""
import logging
from propka.lib import loadOptions
from propka.molecular_container import Molecular_container
from propka.input import read_parameter_file, read_molecule_file
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
_LOGGER = logging.getLogger("PROPKA")
@@ -13,8 +15,10 @@ def main(optargs=None):
optargs = optargs if optargs is not None else []
options = loadOptions(*optargs)
pdbfiles = options.filenames
parameters = read_parameter_file(options.parameters, Parameters())
for pdbfile in pdbfiles:
my_molecule = Molecular_container(pdbfile, options)
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()
@@ -33,9 +37,11 @@ def single(pdbfile, optargs=None):
optargs = optargs if optargs is not None else []
options = loadOptions(*optargs)
pdbfile = options.filenames.pop(0)
parameters = read_parameter_file(options.parameters, Parameters())
if len(options.filenames) > 0:
_LOGGER.warning("Ignoring filenames: {0:s}".format(options.filenames))
my_molecule = Molecular_container(pdbfile, options)
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()
return my_molecule

8
scripts/propka31.py
View File

@@ -11,7 +11,9 @@ is the same as the module name; that's why the new script is called
propka31.)
"""
from propka.lib import loadOptions
from propka.molecular_container import Molecular_container
from propka.input import read_parameter_file, read_molecule_file
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
def main():
@@ -19,9 +21,11 @@ def main():
# loading options, flaggs and arguments
options = loadOptions([])
pdbfiles = options.filenames
parameters = read_parameter_file(options.parameters, Parameters())
for pdbfile in pdbfiles:
my_molecule = Molecular_container(pdbfile, options)
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()

13
tests/test_basic_regression.py
View File

@@ -5,8 +5,10 @@ import re
from pathlib import Path
import pytest
from numpy.testing import assert_almost_equal
import propka.lib
import propka.molecular_container
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
from propka.input import read_parameter_file, read_molecule_file
from propka.lib import loadOptions
_LOGGER = logging.getLogger(__name__)
@@ -64,15 +66,16 @@ def run_propka(options, pdb_path, tmp_path):
tmp_path: path for working directory
"""
options += [str(pdb_path)]
args = propka.lib.loadOptions(options)
args = loadOptions(options)
try:
_LOGGER.warning(
"Working in tmpdir {0:s} because of PROPKA file output; "
"need to fix this.".format(str(tmp_path)))
cwd = Path.cwd()
os.chdir(tmp_path)
molecule = propka.molecular_container.Molecular_container(
str(pdb_path), args)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = read_molecule_file(str(pdb_path), molecule)
molecule.calculate_pka()
molecule.write_pka()
finally: