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Merge pull request #2 from orbeckst/master

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packaged for standalone installation (Python 3 and Python 2)
This commit is contained in:
Jimmy Charnley Kromann
2013-08-10 03:51:24 -07:00
parent 2aaf2d3a48 12e4eeabd8
commit d01659d614
31 changed files with 1465 additions and 610 deletions
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19
INSTALL Normal file
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@@ -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

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MANIFEST.in Normal file
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include README.md INSTALL
include ez_setup.py setup.py
include propka.cfg

56
README.md
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@@ -1,45 +1,69 @@
# PROPKA 3.1
PROPKA predicts the pKa values of ionizable groups in
proteins (version 3.0) and
protein-ligand complexes (version 3.1)
based in the 3D structure.
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:
* 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.

8
Tests/runtest.py
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@@ -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')

258
ez_setup.py Normal file
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@@ -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())

23
propka.py
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@@ -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()

4
Source/__init__.py → propka/__init__.py
View File

@@ -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']

60
Source/atom.py → propka/atom.py
View File

@@ -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:
@@ -8,17 +12,17 @@ class Atom:
def __init__(self, line=None, verbose=False):
self.set_properties(line)
self.set_properties(line)
self.residue_label = "%-3s%4d%2s" % (self.name,self.resNumb, self.chainID)
self.residue_label = "%-3s%4d%2s" % (self.name,self.resNumb, self.chainID)
self.groups_extracted = 0
self.group = None
self.group_type = None
self.number_of_bonded_elements = {}
self.cysteine_bridge = False
self.bonded_atoms = []
self.residue = None
self.conformation_container = None
@@ -39,7 +43,7 @@ class Atom:
self.sybyl_type = ''
self.sybyl_assigned = False
self.marvin_pka = False
return
@@ -122,13 +126,13 @@ class Atom:
return True
return False
def setProperty(self,
numb = None,
name = None,
resName = None,
numb = None,
name = None,
resName = None,
chainID = None,
resNumb = None,
x = None,
@@ -157,7 +161,7 @@ class Atom:
"""
making a copy of this atom
"""
newAtom = Atom()
newAtom.type = self.type
newAtom.numb = self.numb
@@ -191,11 +195,11 @@ class Atom:
if self.group.titratable:
model_pka = '%6.2f'%self.group.model_pka
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,
@@ -213,7 +217,7 @@ class Atom:
def make_conect_line(self):
res = 'CONECT%5d'%self.numb
# extract and sort numbers of bonded residues
bonded = []
for atom in self.bonded_atoms:
@@ -226,9 +230,9 @@ class Atom:
res += '\n'
return res
def get_input_parameters(self):
""" Method for getting the input parameters stored in the
""" Method for getting the input parameters stored in the
occupancy and b-factor fields in input files"""
# Set the group type
@@ -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)
@@ -270,7 +274,7 @@ class Atom:
# set occ and beta to standard values
self.occ = '1.00'
self.beta = '0.00'
return
@@ -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,
@@ -292,17 +296,17 @@ class Atom:
self.z,
self.occ,
self.beta)
return str
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,
@@ -311,7 +315,7 @@ class Atom:
self.resNumb,
self.resName,
0.0)#self.charge)
return str
@@ -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)
@@ -363,25 +367,25 @@ 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):
return '%5d-%4s %5d-%3s (%1s) [%8.3f %8.3f %8.3f] %s' %(self.numb, self.name, self.resNumb, self.resName, self.chainID, self.x, self.y, self.z,self.element)
# def get_element(self):
# """ try to extract element if not already done"""
# if self.element == '':
# self.element = self.name.strip(string.digits)[0]
# return self.element
def set_residue(self, residue):
""" Makes a references to the parent residue"""
if self.residue == None:
self.residue = residue

