Merge pull request #2 from orbeckst/master

packaged for standalone installation (Python 3 and Python 2)

INSTALL

@@ -0,0 +1,19 @@
+## Installation
+
+Clone repository or unpack the tar ball and install with
+[setuptools](http://pythonhosted.org/setuptools/index.html) (note: if
+you don't have setuptools installed you will need an internet
+connection so that the installation procedure can sownload the
+required files):
+
+    cd propka-3.1
+    python setup.py install --user
+
+This will install the `propka31` script in your executable directory,
+as configured for setuptools, for instance `~/.local/bin`. You can
+change the bin directory with the `--install-scripts` option. For
+example, in order to install in my `bin` directory in my home
+directory:
+
+    python setup.py install --user --install-scripts ~/bin
+

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md INSTALL 
+include ez_setup.py setup.py 
+include propka.cfg
+

README.md

@@ -1,45 +1,69 @@
 # PROPKA 3.1
 
-PROPKA predicts the pKa values of ionizable groups in
+PROPKA predicts the pKa values of ionizable groups in proteins
-proteins (version 3.0) and
+(version 3.0) and protein-ligand complexes (version 3.1)
-protein-ligand complexes (version 3.1)
+based on the 3D structure.
-based in the 3D structure.
 
 For proteins without ligands both version should produce the same result.
 
 The method is described in the following papers, which you should cite
 in publications:
 
-* Søndergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
+* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
 
-* Olsson, Mats HM, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
+* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
 
 See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
 using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).
 
+## Modifications 
+
+This release of PROPKA 3.1 was modified by Oliver Beckstein
+<oliver.beckstein@asu.edu> from the released version.
+
+* Included patches from
+  https://github.com/schrodinger/propka-3.1/tree/python27-compat to
+  make it compatible with Python 2.7
+
+* Packaged for installation with setuptools.
+
+
 ## Installation
 
-No installation needed. Just clone and run.
+Clone repository or unpack the tar ball and install with
+[setuptools](http://pythonhosted.org/setuptools/index.html) (note: if
+you don't have setuptools installed you will need an internet
+connection so that the installation procedure can download the
+required files):
+
+    cd propka-3.1
+    python setup.py install --user
+
+This will install the `propka31` script in your executable directory,
+as configured for setuptools, for instance `~/.local/bin`. You can
+change the bin directory with the `--install-scripts` option. For
+example, in order to install in my `bin` directory in my home
+directory:
+
+    python setup.py install --user --install-scripts ~/bin
+
 
 ## Requirements
 
-* Python 3.1 or higher
+* Python 2.7 or higher or Python 3.1 or higher 
 
 ## Getting started
 
 1. Clone the code from GitHub
-2. Run 'propka.py' with a .pdb file (see Examples)
+2. `python setup.py install --user`
+2. Run `propka31` with a .pdb file (see Examples)
 
 ## Examples
 
 Calculate using pdb file
 
-    ./propka.py 1hpx.pdb
+    propka31 1hpx.pdb
 
-If for some reason your setup with python3.1+ is
-not located in '/usr/bin/python3', run the script
-
-    python3.2 propka.py 1hpx.pdb
 
 ## Testing (for developers)
 
@@ -49,9 +73,9 @@ Please run `Tests/runtest.py/` after changes before pushing commits.
 
 Please cite these references in publications:
 
-* Søndergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
+* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
 
-* Olsson, Mats HM, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
+* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
 
 
 

Tests/runtest.py

@@ -1,9 +1,13 @@
-#!/usr/bin/python3
+#!/usr/bin/env python
 
 """ Run test for test pdbs """
 
+from __future__ import division
+from __future__ import print_function
+
 from subprocess import call
 import os, re
+import sys
 
 pdbs = ['1FTJ-Chain-A',
         '1HPX',
@@ -14,7 +18,7 @@ for pdb in pdbs:
   print('RUNNING '+pdb)
 
   # Run pka calculation
-  call(['../propka.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
+  call([sys.executable, '../scripts/propka31.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
 
   # Test pka predictiona
   result = open('results/'+pdb+'.dat','r')

ez_setup.py

@@ -0,0 +1,258 @@
+#!python
+"""Bootstrap setuptools installation
+
+If you want to use setuptools in your package's setup.py, just include this
+file in the same directory with it, and add this to the top of your setup.py::
+
+    from ez_setup import use_setuptools
+    use_setuptools()
+
+If you want to require a specific version of setuptools, set a download
+mirror, or use an alternate download directory, you can do so by supplying
+the appropriate options to ``use_setuptools()``.
+
+This file can also be run as a script to install or upgrade setuptools.
+"""
+import os
+import shutil
+import sys
+import tempfile
+import tarfile
+import optparse
+import subprocess
+
+from distutils import log
+
+try:
+    from site import USER_SITE
+except ImportError:
+    USER_SITE = None
+
+DEFAULT_VERSION = "0.9.6"
+DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
+
+def _python_cmd(*args):
+    args = (sys.executable,) + args
+    return subprocess.call(args) == 0
+
+def _install(tarball, install_args=()):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+
+        # installing
+        log.warn('Installing Setuptools')
+        if not _python_cmd('setup.py', 'install', *install_args):
+            log.warn('Something went wrong during the installation.')
+            log.warn('See the error message above.')
+            # exitcode will be 2
+            return 2
+    finally:
+        os.chdir(old_wd)
+        shutil.rmtree(tmpdir)
+
+
+def _build_egg(egg, tarball, to_dir):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+
+        # building an egg
+        log.warn('Building a Setuptools egg in %s', to_dir)
+        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+
+    finally:
+        os.chdir(old_wd)
+        shutil.rmtree(tmpdir)
+    # returning the result
+    log.warn(egg)
+    if not os.path.exists(egg):
+        raise IOError('Could not build the egg.')
+
+
+def _do_download(version, download_base, to_dir, download_delay):
+    egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
+                       % (version, sys.version_info[0], sys.version_info[1]))
+    if not os.path.exists(egg):
+        tarball = download_setuptools(version, download_base,
+                                      to_dir, download_delay)
+        _build_egg(egg, tarball, to_dir)
+    sys.path.insert(0, egg)
+    import setuptools
+    setuptools.bootstrap_install_from = egg
+
+
+def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                   to_dir=os.curdir, download_delay=15):
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    was_imported = 'pkg_resources' in sys.modules or \
+        'setuptools' in sys.modules
+    try:
+        import pkg_resources
+    except ImportError:
+        return _do_download(version, download_base, to_dir, download_delay)
+    try:
+        pkg_resources.require("setuptools>=" + version)
+        return
+    except pkg_resources.VersionConflict:
+        e = sys.exc_info()[1]
+        if was_imported:
+            sys.stderr.write(
+            "The required version of setuptools (>=%s) is not available,\n"
+            "and can't be installed while this script is running. Please\n"
+            "install a more recent version first, using\n"
+            "'easy_install -U setuptools'."
+            "\n\n(Currently using %r)\n" % (version, e.args[0]))
+            sys.exit(2)
+        else:
+            del pkg_resources, sys.modules['pkg_resources']    # reload ok
+            return _do_download(version, download_base, to_dir,
+                                download_delay)
+    except pkg_resources.DistributionNotFound:
+        return _do_download(version, download_base, to_dir,
+                            download_delay)
+
+
+def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                        to_dir=os.curdir, delay=15):
+    """Download setuptools from a specified location and return its filename
+
+    `version` should be a valid setuptools version number that is available
+    as an egg for download under the `download_base` URL (which should end
+    with a '/'). `to_dir` is the directory where the egg will be downloaded.
+    `delay` is the number of seconds to pause before an actual download
+    attempt.
+    """
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+    tgz_name = "setuptools-%s.tar.gz" % version
+    url = download_base + tgz_name
+    saveto = os.path.join(to_dir, tgz_name)
+    src = dst = None
+    if not os.path.exists(saveto):  # Avoid repeated downloads
+        try:
+            log.warn("Downloading %s", url)
+            src = urlopen(url)
+            # Read/write all in one block, so we don't create a corrupt file
+            # if the download is interrupted.
+            data = src.read()
+            dst = open(saveto, "wb")
+            dst.write(data)
+        finally:
+            if src:
+                src.close()
+            if dst:
+                dst.close()
+    return os.path.realpath(saveto)
+
+
+def _extractall(self, path=".", members=None):
+    """Extract all members from the archive to the current working
+       directory and set owner, modification time and permissions on
+       directories afterwards. `path' specifies a different directory
+       to extract to. `members' is optional and must be a subset of the
+       list returned by getmembers().
+    """
+    import copy
+    import operator
+    from tarfile import ExtractError
+    directories = []
+
+    if members is None:
+        members = self
+
+    for tarinfo in members:
+        if tarinfo.isdir():
+            # Extract directories with a safe mode.
+            directories.append(tarinfo)
+            tarinfo = copy.copy(tarinfo)
+            tarinfo.mode = 448  # decimal for oct 0700
+        self.extract(tarinfo, path)
+
+    # Reverse sort directories.
+    if sys.version_info < (2, 4):
+        def sorter(dir1, dir2):
+            return cmp(dir1.name, dir2.name)
+        directories.sort(sorter)
+        directories.reverse()
+    else:
+        directories.sort(key=operator.attrgetter('name'), reverse=True)
+
+    # Set correct owner, mtime and filemode on directories.
+    for tarinfo in directories:
+        dirpath = os.path.join(path, tarinfo.name)
+        try:
+            self.chown(tarinfo, dirpath)
+            self.utime(tarinfo, dirpath)
+            self.chmod(tarinfo, dirpath)
+        except ExtractError:
+            e = sys.exc_info()[1]
+            if self.errorlevel > 1:
+                raise
+            else:
+                self._dbg(1, "tarfile: %s" % e)
+
+
+def _build_install_args(options):
+    """
+    Build the arguments to 'python setup.py install' on the setuptools package
+    """
+    install_args = []
+    if options.user_install:
+        if sys.version_info < (2, 6):
+            log.warn("--user requires Python 2.6 or later")
+            raise SystemExit(1)
+        install_args.append('--user')
+    return install_args
+
+def _parse_args():
+    """
+    Parse the command line for options
+    """
+    parser = optparse.OptionParser()
+    parser.add_option(
+        '--user', dest='user_install', action='store_true', default=False,
+        help='install in user site package (requires Python 2.6 or later)')
+    parser.add_option(
+        '--download-base', dest='download_base', metavar="URL",
+        default=DEFAULT_URL,
+        help='alternative URL from where to download the setuptools package')
+    options, args = parser.parse_args()
+    # positional arguments are ignored
+    return options
+
+def main(version=DEFAULT_VERSION):
+    """Install or upgrade setuptools and EasyInstall"""
+    options = _parse_args()
+    tarball = download_setuptools(download_base=options.download_base)
+    return _install(tarball, _build_install_args(options))
+
+if __name__ == '__main__':
+    sys.exit(main())

propka.py

@@ -1,23 +0,0 @@
-#!/usr/bin/python3
-
-import string,re,sys,os,math
-import Source.lib, Source.molecular_container 
-
-def main():
-    """
-    Reads in structure files, calculates pKa values, and prints pKa files
-    """
-    # loading options, flaggs and arguments
-    options, pdbfiles = Source.lib.loadOptions()
-
-    for pdbfile in pdbfiles:
-        my_molecule = Source.molecular_container.Molecular_container(pdbfile, options)
-        my_molecule.calculate_pka()
-        my_molecule.write_pka()
-
-
-if __name__ == '__main__': 
-    #import cProfile
-    #cProfile.run('main()',sort=1)
-    main()
-

propka/__init__.py

@@ -1,3 +1,5 @@
-#
+# propka 3.1
+# (Module renamed from original Source to propka to facilitate setuptools installation)
+
 __all__ = ['coupled_residues', 'lib', 'parameters', 'residue', 'bonds', 'debug', 'ligand', 'pdb', 'calculator', 'determinants', 'mutate', 'protein', 'chain', 'iterative', 'output', 'protonate']
 

propka/atom.py

@@ -1,4 +1,8 @@
-import string, Source.lib, Source.group
+
+from __future__ import division
+from __future__ import print_function
+
+import string, propka.lib, propka.group
 
 
 class Atom:
@@ -195,7 +199,7 @@ class Atom:
 
         str  = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s \n" % (self.type.upper(),
                                                                     self.numb,
-                                                                    Source.lib.makeTidyAtomLabel(self.name,
+                                                                    propka.lib.makeTidyAtomLabel(self.name,
                                                                                                  self.element),
                                                                     self.resName,
                                                                     self.chainID,
@@ -258,7 +262,7 @@ class Atom:
 
             # try to initialise the group
             try:
-                exec('self.group = Source.group.%s_group(self)'%self.occ)
+                exec('self.group = propka.group.%s_group(self)'%self.occ)
             except:
                 raise Exception('%s in input_file is not recognized as a group'%self.occ)
 
@@ -282,7 +286,7 @@ class Atom:
         # making string
         str  = "%-6s%5d %s %s%2s%4d%12.3lf%8.3lf%8.3lf%6s%6s\n" % (self.type.upper(),
                                                                    self.numb,
-                                                                   Source.lib.makeTidyAtomLabel(self.name,
+                                                                   propka.lib.makeTidyAtomLabel(self.name,
                                                                                                 self.element),
                                                                    self.resName,
                                                                    self.chainID,
@@ -299,10 +303,10 @@ class Atom:
 
 
     def make_mol2_line(self,id):
-#1	S1     3.6147     2.0531     1.4795	S.3	1	noname	-0.1785
+#1      S1     3.6147     2.0531     1.4795     S.3     1       noname  -0.1785
         # making string
         str  = "%-4d %-4s %10.4f %10.4f %10.4f %6s %6d %10s %10.4f\n" % (id,
-                                                                         Source.lib.makeTidyAtomLabel(self.name,
+                                                                         propka.lib.makeTidyAtomLabel(self.name,
                                                                                                       self.element),
                                                                          self.x,
                                                                          self.y,
@@ -346,7 +350,7 @@ class Atom:
         # making string
         str  = "ATOM "
         str += "%6d" % (numb)
-        str += " %s" % (Source.lib.makeTidyAtomLabel(name,self.element))
+        str += " %s" % (propka.lib.makeTidyAtomLabel(name,self.element))
         str += " %s" % (resName)
         str += "%2s" % (chainID)
         str += "%4d" % (resNumb)
@@ -363,7 +367,7 @@ class Atom:
         """
         Returns a 'tidier' atom label for printing the new pdbfile
         """
-        return Source.lib.makeTidyAtomLabel(self.name,self.element)
+        return propka.lib.makeTidyAtomLabel(self.name,self.element)
 
 
     def __str__(self):

propka/bonds.py

@@ -1,5 +1,10 @@
-import pickle,sys,os,math,Source.calculations
 
+from __future__ import division
+from __future__ import print_function
+
+import pickle,sys,os,math,propka.calculations
+
+import pkg_resources
 
 class bondmaker:
     def __init__(self):
@@ -22,8 +27,7 @@ class bondmaker:
         self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
 
         # protein bonding data
-        path = os.path.split(__file__)[0]
+        self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.dat')
-        self.data_file_name = os.path.join(path,'protein_bonds.dat')
 
         data = open(self.data_file_name,'rb')
         self.protein_bonds = pickle.load(data)
@@ -145,7 +149,7 @@ class bondmaker:
             if atom1.name == 'SG':
                 for atom2 in cys2.atoms:
                     if atom2.name == 'SG':
-                        if Source.calculations.squared_distance(atom1,atom2) < self.SS_dist_squared:
+                        if propka.calculations.squared_distance(atom1,atom2) < self.SS_dist_squared:
                             self.make_bond(atom1, atom2)
 
 
@@ -174,7 +178,7 @@ class bondmaker:
             if atom1.name == 'C':
                 for atom2 in residue2.atoms:
                     if atom2.name == 'N':
-                        if Source.calculations.squared_distance(atom1,atom2) < self.default_dist_squared:
+                        if propka.calculations.squared_distance(atom1,atom2) < self.default_dist_squared:
                             self.make_bond(atom1, atom2)
 
         return
@@ -283,7 +287,7 @@ class bondmaker:
 
 
     def check_distance(self, atom1, atom2):
-        sq_dist = Source.calculations.squared_distance(atom1, atom2)
+        sq_dist = propka.calculations.squared_distance(atom1, atom2)
 
         if sq_dist > self.max_sq_distance:
             return False
@@ -350,9 +354,11 @@ class bondmaker:
         #print('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
 
         # how many boxes do we need in each dimension?
-        self.no_box_x = max(1, math.ceil(xlen/box_size))
+        # NOTE: math.ceil() returns an int in python3 and a float in python2,
-        self.no_box_y = max(1, math.ceil(ylen/box_size))
+        # so we need to cast it to int for range() to work.
-        self.no_box_z = max(1, math.ceil(zlen/box_size))
+        self.no_box_x = max(1, int(math.ceil(xlen/box_size)))
+        self.no_box_y = max(1, int(math.ceil(ylen/box_size)))
+        self.no_box_z = max(1, int(math.ceil(zlen/box_size)))
 
         #print('No. box x: %6.2f'%self.no_box_x)
         #print('No. box y: %6.2f'%self.no_box_y)

propka/calculations.py

@@ -1,6 +1,8 @@
 
+from __future__ import division
+from __future__ import print_function
 
-import math, Source.protonate, Source.bonds,copy, sys
+import math, propka.protonate, propka.bonds,copy, sys
 
 
 #
@@ -19,7 +21,7 @@ def setup_bonding_and_protonation(parameters, molecular_container):
 
     # Protonate atoms
     if molecular_container.options.protonate_all:
-        my_protonator = Source.protonate.Protonate(verbose=False)
+        my_protonator = propka.protonate.Protonate(verbose=False)
         my_protonator.protonate(molecular_container)
 
 
@@ -29,7 +31,7 @@ def setup_bonding_and_protonation(parameters, molecular_container):
 
 def setup_bonding(parameters, molecular_container):
     # make bonds
-    my_bond_maker = Source.bonds.bondmaker()
+    my_bond_maker = propka.bonds.bondmaker()
     my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
 
     return my_bond_maker
@@ -50,7 +52,7 @@ def setup_bonding_and_protonation_30_style(parameters, molecular_container):
     protonate_30_style(molecular_container)
 
     # make bonds
-    my_bond_maker = Source.bonds.bondmaker()
+    my_bond_maker = propka.bonds.bondmaker()
     my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
 
     return
@@ -307,7 +309,7 @@ def protonateSP2(list):
 
 def make_new_H(atom, x,y,z):
 
-    new_H = Source.atom.Atom()
+    new_H = propka.atom.Atom()
     new_H.setProperty(numb    = None,
                       name    = 'H%s'%atom.name[1:],
                       resName = atom.resName,
@@ -569,7 +571,7 @@ def hydrogen_bond_interaction(group1, group2, version):
     # find the smallest distance between interacting atoms
     atoms1 = group1.get_interaction_atoms(group2)
     atoms2 = group2.get_interaction_atoms(group1)
-    [closest_atom1, distance, closest_atom2] = Source.calculations.get_smallest_distance(atoms1, atoms2)
+    [closest_atom1, distance, closest_atom2] = propka.calculations.get_smallest_distance(atoms1, atoms2)
 
     if None in [closest_atom1, closest_atom2]:
         print('Warning: Side chain interaction failed for %s and %s'%(group1.label, group2.label))
@@ -602,7 +604,7 @@ def hydrogen_bond_interaction(group1, group2, version):
         if closest_atom2.element == 'H':
             heavy_atom = closest_atom2.bonded_atoms[0]
             hydrogen   = closest_atom2
-            distance, f_angle, nada = Source.calculations.AngleFactorX(closest_atom1, hydrogen, heavy_atom)   
+            distance, f_angle, nada = propka.calculations.AngleFactorX(closest_atom1, hydrogen, heavy_atom)
         else:
             # Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
             # the titratable atom than the hydrogen. In either case we set the angle factor
@@ -613,7 +615,7 @@ def hydrogen_bond_interaction(group1, group2, version):
         if closest_atom1.element == 'H':
             heavy_atom = closest_atom1.bonded_atoms[0]
             hydrogen   = closest_atom1
-            distance, f_angle, nada = Source.calculations.AngleFactorX(closest_atom2, hydrogen, heavy_atom)  
+            distance, f_angle, nada = propka.calculations.AngleFactorX(closest_atom2, hydrogen, heavy_atom)
         else:
             # Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
             # the titratable atom than the hydrogen. In either case we set the angle factor

propka/conformation_container.py

@@ -2,7 +2,10 @@
 # Container for molecular conformations
 #
 
-import Source.group, Source.determinants, Source.determinant, Source.ligand, Source.output, Source.coupled_groups, functools
+from __future__ import division
+from __future__ import print_function
+
+import propka.group, propka.determinants, propka.determinant, propka.ligand, propka.output, propka.coupled_groups, functools
 
 class Conformation_container:
     def __init__(self, name='', parameters=None, molecular_container=None):
@@ -28,7 +31,7 @@ class Conformation_container:
         for atom in self.get_non_hydrogen_atoms():
             # has this atom been checked for groups?
             if atom.groups_extracted == 0:
-                self.validate_group(Source.group.is_group(self.parameters, atom))
+                self.validate_group(propka.group.is_group(self.parameters, atom))
             # if the atom has been checked in a another conformation, check if it has a
             # group that should be used in this conformation as well
             elif atom.group:
@@ -42,7 +45,7 @@ class Conformation_container:
         # some more configuration might be needed
 
         # print coupling map
-        map = Source.output.make_interaction_map('Covalent coupling map for %s'%self,
+        map = propka.output.make_interaction_map('Covalent coupling map for %s'%self,
                                                  self.get_covalently_coupled_groups(),
                                                  lambda g1,g2: g1 in g2.covalently_coupled_groups)
         print(map)
@@ -54,7 +57,7 @@ class Conformation_container:
         return
 
     def set_common_charge_centres(self):
-        for system in self.get_coupled_systems(self.get_covalently_coupled_groups(), Source.group.Group.get_covalently_coupled_groups):
+        for system in self.get_coupled_systems(self.get_covalently_coupled_groups(), propka.group.Group.get_covalently_coupled_groups):
             # make a list of the charge centre coordinates
             all_coordinates = list(map(lambda g: [g.x, g.y, g.z], system))
             # find the common charge center
@@ -88,7 +91,7 @@ class Conformation_container:
             self.set_common_charge_centres()
 
         # print coupling map
-        map = Source.output.make_interaction_map('Covalent coupling map for %s'%self,
+        map = propka.output.make_interaction_map('Covalent coupling map for %s'%self,
                                                  #self.get_titratable_groups(),
                                                  self.get_covalently_coupled_groups(),
                                                  lambda g1,g2: g1 in g2.covalently_coupled_groups)
@@ -103,7 +106,7 @@ class Conformation_container:
         if len(list(filter(lambda g: len(g.non_covalently_coupled_groups)>0, self.get_titratable_groups())))>0:
             self.non_covalently_coupled_groups = True
 
-        Source.coupled_groups.nccg.identify_non_covalently_coupled_groups(self,verbose=verbose)
+        propka.coupled_groups.nccg.identify_non_covalently_coupled_groups(self,verbose=verbose)
 
         # re-do the check
         if len(list(filter(lambda g: len(g.non_covalently_coupled_groups)>0, self.get_titratable_groups())))>0:
@@ -163,16 +166,16 @@ class Conformation_container:
             version.calculate_desolvation(group)
 
         # calculate backbone interactions
-        Source.determinants.setBackBoneDeterminants(self.get_titratable_groups(), self.get_backbone_groups(), version)
+        propka.determinants.setBackBoneDeterminants(self.get_titratable_groups(), self.get_backbone_groups(), version)
 
         # setting ion determinants
-        Source.determinants.setIonDeterminants(self, version)
+        propka.determinants.setIonDeterminants(self, version)
 
         # calculating the back-bone reorganization/desolvation term
         version.calculateBackBoneReorganization(self)
 
         # setting remaining non-iterative and iterative side-chain & Coulomb interaction determinants
-        Source.determinants.setDeterminants(self.get_sidechain_groups(), version=version, options=options)
+        propka.determinants.setDeterminants(self.get_sidechain_groups(), version=version, options=options)
 
         # calculating the total pKa values
         for group in self.groups: group.calculate_total_pka()
@@ -208,7 +211,7 @@ class Conformation_container:
         penalised_labels = []
 
         for all_groups in self.get_coupled_systems(self.get_covalently_coupled_groups(),
-                                                   Source.group.Group.get_covalently_coupled_groups):
+                                                   propka.group.Group.get_covalently_coupled_groups):
 
             # check if we should share determinants
             if self.parameters.shared_determinants:
@@ -250,7 +253,7 @@ class Conformation_container:
 
              # overwrite/add maximum value for each determinant
             for det_group in max_dets.keys():
-                new_determinant = Source.determinant.Determinant(det_group, max_dets[det_group])
+                new_determinant = propka.determinant.Determinant(det_group, max_dets[det_group])
                 for g in groups:
                     g.set_determinant(new_determinant,type)
 
@@ -410,7 +413,7 @@ class Conformation_container:
 
     def set_ligand_atom_names(self):
         for atom in self.get_ligand_atoms():
-            Source.ligand.assign_sybyl_type(atom)
+            propka.ligand.assign_sybyl_type(atom)
         return
 
 

propka/coupled_groups.py

@@ -1,5 +1,8 @@
 
-import math, Source.output, Source.group, Source.lib, itertools
+from __future__ import division
+from __future__ import print_function
+
+import math, propka.output, propka.group, propka.lib, itertools
 
 
 class non_covalently_couple_groups:
@@ -163,12 +166,12 @@ class non_covalently_couple_groups:
         return
 
     def print_out_swaps(self, conformation, verbose=True):
-        map = Source.output.make_interaction_map('Non-covalent coupling map for %s'%conformation,
+        map = propka.output.make_interaction_map('Non-covalent coupling map for %s'%conformation,
                                                  conformation.get_non_covalently_coupled_groups(),
                                                  lambda g1,g2: g1 in g2.non_covalently_coupled_groups)
         print(map)
 
-        for system in conformation.get_coupled_systems(conformation.get_non_covalently_coupled_groups(),Source.group.Group.get_non_covalently_coupled_groups):
+        for system in conformation.get_coupled_systems(conformation.get_non_covalently_coupled_groups(),propka.group.Group.get_non_covalently_coupled_groups):
             self.print_system(conformation, list(system))
         return
 
@@ -187,7 +190,7 @@ class non_covalently_couple_groups:
         print(coup_info)
 
         # make list of possible combinations of swap to try out
-        combinations = Source.lib.generate_combinations(interactions)
+        combinations = propka.lib.generate_combinations(interactions)
 
