Resolve cyclic import problem.

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

propka/__init__.py

@@ -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",
+           "hybrid36", "iterative", "input", "lib", "ligand_pka_values",
-           "molecular_container", "output", "parameters", "pdb", "protonate",
+           "ligand", "molecular_container", "output", "parameters",
-           "run", "vector_algebra", "version"]
+           "protonate", "run", "vector_algebra", "version"]

propka/atom.py

@@ -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):

propka/conformation_container.py

@@ -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
 

propka/input.py

@@ -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]
-
-

propka/ligand_pka_values.py

@@ -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,
+    def get_marvin_pkas_for_pdb_file(
-                                     max_ph=20):
+            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
-

propka/molecular_container.py

@@ -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
+        self.name = None
-        # 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)
         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."""

propka/output.py

@@ -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:

propka/parameters.py

@@ -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)),

propka/run.py

@@ -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

scripts/propka31.py

@@ -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()
 

tests/test_basic_regression.py

@@ -5,8 +5,10 @@ import re
 from pathlib import Path
 import pytest
 from numpy.testing import assert_almost_equal
-import propka.lib
+from propka.parameters import Parameters
-import propka.molecular_container
+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(
+        parameters = read_parameter_file(args.parameters, Parameters())
-            str(pdb_path), args)
+        molecule = MolecularContainer(parameters, args)
+        molecule = read_molecule_file(str(pdb_path), molecule)
         molecule.calculate_pka()
         molecule.write_pka()
     finally: