Remove cyclic import based on atom.py

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

propka/atom.py

@@ -1,8 +1,7 @@
 """Atom class - contains all atom information found in the PDB file"""
 import string
-import propka.lib
-import propka.group
 from . import hybrid36
+from propka.lib import make_tidy_atom_label
 
 
 # Format strings that get used in multiple places (or are very complex)
@@ -50,6 +49,9 @@ class Atom(object):
         self.z = None
         self.group = None
         self.group_type = None
+        self.group_label = None
+        self.group_model_pka = None
+        self.group_model_pka_set = None
         self.number_of_bonded_elements = {}
         self.cysteine_bridge = False
         self.bonded_atoms = []
@@ -267,7 +269,7 @@ class Atom(object):
                 model_pka = PKA_FMT.format(self.group.model_pka)
         str_ = INPUT_LINE_FMT.format(
             type=self.type.upper(), r=self,
-            atom_label=propka.lib.make_tidy_atom_label(self.name, self.element),
+            atom_label=make_tidy_atom_label(self.name, self.element),
             group=group, pka=model_pka)
         return str_
 
@@ -313,21 +315,11 @@ class Atom(object):
             self.occ = self.occ.replace('ALG', 'titratable_ligand')
             self.occ = self.occ.replace('BLG', 'titratable_ligand')
             self.occ = self.occ.replace('LG', 'non_titratable_ligand')
-            # try to initialise the group
+            self.group_label = "{0:s}_group".format(self.occ)
-            try:
-                group_attr = "{0:s}_group".format(self.occ)
-                group_attr = getattr(propka.group, group_attr)
-                self.group = group_attr(self)
-            except:
-                # TODO - be more specific with expection handling here
-                str_ = (
-                    '{0:s} in input_file is not recognized as a group'.format(
-                        self.occ))
-                raise Exception(str_)
         # set the model pKa value
         if self.beta != '-':
-            self.group.model_pka = float(self.beta)
+            self.group_model_pka = float(self.beta)
-            self.group.model_pka_set = True
+            self.group_model_pka_set = True
         # set occ and beta to standard values
         self.occ = '1.00'
         self.beta = '0.00'
@@ -344,7 +336,7 @@ class Atom(object):
         """
         str_ = PDB_LINE_FMT1.format(
             type=self.type.upper(), r=self,
-            atom_label=propka.lib.make_tidy_atom_label(self.name, self.element))
+            atom_label=make_tidy_atom_label(self.name, self.element))
         return str_
 
     def make_mol2_line(self, id_):
@@ -359,7 +351,7 @@ class Atom(object):
         """
         str_ = MOL2_LINE_FMT.format(
             id=id_, r=self,
-            atom_label=propka.lib.make_tidy_atom_label(self.name, self.element))
+            atom_label=make_tidy_atom_label(self.name, self.element))
         return str_
 
     def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None,
@@ -397,7 +389,7 @@ class Atom(object):
         str_ = PDB_LINE_FMT2.format(
             numb=numb, res_name=res_name, chain_id=chain_id, res_num=res_num,
             x=x, y=y, z=z, occ=occ, beta=beta,
-            atom_label=propka.lib.make_tidy_atom_label(name, self.element)
+            atom_label=make_tidy_atom_label(name, self.element)
         )
         return str_
 
@@ -408,7 +400,7 @@ class Atom(object):
 
         Returns:
             String with label"""
-        return propka.lib.make_tidy_atom_label(self.name, self.element)
+        return make_tidy_atom_label(self.name, self.element)
 
     def __str__(self):
         """Return an undefined-format string version of this atom."""

propka/calculations.py

@@ -1,8 +1,5 @@
 """PROPKA calculations."""
 import math
-import propka.protonate
-import propka.bonds
-from propka.lib import warning, info
 
 
 # TODO - this file should be broken into three separate files:

propka/group.py

@@ -6,6 +6,7 @@ from propka.ligand_pka_values import LigandPkaValues
 from propka.determinant import Determinant
 from propka.lib import info, warning
 
+
 # Constants that start with "UNK_" are a mystery to me
 UNK_PKA_SCALING = -1.36
 PROTONATOR = propka.protonate.Protonate(verbose=False)
@@ -1417,3 +1418,15 @@ def is_ion_group(parameters, atom):
     if atom.res_name.strip() in parameters.ions.keys():
         return IonGroup(atom)
     return None
+
+def initialize_atom_group(atom):
+    """Initialize an atom group.
+
+    Args:
+        atom:  atom to initialize
+    """
+        # try to initialise the group
+    group_attr = globals()[atom.group_label]
+    atom.group = group_attr(atom)
+    atom.group.model_pka = atom.group_model_pka
+    atom.group.model_pka_set = atom.group_model_pka_set

propka/ligand_pka_values.py

@@ -6,7 +6,7 @@ import propka.molecular_container
 import propka.calculations
 import propka.parameters
 import propka.pdb
-import propka.lib
+from propka.output import write_mol2_for_atoms
 from propka.lib import info, warning
 
 
@@ -133,7 +133,7 @@ class LigandPkaValues:
         """
         # print out structure unless we are using user-modified structure
         if not reuse:
-            propka.pdb.write_mol2_for_atoms(atoms, filename)
+            write_mol2_for_atoms(atoms, filename)
         # check that we actually have a file to work with
         if not os.path.isfile(filename):
             errstr = (
@@ -141,7 +141,7 @@ class LigandPkaValues:
                 "- generating one".format(
                     filename))
             warning(errstr)
-            propka.pdb.write_mol2_for_atoms(atoms, filename)
+            write_mol2_for_atoms(atoms, filename)
         # Marvin calculate pKa values
         fmt = (
             'pka -a {num1} -b {num2} --min {min_ph} '
@@ -197,3 +197,4 @@ 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

@@ -1,13 +1,11 @@
 """Molecular container for storing all contents of PDB files."""
 import os
 import sys
-import propka.pdb
 import propka.version
-import propka.output
+from propka.pdb import read_input
-import propka.group
+from propka.output import write_input
-import propka.lib
 from propka.conformation_container import ConformationContainer
-from propka.lib import info, warning
+from propka.lib import info, warning, make_grid
 
 
 # TODO - these are constants whose origins are a little murky
@@ -78,7 +76,7 @@ class Molecular_container:
             self.find_covalently_coupled_groups()
             # write out the input file
             filename = self.file.replace(input_file_extension, '.propka_input')
-            propka.pdb.write_input(self, filename)
+            write_input(self, filename)
         elif input_file_extension == '.propka_input':
             #input is a propka_input file
             [self.conformations, self.conformation_names] = (
@@ -155,7 +153,7 @@ class Molecular_container:
                 else:
                     str_ = (
                         'Group {0:s} could not be found in '
-                        'conformation {0:s}.'.format(
+                        'conformation {1:s}.'.format(
                             group.atom.residue_label, name))
                     warning(str_)
             # ... and store the average value
@@ -214,7 +212,7 @@ class Molecular_container:
         """
         # calculate stability profile
         profile = []
-        for ph in propka.lib.make_grid(*grid):
+        for ph in make_grid(*grid):
             conf = self.conformations[conformation]
             ddg = conf.calculate_folding_energy(ph=ph, reference=reference)
             profile.append([ph, ddg])
@@ -244,7 +242,7 @@ class Molecular_container:
             list of charge state values
         """
         charge_profile = []
-        for ph in propka.lib.make_grid(*grid):
+        for ph in make_grid(*grid):
             conf = self.conformations[conformation]
             q_unfolded, q_folded = conf.calculate_charge(
                 self.version.parameters, ph=ph)

propka/output.py

@@ -1,6 +1,6 @@
 """Output routines."""
 from datetime import date
-from propka.lib import info
+from propka.lib import info, open_file_for_writing
 
 
 def print_header():
@@ -11,8 +11,8 @@ def print_header():
     info(str_)
 
 
-def write_pdb(protein, pdbfile=None, filename=None, include_hydrogens=False,
+def write_pdb_for_protein(
-              _=None):
+        protein, pdbfile=None, filename=None, include_hydrogens=False, _=None):
     """Write a residue to the new PDB file.
 
     Args:
@@ -50,6 +50,16 @@ def write_pdb(protein, pdbfile=None, filename=None, include_hydrogens=False,
         pdbfile.close()
 