         # Make possible swap combinations
         swap_info = ''

propka/determinant.py

@@ -1,4 +1,7 @@
 
+from __future__ import division
+from __future__ import print_function
+
 class Determinant:
     """
         Determinant class - set up for later structurization

propka/determinants.py

@@ -1,8 +1,12 @@
+
+from __future__ import division
+from __future__ import print_function
+
 import math, time
 
-import Source.iterative, Source.lib, Source.vector_algebra
+import propka.iterative, propka.lib, propka.vector_algebra
-import Source.calculations
+import propka.calculations
-from Source.determinant import Determinant
+from propka.determinant import Determinant
 
 
 def setDeterminants(propka_groups, version=None, options=None):
@@ -20,18 +24,18 @@ def setDeterminants(propka_groups, version=None, options=None):
             if group2 in group1.covalently_coupled_groups:
                 break
 
-            distance = Source.calculations.distance(group1, group2)
+            distance = propka.calculations.distance(group1, group2)
 
             if distance < version.parameters.coulomb_cutoff2:
                 interaction_type = version.parameters.interaction_matrix.get_value(group1.type,group2.type)
                 if interaction_type == 'I':
-                    Source.iterative.addtoDeterminantList(group1, group2, distance, iterative_interactions, version=version)
+                    propka.iterative.addtoDeterminantList(group1, group2, distance, iterative_interactions, version=version)
                 elif interaction_type == 'N':
                     addDeterminants(group1, group2, distance, version)
 
 
     # --- Iterative section ---#
-    Source.iterative.addDeterminants(iterative_interactions, version, options=options)
+    propka.iterative.addDeterminants(iterative_interactions, version, options=options)
 
 
 def addDeterminants(group1, group2, distance, version):
@@ -151,7 +155,7 @@ def setIonDeterminants(conformation_container, version):
     """
     for titratable_group in conformation_container.get_titratable_groups():
         for ion_group in conformation_container.get_ions():
-            squared_distance = Source.calculations.squared_distance(titratable_group, ion_group)
+            squared_distance = propka.calculations.squared_distance(titratable_group, ion_group)
             if squared_distance < version.parameters.coulomb_cutoff2_squared:
                 weight = version.calculatePairWeight(titratable_group.Nmass, ion_group.Nmass)
                 # the pKa of both acids and bases are shifted up by negative ions (and vice versa)
@@ -171,7 +175,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
             titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids
 
             # find the smallest distance
-            [backbone_atom, distance, titratable_atom] = Source.calculations.get_smallest_distance(backbone_interaction_atoms,
+            [backbone_atom, distance, titratable_atom] = propka.calculations.get_smallest_distance(backbone_interaction_atoms,
                                                                                                    titratable_group_interaction_atoms)
             # get the parameters
             parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom, titratable_atom)
@@ -197,7 +201,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
                         if titratable_atom.element == 'H':
                             heavy_atom    = titratable_atom.bonded_atoms[0]
                             hydrogen_atom = titratable_atom
-                            [d1, f_angle, d2] = Source.calculations.AngleFactorX(atom1=heavy_atom,
+                            [d1, f_angle, d2] = propka.calculations.AngleFactorX(atom1=heavy_atom,
                                                                                  atom2=hydrogen_atom,
                                                                                  atom3=backbone_atom)
                         else:
@@ -218,7 +222,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
                     if backbone_atom.element == 'H':
                         backbone_N = backbone_atom.bonded_atoms[0]
                         backbone_H = backbone_atom
-                        [d1, f_angle, d2] = Source.calculations.AngleFactorX(atom1=titratable_atom,
+                        [d1, f_angle, d2] = propka.calculations.AngleFactorX(atom1=titratable_atom,
                                                                              atom2=backbone_H,
                                                                              atom3=backbone_N)
                     else:
@@ -229,7 +233,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
 
 
                 if f_angle > 0.001:
-                    value = titratable_group.charge * Source.calculations.HydrogenBondEnergy(distance, dpKa_max, [cutoff1,cutoff2], f_angle)
+                    value = titratable_group.charge * propka.calculations.HydrogenBondEnergy(distance, dpKa_max, [cutoff1,cutoff2], f_angle)
 
                     newDeterminant = Determinant(backbone_group, value)
                     titratable_group.determinants['backbone'].append(newDeterminant)

propka/group.py

@@ -2,9 +2,12 @@
 # Class for storing groups important for propka calculations
 #
 
-import Source.ligand, Source.determinant, Source.ligand_pka_values, math, Source.protonate
+from __future__ import division
+from __future__ import print_function
 
-my_protonator = Source.protonate.Protonate(verbose=False)
+import propka.ligand, propka.determinant, propka.ligand_pka_values, math, propka.protonate
+
+my_protonator = propka.protonate.Protonate(verbose=False)
 
 expected_atoms_acid_interactions = {
     'COO':{'O':2},
@@ -190,7 +193,7 @@ class Group:
 
         # otherwise we just add the determinant to our list
         if not added:
-            self.determinants[type].append(Source.determinant.Determinant(new_determinant.group, 
+            self.determinants[type].append(propka.determinant.Determinant(new_determinant.group,
                                                                           new_determinant.value))
 
         return
@@ -283,7 +286,7 @@ class Group:
                 return
 
         # otherwise we just add the determinant to our list
-        self.determinants[type].append(Source.determinant.Determinant(new_determinant.group, 
+        self.determinants[type].append(propka.determinant.Determinant(new_determinant.group,
                                                                       new_determinant.value))
 
         return
@@ -298,7 +301,7 @@ class Group:
                 return
 
         # otherwise we just add the determinant to our list
-        self.determinants[type].append(Source.determinant.Determinant(new_determinant.group, 
+        self.determinants[type].append(propka.determinant.Determinant(new_determinant.group,
                                                                       new_determinant.value))
 
         return
@@ -624,7 +627,7 @@ class HIS_group(Group):
 
     def setup_atoms(self):
         # Find the atoms in the histidine ring
-        ring_atoms = Source.ligand.is_ring_member(self.atom)
+        ring_atoms = propka.ligand.is_ring_member(self.atom)
         if len(ring_atoms) != 5:
             print('Warning: His group does not seem to contain a ring',self)
 
@@ -1284,7 +1287,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
     # calculate Marvin ligand pkas for this conformation container
     # if not already done
     if not atom.conformation_container.marvin_pkas_calculated:
-        lpka = Source.ligand_pka_values.ligand_pka_values(parameters)
+        lpka = propka.ligand_pka_values.ligand_pka_values(parameters)
         lpka.get_marvin_pkas_for_molecular_container(atom.molecular_container,
                                                      min_pH=parameters.min_ligand_model_pka,
                                                      max_pH=parameters.max_ligand_model_pka)

propka/iterative.py

@@ -1,7 +1,12 @@
+
+from __future__ import division
+from __future__ import print_function
+
 import math, time
-import Source.lib as lib
+
-from Source.determinant import Determinant
+import propka.lib as lib
-import Source.calculations
+from propka.determinant import Determinant
+import propka.calculations
 
 # Some library functions for the interative pKa determinants
 

propka/lib.py

@@ -1,20 +1,24 @@
-#!/usr/bin/python
+from __future__ import division
+from __future__ import print_function
 
 import string, sys, copy, math, os
 
+import pkg_resources
 
 #
 # file I/O
 #
 def open_file_for_reading(filename):
-    if not os.path.isfile(filename):
+    try:
+        f = open(filename,'r')
+    except:
         raise Exception('Cannot find file %s' %filename)
-    
+    return f
-    return open(filename,'r')
 
 def open_file_for_writing(filename):
-    res = open(filename,'w')
+    try:
-    if not res:
+        res = open(filename,'w')
+    except:
         raise Exception('Could not open %s'%filename)
     return res
 
@@ -99,8 +103,8 @@ def loadOptions():
            help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
     parser.add_option("-v", "--version", dest="version_label", default="Jan15",
            help="specifying the sub-version of propka [Jan15/Dec19]")
-    parser.add_option("-p", "--parameters",dest="parameters", default="propka.cfg",
+    parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
-                      help="set the parameter file")
+                      help="set the parameter file [%default]")
     parser.add_option("-z", "--verbose", dest="verbose", action="store_true", default=True,
            help="sleep during calculations")
     parser.add_option("-q", "--quiet", dest="verbose", action="store_false",

propka/ligand.py

@@ -1,7 +1,12 @@
 #!/usr/bin/python
 
-import sys, Source.calculations
+from __future__ import division
-from Source.vector_algebra import *
+from __future__ import print_function
+
+import sys
+
+import propka.calculations
+from propka.vector_algebra import *
 
 
 all_sybyl_types = [
@@ -217,7 +222,7 @@ def assign_sybyl_type(atom):
         # sp carbon
         if len(atom.bonded_atoms)<=2:
             for b in atom.bonded_atoms:
-                if Source.calculations.squared_distance(atom, b) < max_C_triple_bond_squared:
+                if propka.calculations.squared_distance(atom, b) < max_C_triple_bond_squared:
                     set_type(atom,'C.1')
                     set_type(b,b.element+'.1')
             if atom.sybyl_assigned:
@@ -270,7 +275,7 @@ def assign_sybyl_type(atom):
                         return
 
             # check for X=O
-            if Source.calculations.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
+            if propka.calculations.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
                 set_type(atom,'O.2')
                 if atom.bonded_atoms[0].element=='C':
                     set_type(atom.bonded_atoms[0],'C.2')
@@ -316,7 +321,7 @@ def assign_sybyl_type(atom):
 #             bonded_oxygens_1 = [o for o in bonded_oxygens if len(o.get_bonded_heavy_atoms())==1]
 #             # find the closest oxygen ...
 #             closest_oxygen = min(bonded_oxygens_1,
-#                                  key= lambda o:Source.calculations.squared_distance(atom,o))
+#                                  key= lambda o:propka.calculations.squared_distance(atom,o))
 #             # ... and set it to O.2
 #             set_type(closest_oxygen,'O.2')
 

propka/ligand_pka_values.py

@@ -1,6 +1,9 @@
 #!/usr/bin/env python
 
-import Source.molecular_container, Source.calculations, Source.calculations, Source.parameters, Source.pdb, Source.lib, os, subprocess, sys
+from __future__ import division
+from __future__ import print_function
+
+import propka.molecular_container, propka.calculations, propka.calculations, propka.parameters, propka.pdb, propka.lib, os, subprocess, sys
 
 class ligand_pka_values:
     def __init__(self, parameters):
@@ -29,7 +32,7 @@ class ligand_pka_values:
         return l[0]
 
     def get_marvin_pkas_for_pdb_file(self, file, no_pkas=10, min_pH =-10, max_pH=20):
-        molecule = Source.molecular_container.Molecular_container(file)
+        molecule = propka.molecular_container.Molecular_container(file)
         self.get_marvin_pkas_for_molecular_container(molecule, no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
         return
 
@@ -50,7 +53,7 @@ class ligand_pka_values:
 
     def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
         # do one molecule at the time so we don't confuse marvin
-        molecules = Source.lib.split_atoms_into_molecules(atoms)
+        molecules = propka.lib.split_atoms_into_molecules(atoms)
         for i in range(len(molecules)):
             filename = '%s_%d.mol2'%(name, i+1)
             self.get_marvin_pkas_for_molecule(molecules[i], filename=filename, reuse=reuse, no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
@@ -61,11 +64,11 @@ class ligand_pka_values:
     def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
         # print out structure unless we are using user-modified structure
         if not reuse:
-            Source.pdb.write_mol2_for_atoms(atoms, filename)
+            propka.pdb.write_mol2_for_atoms(atoms, filename)
         # check that we actually have a file to work with
         if not os.path.isfile(filename):
             print('Warning: Didn\'t find a user-modified file \'%s\' - generating one'%filename)
-            Source.pdb.write_mol2_for_atoms(atoms, filename)
+            propka.pdb.write_mol2_for_atoms(atoms, filename)
 
 
 

propka/molecular_container.py

@@ -3,13 +3,17 @@
 # Molecular container for storing all contents of pdb files
 #
 #
+from __future__ import division
+from __future__ import print_function
 
-import os, Source.pdb, sys, Source.version, Source.output, Source.conformation_container, Source.group, Source.lib
+import os, sys
+
+import propka.pdb, propka.version, propka.output, propka.conformation_container, propka.group, propka.lib
 
 class Molecular_container:
     def __init__(self, input_file, options=None):
         # printing out header before parsing input
-        Source.output.printHeader()
+        propka.output.printHeader()
 
         # set up some values
         self.options = options
@@ -21,11 +25,11 @@ class Molecular_container:
 
         # set the version
         if options:
-            parameters = Source.parameters.Parameters(self.options.parameters)
+            parameters = propka.parameters.Parameters(self.options.parameters)
         else:
-            parameters = Source.parameters.Parameters('propka.cfg')
+            parameters = propka.parameters.Parameters('propka.cfg')
         try:
-            exec('self.version = Source.version.%s(parameters)'%parameters.version)
+            exec('self.version = propka.version.%s(parameters)'%parameters.version)
         except:
             raise Exception('Error: Version %s does not exist'%parameters.version)
 
@@ -33,7 +37,7 @@ class Molecular_container:
         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] = Source.pdb.read_pdb(input_file, self.version.parameters,self)
+            [self.conformations, self.conformation_names] = propka.pdb.read_pdb(input_file, self.version.parameters,self)
             if len(self.conformations)==0:
                 print('Error: The pdb file does not seems to contain any molecular conformations')
                 sys.exit(-1)
@@ -41,7 +45,7 @@ class Molecular_container:
             self.top_up_conformations()
 
             # make a structure precheck
-            Source.pdb.protein_precheck(self.conformations, self.conformation_names)
+            propka.pdb.protein_precheck(self.conformations, self.conformation_names)
 
             # set up atom bonding and protonation
             self.version.setup_bonding_and_protonation(self)
@@ -58,12 +62,12 @@ class Molecular_container:
 
             # write out the input file
             filename = self.file.replace(input_file_extension,'.propka_input')
-            Source.pdb.write_input(self, filename)
+            propka.pdb.write_input(self, filename)
 
 
         elif input_file_extension == '.propka_input':
             #input is a propka_input file
-            [self.conformations, self.conformation_names] = Source.pdb.read_input(input_file, self.version.parameters, self)
+            [self.conformations, self.conformation_names] = propka.pdb.read_input(input_file, self.version.parameters, self)
 
             # Extract groups - this merely sets up the groups found in the input file
             self.extract_groups()
@@ -125,13 +129,13 @@ class Molecular_container:
         self.average_of_conformations()
 
         # print out the conformation-average results
-        Source.output.printResult(self, 'AVR', self.version.parameters)
+        propka.output.printResult(self, 'AVR', self.version.parameters)
 
         return
 
     def average_of_conformations(self):
         # make a new configuration to hold the average values
-        avr_conformation = Source.conformation_container.Conformation_container(name='average',
+        avr_conformation = propka.conformation_container.Conformation_container(name='average',
                                                                                 parameters=self.conformations[self.conformation_names[0]].parameters,
                                                                                 molecular_container=self)
 
@@ -161,7 +165,7 @@ class Molecular_container:
 
     def write_pka(self, filename=None, reference="neutral", direction="folding", options=None):
         #for name in self.conformation_names:
-        #    Source.output.writePKA(self, self.version.parameters, filename='%s_3.1_%s.pka'%(self.name, name), 
+        #    propka.output.writePKA(self, self.version.parameters, filename='%s_3.1_%s.pka'%(self.name, name),
         #                           conformation=name,reference=reference,
         #                           direction=direction, options=options)
 
@@ -176,7 +180,7 @@ class Molecular_container:
         if hasattr(self.version.parameters, 'output_file_tag') and len(self.version.parameters.output_file_tag)>0:
             filename=os.path.join('%s_%s.pka'%(self.name,self.version.parameters.output_file_tag))
 
-        Source.output.writePKA(self, self.version.parameters, filename=filename,
+        propka.output.writePKA(self, self.version.parameters, filename=filename,
                                conformation='AVR',reference=reference,
                                direction=direction, options=options)
 
@@ -185,7 +189,7 @@ class Molecular_container:
     def getFoldingProfile(self, conformation='AVR',reference="neutral", direction="folding", grid=[0., 14., 0.1], options=None):
         # calculate stability profile
         profile = []
-        for ph in Source.lib.make_grid(*grid):
+        for ph in propka.lib.make_grid(*grid):
             ddg = self.conformations[conformation].calculate_folding_energy( pH=ph, reference=reference)
             #print(ph,ddg)
             profile.append([ph, ddg])
@@ -213,7 +217,7 @@ class Molecular_container:
 
     def getChargeProfile(self, conformation='AVR', grid=[0., 14., .1]):
         charge_profile = []
-        for ph in Source.lib.make_grid(*grid):
+        for ph in propka.lib.make_grid(*grid):
             q_unfolded, q_folded = self.conformations[conformation].calculate_charge(self.version.parameters, pH=ph)
             charge_profile.append([ph, q_unfolded, q_folded])
 

propka/output.py

@@ -1,5 +1,10 @@
+
+from __future__ import division
+from __future__ import print_function
+
 import sys
-import Source.lib
+
+import propka.lib
 
 
 def printHeader():

propka/parameters.py

@@ -1,7 +1,12 @@
+
+from __future__ import division
+from __future__ import print_function
+
 import math
-import Source.lib as lib
+import propka.lib as lib
 import sys, os
 
+import pkg_resources
 
 # names and types of all key words in configuration file
 matrices =            ['interaction_matrix']
@@ -53,8 +58,7 @@ class Parameters:
     def read_parameters(self, file):
         # try to locate the parameters file
         try:
-            path = os.path.dirname(__file__)
+            ifile = pkg_resources.resource_filename(__name__, file)
-            ifile = os.path.join(path,'../'+file)
             input = lib.open_file_for_reading(ifile)
         except:
             input = lib.open_file_for_reading(file)

propka/pdb.py

@@ -1,6 +1,12 @@
-import string, sys, copy, Source.lib
+
-from Source.atom import Atom
+from __future__ import division
-from Source.conformation_container import Conformation_container
+from __future__ import print_function
+
+import string, sys, copy
+
+import propka.lib
+from propka.atom import Atom
+from propka.conformation_container import Conformation_container
 
 expected_atom_numbers = {'ALA':5,
                          'ARG':11,
@@ -35,7 +41,7 @@ def read_pdb(pdb_file, parameters, molecule):
         conformations[name].add_atom(atom)
 