 
+def write_pdb_for_conformation(conformation, filename):
+    """Write PDB conformation to a file.
+
+    Args:
+        conformation:  conformation container
+        filename:  filename for output
+    """
+    write_pdb_for_atoms(conformation.atoms, filename)
+
+
 def write_pka(protein, parameters, filename=None, conformation='1A',
               reference="neutral", _="folding", verbose=False,
               __=None):
@@ -461,3 +471,104 @@ def make_interaction_map(name, list_, interaction):
                 tag = '    X     '
             res += '{0:>10s}| '.format(tag)
     return res
+
+
+def write_pdb_for_atoms(atoms, filename, make_conect_section=False):
+    """Write out PDB file for atoms.
+
+    Args:
+        atoms:  list of atoms
+        filename:  name of file
+        make_conect_section:  generate a CONECT PDB section
+    """
+    out = open_file_for_writing(filename)
+    for atom in atoms:
+        out.write(atom.make_pdb_line())
+    if make_conect_section:
+        for atom in atoms:
+            out.write(atom.make_conect_line())
+    out.close()
+
+
+def get_bond_order(atom1, atom2):
+    """Get the order of a bond between two atoms.
+
+    Args:
+        atom1:  first atom in bond
+        atom2:  second atom in bond
+    Returns:
+        string with bond type
+    """
+    type_ = '1'
+    pi_electrons1 = atom1.num_pi_elec_2_3_bonds
+    pi_electrons2 = atom2.num_pi_elec_2_3_bonds
+    if '.ar' in atom1.sybyl_type:
+        pi_electrons1 -= 1
+    if '.ar' in atom2.sybyl_type:
+        pi_electrons2 -= 1
+    if pi_electrons1 > 0 and pi_electrons2 > 0:
+        type_ = '{0:d}'.format(min(pi_electrons1, pi_electrons2)+1)
+    if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type:
+        type_ = 'ar'
+    return type_
+
+
+def write_mol2_for_atoms(atoms, filename):
+    """Write out MOL2 file for atoms.
+
+    Args:
+        atoms:  list of atoms
+        filename:  name of file
+    """
+    # TODO - header needs to be converted to format string
+    header = '@<TRIPOS>MOLECULE\n\n{natom:d} {id:d}\nSMALL\nUSER_CHARGES\n'
+    atoms_section = '@<TRIPOS>ATOM\n'
+    for i, atom in enumerate(atoms):
+        atoms_section += atom.make_mol2_line(i+1)
+    bonds_section = '@<TRIPOS>BOND\n'
+    id_ = 1
+    for i, atom1 in enumerate(atoms):
+        for j, atom2 in enumerate(atoms, i+1):
+            if atom1 in atom2.bonded_atoms:
+                type_ = get_bond_order(atom1, atom2)
+                bonds_section += '{0:>7d} {1:>7d} {2:>7d} {3:>7s}\n'.format(
+                    id_, i+1, j+1, type_)
+                id_ += 1
+    substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
+    if len(atoms) > 0:
+        substructure_section = (
+            '@<TRIPOS>SUBSTRUCTURE\n{0:<7d} {1:>10s} {2:>7d}\n'.format(
+                atoms[0].res_num, atoms[0].res_name, atoms[0].numb))
+    out = open_file_for_writing(filename)
+    out.write(header.format(natom=len(atoms), id=id_-1))
+    out.write(atoms_section)
+    out.write(bonds_section)
+    out.write(substructure_section)
+    out.close()
+
+def write_input(molecular_container, filename):
+    """Write PROPKA input file for molecular container.
+
+    Args:
+        molecular_container:  molecular container
+        filename:  output file name
+    """
+    out = open_file_for_writing(filename)
+    for conformation_name in molecular_container.conformation_names:
+        out.write('MODEL {0:s}\n'.format(conformation_name))
+        # write atoms
+        for atom in molecular_container.conformations[conformation_name].atoms:
+            out.write(atom.make_input_line())
+        # write bonds
+        for atom in molecular_container.conformations[conformation_name].atoms:
+            out.write(atom.make_conect_line())
+        # write covalently coupled groups
+        for group in (
+                molecular_container.conformations[conformation_name].groups):
+            out.write(group.make_covalently_coupled_line())
+        # write non-covalently coupled groups
+        for group in (
+                molecular_container.conformations[conformation_name].groups):
+            out.write(group.make_non_covalently_coupled_line())
+        out.write('ENDMDL\n')
+    out.close()

propka/pdb.py

@@ -1,7 +1,8 @@
-"""PDB parsing functionality."""
+"""Read and parse PDB-like input files."""
 import propka.lib
 from propka.lib import warning
 from propka.atom import Atom
+from propka.group import initialize_atom_group
 from propka.conformation_container import ConformationContainer
 
 
@@ -158,118 +159,6 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
             terminal = None
 