     # make a sorted list of conformation names
-    names = sorted(conformations.keys(), key=Source.lib.conformation_sorter)
+    names = sorted(conformations.keys(), key=propka.lib.conformation_sorter)
 
     return [conformations, names]
 
@@ -74,7 +80,7 @@ def resid_from_atom(a):
 
 def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False, tags = ['ATOM  ', 'HETATM'], chains=None):
 
-    lines = Source.lib.open_file_for_reading(pdb_file).readlines()
+    lines = propka.lib.open_file_for_reading(pdb_file).readlines()
     nterm_residue = 'next_residue'
     old_residue = None
     terminal = None
@@ -147,7 +153,7 @@ def write_pdb(conformation, filename):
     return
 
 def write_pdb_for_atoms(atoms, filename, make_conect_section=False):
-    out = Source.lib.open_file_for_writing(filename)
+    out = propka.lib.open_file_for_writing(filename)
 
     for atom in atoms:
         out.write(atom.make_pdb_line())
@@ -185,7 +191,7 @@ def write_mol2_for_atoms(atoms, filename):
     if len(atoms)>0:
         substructure_section = '@<TRIPOS>SUBSTRUCTURE\n%-7d %10s %7d\n'%(atoms[0].resNumb,atoms[0].resName,atoms[0].numb)
 
-    out = Source.lib.open_file_for_writing(filename)
+    out = propka.lib.open_file_for_writing(filename)
     out.write(header%(len(atoms),id-1))
     out.write(atoms_section)
     out.write(bonds_section)
@@ -216,7 +222,7 @@ def get_bond_order(atom1, atom2):
 
 
 def write_input(molecular_container, filename):
-    out = Source.lib.open_file_for_writing(filename)
+    out = propka.lib.open_file_for_writing(filename)
 
     for conformation_name in molecular_container.conformation_names:
         out.write('MODEL %s\n'%conformation_name)
@@ -250,14 +256,14 @@ def read_input(input_file, parameters,molecule):
         conformations[name].add_atom(atom)
 
     # make a sorted list of conformation names
-    names = sorted(conformations.keys(), key=Source.lib.conformation_sorter)
+    names = sorted(conformations.keys(), key=propka.lib.conformation_sorter)
 
     return [conformations, names]
 
 
 
 def get_atom_lines_from_input(input_file, tags = ['ATOM  ','HETATM']):
-    lines = Source.lib.open_file_for_reading(input_file).readlines()
+    lines = propka.lib.open_file_for_reading(input_file).readlines()
     conformation = ''
 
     atoms = {}

propka/propka.cfg

@@ -0,0 +1,398 @@
+# PropKa configuration file
+
+version version_A
+
+# Model pKa values
+model_pkas C-   3.20
+model_pkas ASP  3.80
+model_pkas GLU  4.50
+model_pkas HIS  6.50
+model_pkas CYS  9.00
+model_pkas TYR 10.00
+model_pkas LYS 10.50
+model_pkas ARG 12.50
+#model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London
+model_pkas N+   8.00
+model_pkas CG  11.50
+model_pkas C2N 11.50
+model_pkas N30 10.00
+model_pkas N31 10.00
+model_pkas N32 10.00
+model_pkas N33 10.00
+model_pkas NAR  5.00
+model_pkas OCO  4.50
+model_pkas SH  10.00
+model_pkas OP   6.00
+
+# Custom ligand pKa values
+#  P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya:
+#  Measurement of Nucleobase pKa Values in Model Mononucleotides 
+#  Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
+#  Journal of the American Chemical Society 2004 126 (9), 2862-2869
+# 
+custom_model_pkas DA-N1   3.82
+custom_model_pkas DA-N3   3.82
+custom_model_pkas DA-N7   3.82
+custom_model_pkas DA-OP1  1.00
+custom_model_pkas DA-OP2  1.00
+
+custom_model_pkas DG-N1   9.59
+custom_model_pkas DG-N3   9.59
+custom_model_pkas DG-N7   9.59
+custom_model_pkas DG-OP1  1.00
+custom_model_pkas DG-OP2  1.00
+
+custom_model_pkas DC-N3   4.34
+custom_model_pkas DC-OP1  1.00
+custom_model_pkas DC-OP2  1.00
+
+custom_model_pkas DT-N3  10.12
+custom_model_pkas DT-OP1  1.00
+custom_model_pkas DT-OP2  1.00
+
+
+# protein group mapping
+protein_group_mapping ASP-CG  COO
+protein_group_mapping GLU-CD  COO
+protein_group_mapping HIS-CG  HIS
+protein_group_mapping CYS-SG  CYS
+protein_group_mapping TYR-OH  TYR
+protein_group_mapping LYS-NZ  LYS
+protein_group_mapping ARG-CZ  ARG
+#protein_group_mapping SER-OG  SER
+protein_group_mapping THR-OG1 ROH
+protein_group_mapping SER-OG  ROH#
+protein_group_mapping ASN-CG  AMD
+protein_group_mapping GLN-CD  AMD
+protein_group_mapping TRP-NE1 TRP
+
+
+# matrix for propka interactions
+#   'N'   non-iterative interaction
+#   'I'   iterative interaction
+#   '-'   no interaction
+                      #CYS
+interaction_matrix CYS I#N+ 
+interaction_matrix N+  N I#HIS 
+interaction_matrix HIS I N I#LYS 
+interaction_matrix LYS N N N I#AMD 
+interaction_matrix AMD N - N - -#COO 
+interaction_matrix COO I N I N N I#ARG 
+interaction_matrix ARG N N N N - N I#TRP 
+interaction_matrix TRP N - - - - N - -#ROH 
+interaction_matrix ROH N - - - - N - - -#TYR 
+interaction_matrix TYR N I I I N N N N N I#SER
+interaction_matrix SER N N N N N N I N N N I #CG
+interaction_matrix CG  N N N N - N I - - N I I#C2N
+interaction_matrix C2N N N N N - N I - - N I I I#N30
+interaction_matrix N30 N I N N - N N - - I N I I I#N31
+interaction_matrix N31 N I N N - N N - - I N I I I I#N32
+interaction_matrix N32 N I N N - N N - - I N I I I I I#N33
+interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR
+interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO
+interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1
+interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH
+interaction_matrix OH  N - - - - N - - - N N - - - - - - - N - -#O3
+interaction_matrix O3  N - N - - N - - - N N - - - - - - N N - - -#CL
+interaction_matrix CL  N - N - - N - - - N N - - - - - - N N - - - -#F
+interaction_matrix F   N - N - - N - - - N N - - - - - - N N - - - - -#NAM
+interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1
+interaction_matrix N1  N - N - - N - - - N N - - - - - - N N - - - - - - -#O2
+interaction_matrix O2  N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP
+interaction_matrix OP  I N I N N I N N N N N N N N N N N I I N N N N N N N N I#SH
+interaction_matrix SH  I N N N N N N N N N N I I I I I I N N N N N N N N N N N I
+
+# Cutoff values for side chain interactions
+# default value
+sidechain_cutoffs default 3.0  4.0  
+# COO
+sidechain_cutoffs COO COO 2.5  3.5
+Sidechain_cutoffs COO SER 2.65 3.65
+sidechain_cutoffs COO ARG 1.85 2.85
+sidechain_cutoffs COO LYS 2.85 3.85
+sidechain_cutoffs COO HIS 2.0  3.0
+sidechain_cutoffs COO AMD 2.0  3.0
+sidechain_cutoffs COO TRP 2.0  3.0
+sidechain_cutoffs COO ROH 2.65 3.65
+sidechain_cutoffs COO TYR 2.65 3.65
+sidechain_cutoffs COO  N+ 2.85 3.85
+sidechain_cutoffs COO  CG 1.85 2.85
+sidechain_cutoffs COO C2N 1.85 2.85
+sidechain_cutoffs COO N30 2.85 3.85
+sidechain_cutoffs COO N31 2.85 3.85
+sidechain_cutoffs COO N32 2.85 3.85
+sidechain_cutoffs COO N33 2.85 3.85
+sidechain_cutoffs COO NAR 2.0  3.0
+sidechain_cutoffs COO OCO 2.5  3.5
+sidechain_cutoffs COO  OH 2.65 3.65
+sidechain_cutoffs COO NAM 2.0  3.0
+# SER
+sidechain_cutoffs SER SER 3.5  4.5
+sidechain_cutoffs SER ARG 2.5  4.0
+sidechain_cutoffs SER HIS 2.0  3.0
+sidechain_cutoffs SER AMD 2.5  3.5
+sidechain_cutoffs SER CYS 3.5  4.5
+sidechain_cutoffs SER TRP 2.5  3.5
+sidechain_cutoffs SER ROH 3.5  4.5
+sidechain_cutoffs SER  CG 2.5  4.0
+sidechain_cutoffs SER C2N 2.5  4.0
+sidechain_cutoffs SER NAR 2.0  3.0
+sidechain_cutoffs SER  OH 3.5  4.5
+sidechain_cutoffs SER  SH 3.5  4.5
+sidechain_cutoffs SER TYR 3.5  4.5
+sidechain_cutoffs SER  N+ 3.0  4.5
+sidechain_cutoffs SER NAM 2.5  3.5
+# ARG
+sidechain_cutoffs ARG CYS 2.5  4.0
+sidechain_cutoffs ARG TYR 2.5  4.0
+sidechain_cutoffs ARG OCO 1.85 2.85
+sidechain_cutoffs ARG  SH 2.5  4.0
+# HIS
+sidechain_cutoffs HIS AMD 2.0  3.0
+sidechain_cutoffs HIS TYR 2.0  3.0
+sidechain_cutoffs HIS OCO 2.0  3.0
+# CYS
+sidechain_cutoffs CYS CYS 3.0  5.0
+sidechain_cutoffs CYS TRP 2.5  3.5
+sidechain_cutoffs CYS ROH 3.5  4.5
+sidechain_cutoffs CYS AMD 2.5  3.5
+sidechain_cutoffs CYS TYR 3.5  4.5
+sidechain_cutoffs CYS  N+ 3.0  4.5
+sidechain_cutoffs CYS  CG 2.5  4.0
+sidechain_cutoffs CYS C2N 2.5  4.0
+sidechain_cutoffs CYS N30 3.0  4.5
+sidechain_cutoffs CYS N31 3.0  4.5
+sidechain_cutoffs CYS N32 3.0  4.5
+sidechain_cutoffs CYS N33 3.0  4.5
+sidechain_cutoffs CYS  OH 3.5  4.5
+sidechain_cutoffs CYS NAM 2.5  3.5
+sidechain_cutoffs CYS  SH 3.0  5.0
+# TYR
+sidechain_cutoffs TYR TYR 3.5  4.5
+sidechain_cutoffs TYR  N+ 3.0  4.5
+sidechain_cutoffs TYR AMD 2.5  3.5
+sidechain_cutoffs TYR TRP 2.5  3.5
+sidechain_cutoffs TYR ROH 3.5  4.5
+sidechain_cutoffs TYR  CG 2.5  4.0
+sidechain_cutoffs TYR C2N 2.5  4.0
+sidechain_cutoffs TYR OCO 2.65 3.65
+sidechain_cutoffs TYR NAR 2.0  3.0
+sidechain_cutoffs TYR  OH 3.5  4.5
+sidechain_cutoffs TYR NAM 2.5  3.5
+sidechain_cutoffs TYR  SH 3.5  4.5
+# N+
+sidechain_cutoffs  N+ OCO 2.85 3.85
+sidechain_cutoffs  N+  SH 3.0  4.5
+# LYS
+sidechain_cutoffs LYS OCO 2.85 3.85
+# OCO
+sidechain_cutoffs OCO OCO 2.5  3.5
+sidechain_cutoffs OCO TRP 2.0  3.0
+sidechain_cutoffs OCO ROH 2.65 3.65
+sidechain_cutoffs OCO AMD 2.0  3.0
+sidechain_cutoffs OCO  CG 1.85 2.85
+sidechain_cutoffs OCO C2N 1.85 2.85
+sidechain_cutoffs OCO N30 2.85 3.85
+sidechain_cutoffs OCO N31 2.85 3.85
+sidechain_cutoffs OCO N32 2.85 3.85
+sidechain_cutoffs OCO N33 2.85 3.85
+sidechain_cutoffs OCO NAR 2.0  3.0 
+sidechain_cutoffs OCO  OH 2.65 3.65
+sidechain_cutoffs OCO NAM 2.0  3.0
+# NAR
+sidechain_cutoffs NAR AMD 2.0  3.0
+# SH
+sidechain_cutoffs  SH ROH 3.5  4.5
+sidechain_cutoffs  SH TRP 2.5  3.5
+sidechain_cutoffs  SH AMD 2.5  3.5
+sidechain_cutoffs  SH NAM 2.5  3.5
+sidechain_cutoffs  SH  CG 2.5  4.0
+sidechain_cutoffs  SH C2N 2.5  4.0
+sidechain_cutoffs  SH  OH 3.5  4.5
+sidechain_cutoffs  SH  SH 3.0  5.0
+
+
+
+# Maximal interaction energies for side chains
+sidechain_interaction 0.85  
+
+# Angular dependent sidechain interactions
+angular_dependent_sidechain_interactions HIS
+angular_dependent_sidechain_interactions ARG
+angular_dependent_sidechain_interactions AMD
+angular_dependent_sidechain_interactions TRP
+
+# exception interaction values
+COO_HIS_exception 1.60
+OCO_HIS_exception 1.60
+CYS_HIS_exception 1.60
+CYS_CYS_exception 3.60
+
+# Coulomb interaction parameters
+coulomb_cutoff1  4.0  
+coulomb_cutoff2 10.0
+coulomb_diel    80.0
+
+# Backbone hydrogen bond parameters 
+backbone_NH_hydrogen_bond COO -0.85 2.00 3.00
+#backbone_NH_hydrogen_bond C-  -0.85 2.00 3.00
+backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00
+backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20
+backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50
+backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50
+
+backbone_CO_hydrogen_bond HIS  0.85 2.00 3.00
+backbone_CO_hydrogen_bond OCO  0.85 3.00 4.00
+backbone_CO_hydrogen_bond CG   0.85 2.00 4.00
+backbone_CO_hydrogen_bond C2N  0.85 2.00 4.00
+backbone_CO_hydrogen_bond N30  0.85 2.00 4.00
+backbone_CO_hydrogen_bond N31  0.85 2.00 4.00
+backbone_CO_hydrogen_bond N32  0.85 2.00 4.00
+backbone_CO_hydrogen_bond N33  0.85 2.00 4.00
+backbone_CO_hydrogen_bond NAR  0.85 2.00 3.50
+
+# Group charges
+charge COO -1
+charge HIS +1
+charge CYS -1
+charge TYR -1
+charge LYS +1
+charge ARG +1
+charge N+  +1
+charge C-  -1
+charge OCO -1
+charge SER -1
+charge CG  +1
+charge C2N +1
+charge N30 +1
+charge N31 +1
+charge N32 +1
+charge N33 +1
+charge NAR +1
+charge SH  -1
+charge OP  -1
+
+# list of acids
+acid_list ASP
+acid_list GLU
+acid_list CYS
+acid_list TYR
+acid_list SER
+acid_list C-
+acid_list OCO
+acid_list OP
+acid_list SH
+
+# list of bases
+base_list ARG
+base_list LYS
+base_list HIS
+base_list N+
+base_list CG
+base_list C2N
+base_list N30
+base_list N31
+base_list N32
+base_list N33
+base_list NAR
+
+# list of groups used in backbone reorganisation calculations
+backbone_reorganisation_list ASP
+backbone_reorganisation_list GLU
+
+# Residues that should be ignored
+ignore_residues HOH
+ignore_residues H2O
+ignore_residues HOH
+ignore_residues SO4
+ignore_residues PO4
+ignore_residues PEG
+ignore_residues EPE
+#ignore_residues NAG
+ignore_residues TRS
+
+# Relative Van der Waals volume parameters for the radial volume model
+# Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51
+VanDerWaalsVolume C  1.40  # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms
+VanDerWaalsVolume C4 2.64  # 38.79 hydrodphobic carbon atoms + unidentified atoms
+VanDerWaalsVolume N  1.06  # radius: 1.55, volume: 15.60 all nitrogen atoms
+VanDerWaalsVolume O  1.00  # radius: 1.52, volume: 14.71 all oxygen atoms
+VanDerWaalsVolume S  1.66  # radius: 1.80, volume: 24.43 all sulphur atoms
+VanDerWaalsVolume F  0.90  # raidus: 1.47, volume: 13.30 for fluorine 
+VanDerWaalsVolume Cl 1.53  # radius: 1.75, volume: 22.44 for chlorine
+VanDerWaalsVolume P  1.66  # radius: 1.80, volume: 24.42 for phosphorus
+
+# Other desolvation parameters
+desolvationSurfaceScalingFactor	   0.25
+desolvationPrefactor		  -13.0
+desolvationAllowance		    0.0
+desolv_cutoff 			   20.0
+buried_cutoff 			   15.0
+Nmin	      			    280
+Nmax	      			    560
+
+# Ligand groups
+ligand_typing groups 
+min_bond_distance_for_hydrogen_bonds 4
+
+# covalent coupling
+coupling_max_number_of_bonds     3
+shared_determinants              0
+common_charge_centre             0
+remove_penalised_group	         1
+
+# non-covalent coupling
+max_intrinsic_pKa_diff         2.0
+min_interaction_energy         0.5
+max_free_energy_diff           1.0
+min_swap_pka_shift             1.0
+min_pka                        0.0
+max_pka                       10.0
+pH                        variable
+reference                  neutral
+
+# ions
+ions 1P   1 # generic charged atoms
+ions 2P   2
+ions 1N  -1
+ions 2N  -2
+
+ions MG   2 #Magnesium Ion
+ions CA   2 #Calcium Ion
+ions ZN   2 #Zinc Ion
+ions NA   1 #Sodium Ion
+ions CL  -1 #Chloride Ion
+ions MN   2 #Manganese (ii) Ion
+ions K    1 #Potassium Ion
+ions CD   2 #Cadmium Ion
+ions FE   3 #Fe (iii) Ion
+ions SR   2 #Strontium Ion
+ions CU   2 #Copper (ii) Ion
+ions IOD -1 #Iodide Ion
+ions HG   2 #Mercury (ii) Ion
+ions BR  -1 #Bromide Ion
+ions CO   2 #Cobalt (ii) Ion
+ions NI   2 #Nickel (ii) Ion
+ions FE2  2 #Fe (ii) Ion
+
+# write out order of residues
+write_out_order ASP 
+write_out_order GLU
+write_out_order C-
+write_out_order HIS
+write_out_order CYS
+write_out_order TYR
+write_out_order LYS
+write_out_order ARG
+write_out_order SER
+write_out_order N+
+write_out_order CG
+write_out_order C2N
+write_out_order N30
+write_out_order N31
+write_out_order N32
+write_out_order N33
+write_out_order NAR
+write_out_order OCO
+write_out_order SH
+write_out_order OP