 
-def write_pdb(conformation, filename):
-    """Write PDB conformation to a file.
-
-    Args:
-        conformation:  conformation container
-        filename:  filename for output
-    """
-    write_pdb_for_atoms(conformation.atoms, filename)
-
-
-def write_pdb_for_atoms(atoms, filename, make_conect_section=False):
-    """Write out PDB file for atoms.
-
-    Args:
-        atoms:  list of atoms
-        filename:  name of file
-        make_conect_section:  generate a CONECT PDB section
-    """
-    out = propka.lib.open_file_for_writing(filename)
-    for atom in atoms:
-        out.write(atom.make_pdb_line())
-    if make_conect_section:
-        for atom in atoms:
-            out.write(atom.make_conect_line())
-    out.close()
-
-
-def write_mol2_for_atoms(atoms, filename):
-    """Write out MOL2 file for atoms.
-
-    Args:
-        atoms:  list of atoms
-        filename:  name of file
-    """
-    # TODO - header needs to be converted to format string
-    header = '@<TRIPOS>MOLECULE\n\n{natom:d} {id:d}\nSMALL\nUSER_CHARGES\n'
-    atoms_section = '@<TRIPOS>ATOM\n'
-    for i, atom in enumerate(atoms):
-        atoms_section += atom.make_mol2_line(i+1)
-    bonds_section = '@<TRIPOS>BOND\n'
-    id_ = 1
-    for i, atom1 in enumerate(atoms):
-        for j, atom2 in enumerate(atoms, i+1):
-            if atom1 in atom2.bonded_atoms:
-                type_ = get_bond_order(atom1, atom2)
-                bonds_section += '{0:>7d} {1:>7d} {2:>7d} {3:>7s}\n'.format(
-                    id_, i+1, j+1, type_)
-                id_ += 1
-    substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
-    if len(atoms) > 0:
-        substructure_section = (
-            '@<TRIPOS>SUBSTRUCTURE\n{0:<7d} {1:>10s} {2:>7d}\n'.format(
-                atoms[0].res_num, atoms[0].res_name, atoms[0].numb))
-    out = propka.lib.open_file_for_writing(filename)
-    out.write(header.format(natom=len(atoms), id=id_-1))
-    out.write(atoms_section)
-    out.write(bonds_section)
-    out.write(substructure_section)
-    out.close()
-
-
-def get_bond_order(atom1, atom2):
-    """Get the order of a bond between two atoms.
-
-    Args:
-        atom1:  first atom in bond
-        atom2:  second atom in bond
-    Returns:
-        string with bond type
-    """
-    type_ = '1'
-    pi_electrons1 = atom1.num_pi_elec_2_3_bonds
-    pi_electrons2 = atom2.num_pi_elec_2_3_bonds
-    if '.ar' in atom1.sybyl_type:
-        pi_electrons1 -= 1
-    if '.ar' in atom2.sybyl_type:
-        pi_electrons2 -= 1
-    if pi_electrons1 > 0 and pi_electrons2 > 0:
-        type_ = '{0:d}'.format(min(pi_electrons1, pi_electrons2)+1)
-    if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type:
-        type_ = 'ar'
-    return type_
-
-
-def write_input(molecular_container, filename):
-    """Write PROPKA input file for molecular container.
-
-    Args:
-        molecular_container:  molecular container
-        filename:  output file name
-    """
-    out = propka.lib.open_file_for_writing(filename)
-    for conformation_name in molecular_container.conformation_names:
-        out.write('MODEL {0:s}\n'.format(conformation_name))
-        # write atoms
-        for atom in molecular_container.conformations[conformation_name].atoms:
-            out.write(atom.make_input_line())
-        # write bonds
-        for atom in molecular_container.conformations[conformation_name].atoms:
-            out.write(atom.make_conect_line())
-        # write covalently coupled groups
-        for group in (
-                molecular_container.conformations[conformation_name].groups):
-            out.write(group.make_covalently_coupled_line())
-        # write non-covalently coupled groups
-        for group in (
-                molecular_container.conformations[conformation_name].groups):
-            out.write(group.make_non_covalently_coupled_line())
-        out.write('ENDMDL\n')
-    out.close()
-
-
 def read_input(input_file, parameters, molecule):
     """Read PROPKA input file for molecular container.
 
@@ -316,6 +205,7 @@ def get_atom_lines_from_input(input_file, tags=['ATOM  ', 'HETATM']):
         if tag in tags:
             atom = Atom(line=line)
             atom.get_input_parameters()
+            initialize_atom_group(atom)
             atom.groups_extracted = 1
             atom.is_protonated = True
             atoms[atom.numb] = atom