propka/protonate.py

@@ -1,7 +1,10 @@
 #!/usr/bin/python
 
-from Source.vector_algebra import *
+from __future__ import division
-import Source.bonds, Source.pdb, Source.atom
+from __future__ import print_function
+
+from propka.vector_algebra import *
+import propka.bonds, propka.pdb, propka.atom
 
 class Protonate:
     """ Protonates atoms using VSEPR theory """
@@ -357,7 +360,7 @@ class Protonate:
 
     def add_proton(self, atom, position):
         # Create the new proton
-        new_H = Source.atom.Atom()
+        new_H = propka.atom.Atom()
         new_H.setProperty(numb    = None,
                           name    = 'H%s'%atom.name[1:],
                           resName = atom.resName,

propka/run.py

@@ -0,0 +1,15 @@
+# entry point for propka script
+
+import propka.lib, propka.molecular_container
+
+def main():
+    """
+    Reads in structure files, calculates pKa values, and prints pKa files
+    """
+    # loading options, flaggs and arguments
+    options, pdbfiles = propka.lib.loadOptions()
+
+    for pdbfile in pdbfiles:
+        my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+        my_molecule.calculate_pka()
+        my_molecule.write_pka()

propka/vector_algebra.py

@@ -1,3 +1,5 @@
+from __future__ import division
+from __future__ import print_function
 import math
 
 class vector:

propka/version.py

@@ -1,8 +1,11 @@
+from __future__ import division
+from __future__ import print_function
 import math
-import Source.lib as lib
 import sys, os
-import Source.calculations as calculations
+
-import Source.parameters
+import propka.lib as lib
+import propka.calculations as calculations
+import propka.parameters
 
 
 class version:
@@ -56,8 +59,8 @@ class version_A(version):
         version.__init__(self, parameters)
 
         # atom naming, bonding, and protonation
-        self.molecular_preparation_method = Source.calculations.setup_bonding_and_protonation
+        self.molecular_preparation_method = propka.calculations.setup_bonding_and_protonation
-        self.prepare_bonds = Source.calculations.setup_bonding
+        self.prepare_bonds = propka.calculations.setup_bonding
 
 
         # desolvation related methods
@@ -65,20 +68,20 @@ class version_A(version):
         self.weight_pair_method = calculations.calculatePairWeight
 
         # side chain methods
-        self.sidechain_interaction_model = Source.calculations.HydrogenBondEnergy
+        self.sidechain_interaction_model = propka.calculations.HydrogenBondEnergy
-        self.hydrogen_bond_interaction_model = Source.calculations.hydrogen_bond_interaction
+        self.hydrogen_bond_interaction_model = propka.calculations.hydrogen_bond_interaction
 
         # colomb methods
-        self.electrostatic_interaction_model = Source.calculations.electrostatic_interaction
+        self.electrostatic_interaction_model = propka.calculations.electrostatic_interaction
-        self.check_coulomb_pair_method = Source.calculations.checkCoulombPair
+        self.check_coulomb_pair_method = propka.calculations.checkCoulombPair
-        self.coulomb_interaction_model = Source.calculations.CoulombEnergy
+        self.coulomb_interaction_model = propka.calculations.CoulombEnergy
 
         #backbone
-        self.backbone_interaction_model = Source.calculations.HydrogenBondEnergy
+        self.backbone_interaction_model = propka.calculations.HydrogenBondEnergy
-        self.backbone_reorganisation_method = Source.calculations.BackBoneReorganization
+        self.backbone_reorganisation_method = propka.calculations.BackBoneReorganization
 
         # exception methods
-        self.exception_check_method = Source.calculations.checkExceptions
+        self.exception_check_method = propka.calculations.checkExceptions
         return
 
     def get_hydrogen_bond_parameters(self, atom1, atom2):
@@ -180,24 +183,24 @@ class propka30(version):
         version.__init__(self, parameters)
 
         # atom naming, bonding, and protonation
-        self.molecular_preparation_method = Source.calculations.setup_bonding_and_protonation_30_style
+        self.molecular_preparation_method = propka.calculations.setup_bonding_and_protonation_30_style
 
         # desolvation related methods
         self.desolvation_model = calculations.radial_volume_desolvation
         self.weight_pair_method = calculations.calculatePairWeight
 
         # side chain methods
-        self.sidechain_interaction_model = Source.calculations.HydrogenBondEnergy
+        self.sidechain_interaction_model = propka.calculations.HydrogenBondEnergy
 
         # colomb methods
-        self.check_coulomb_pair_method = Source.calculations.checkCoulombPair
+        self.check_coulomb_pair_method = propka.calculations.checkCoulombPair
-        self.coulomb_interaction_model = Source.calculations.CoulombEnergy
+        self.coulomb_interaction_model = propka.calculations.CoulombEnergy
 
         #backbone
-        self.backbone_reorganisation_method = Source.calculations.BackBoneReorganization
+        self.backbone_reorganisation_method = propka.calculations.BackBoneReorganization
 
         # exception methods
-        self.exception_check_method = Source.calculations.checkExceptions
+        self.exception_check_method = propka.calculations.checkExceptions
 
 
         return

scripts/propka31.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+
+# This is the original propka script. However, this distribute-based
+# installation moved the main() function into propka.run.main and just
+# generates a script called propka31 from the setup.py installation
+# script. You should not need to use this script.
+#
+# (Also note that there can be import problems because the script name
+# is the same as the module name; that's why the new script is called
+# propka31.)
+
+import propka.lib, propka.molecular_container
+
+def main():
+    """
+    Reads in structure files, calculates pKa values, and prints pKa files
+    """
+    # loading options, flaggs and arguments
+    options, pdbfiles = propka.lib.loadOptions()
+
+    for pdbfile in pdbfiles:
+        my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+        my_molecule.calculate_pka()
+        my_molecule.write_pka()
+
+
+if __name__ == '__main__':
+    #import cProfile
+    #cProfile.run('main()',sort=1)
+    main()
+

setup.py

@@ -0,0 +1,51 @@
+# PROPKA 3.1
+#
+#
+# setuptools installation of  PROPKA 3.1
+
+import ez_setup
+ez_setup.use_setuptools()
+from setuptools import setup, find_packages
+
+VERSION = "3.1"
+
+setup(name="PROPKA",
+      version=VERSION,
+      description="Heuristic pKa calculations with ligands",
+      long_description="""
+PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and
+protein-ligand complexes (version 3.1) based on the 3D structure.
+
+For proteins without ligands both version should produce the same result.
+
+The method is described in the following papers, which you should cite
+in publications:
+
+* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan
+  H. Jensen. "Improved Treatment of Ligands and Coupling Effects in
+  Empirical Calculation and Rationalization of pKa Values." Journal of
+  Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
+
+* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan
+  H. Jensen. "PROPKA3: consistent treatment of internal and surface
+  residues in empirical pKa predictions." Journal of Chemical Theory
+  and Computation 7, no. 2 (2011): 525-537.
+
+See http://propka.ki.ku.dk/ for the PROPKA web server,
+using the tutorial http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial .
+""",
+      author="Jan H. Jensen",
+      author_email="jhjensen@chem.ku.dk",
+      license="",
+      url="http://propka.ki.ku.dk/",
+      keywords="science",
+      packages=find_packages(exclude=['scripts']),
+      package_data = {'propka': ['*.dat', '*.cfg']},
+      #scripts = ["scripts/propka31.py"],  # use entry point below
+      entry_points = {
+        'console_scripts': [
+            'propka31 = propka.run:main',
+            ],
+        },
+      zip_safe=True,
+)