86
Source/bonds.py → propka/bonds.py
View File

@@ -1,14 +1,19 @@
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):
# predefined bonding distances
self.distances = {
'S-S':2.5,
'F-F':1.7}
self.distances_squared = {}
for k in self.distances.keys():
self.distances_squared[k]=self.distances[k]*self.distances[k]
@@ -18,12 +23,11 @@ class bondmaker:
self.H_dist_squared = self.H_dist * self.H_dist
self.default_dist_squared = self.default_dist * self.default_dist
self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
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 = os.path.join(path,'protein_bonds.dat')
self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.dat')
data = open(self.data_file_name,'rb')
self.protein_bonds = pickle.load(data)
@@ -104,13 +108,13 @@ class bondmaker:
def find_bonds_for_protein(self, protein):
""" Finds bonds proteins based on the way atoms
""" Finds bonds proteins based on the way atoms
normally bond in proteins"""
print('++++ Side chains ++++')
# side chains
for chain in protein.chains:
for residue in chain.residues:
for residue in chain.residues:
if residue.resName.replace(' ','') not in ['N+','C-']:
self.find_bonds_for_side_chain(residue.atoms)
@@ -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
@@ -209,7 +213,7 @@ class bondmaker:
for atom2 in atoms:
if atom2.name in self.protein_bonds[atom1.resName][atom1.name]:
self.make_bond(atom1,atom2)
return
@@ -270,7 +274,7 @@ class bondmaker:
if atoms[i] in atoms[j].bonded_atoms:
continue
if self.check_distance(atoms[i], atoms[j]):
self.make_bond(atoms[i],atoms[j])
# di-sulphide bonds
@@ -283,14 +287,14 @@ 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
key = '%s-%s'%(atom1.element,atom2.element)
h_count = key.count('H')
if sq_dist < self.H_dist_squared and h_count==1:
return True
if sq_dist < self.default_dist_squared and h_count==0:
@@ -299,8 +303,8 @@ class bondmaker:
if sq_dist < self.distances_squared[key]:
return True
return False
def find_bonds_for_molecules_using_boxes(self, molecules):
@@ -320,7 +324,7 @@ class bondmaker:
def find_bonds_for_atoms_using_boxes(self, atoms):
""" Finds all bonds for a list of atoms"""
box_size = 2.5
# find min and max coordinates
@@ -348,11 +352,13 @@ class bondmaker:
#print('x range: [%6.2f;%6.2f] %6.2f'%(xmin,xmax,xlen))
#print('y range: [%6.2f;%6.2f] %6.2f'%(ymin,ymax,ylen))
#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))
self.no_box_y = max(1, math.ceil(ylen/box_size))
self.no_box_z = max(1, math.ceil(zlen/box_size))
# NOTE: math.ceil() returns an int in python3 and a float in python2,
# so we need to cast it to int for range() to work.
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)
@@ -372,12 +378,12 @@ class bondmaker:
z = math.floor((atom.z-zmin)/box_size)
self.put_atom_in_box(x,y,z,atom)
# assign bonds
# assign bonds
keys = self.boxes.keys()
for key in keys:
self.find_bonds_for_atoms(self.boxes[key])
return
@@ -386,7 +392,7 @@ class bondmaker:
# one side of the x,y,z box in each dimension
for bx in [x,x+1]:
for by in [y,y+1]:
for bz in [z,z+1]:
for bz in [z,z+1]:
key = self.box_key(bx,by,bz)
if key in self.boxes.keys():
self.boxes[key].append(atom)
@@ -397,13 +403,13 @@ class bondmaker:
def box_key(self, x, y, z):
return '%d-%d-%d'%(x,y,z)
def has_bond(self, atom1, atom2):
if atom1 in atom2.bonded_atoms or atom2 in atom1.bonded_atoms:
return True
return False
def make_bond(self, atom1, atom2):
""" Makes a bond between atom1 and atom2 """
@@ -413,13 +419,13 @@ class bondmaker:
#print('making bond for',atom1,atom2)
if not atom1 in atom2.bonded_atoms:
atom2.bonded_atoms.append(atom1)
if not atom2 in atom1.bonded_atoms:
atom1.bonded_atoms.append(atom2)
atom1.bonded_atoms.append(atom2)
return
def generate_protein_bond_dictionary(self, atoms):
for atom in atoms:
@@ -433,25 +439,25 @@ class bondmaker:
not name_j in self.backbone_atoms:
if not name_i in self.terminal_oxygen_names and\
not name_j in self.terminal_oxygen_names:
if not resi_i in list(self.protein_bonds.keys()):
self.protein_bonds[resi_i] = {}
if not name_i in self.protein_bonds[resi_i]:
self.protein_bonds[resi_i][name_i] = []
if not name_j in self.protein_bonds[resi_i][name_i]:
self.protein_bonds[resi_i][name_i].append(name_j)
if not resi_j in list(self.protein_bonds.keys()):
self.protein_bonds[resi_j] = {}
if not name_j in self.protein_bonds[resi_j]:
self.protein_bonds[resi_j][name_j] = []
if not name_i in self.protein_bonds[resi_j][name_j]:
self.protein_bonds[resi_j][name_j].append(name_i)
return
@@ -467,10 +473,10 @@ if __name__ == '__main__':
if not os.path.isfile(filename):
print('Error: Could not find \"%s\"'%filename)
sys.exit(1)
pdblist = pdb.readPDB(filename)
my_protein = protein.Protein(pdblist,'test.pdb')
for chain in my_protein.chains:
for residue in chain.residues:
residue.atoms = [atom for atom in residue.atoms if atom.element != 'H']

134
Source/calculations.py → propka/calculations.py
View File

@@ -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
#
@@ -17,9 +19,9 @@ def setup_bonding_and_protonation(parameters, molecular_container):
# apply information on pi electrons
my_bond_maker.add_pi_electron_information(molecular_container)
# Protonate atoms
# 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
@@ -46,11 +48,11 @@ def set_ligand_atom_names(molecular_container):
# The following methods imitates propka3.0 protonation!
#
def setup_bonding_and_protonation_30_style(parameters, molecular_container):
# Protonate atoms
# Protonate atoms
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
@@ -87,7 +89,7 @@ def protonate_30_style(molecular_container):
residue = []
if atom.type=='atom':
residue.append(atom)
return
def addArgHydrogen(residue):
@@ -117,7 +119,7 @@ def addArgHydrogen(residue):
H4.name = "HN3"
H5 = protonateDirection([NH2, NE, H1])
H5.name = "HN4"
return [H1,H2,H3,H4,H5]
def addHisHydrogen(residue):
@@ -179,7 +181,7 @@ def addAmdHydrogen(residue):
O = atom
elif (atom.resName == "GLN" and atom.name == "NE2") or (atom.resName == "ASN" and atom.name == "ND2"):
N = atom
if C == None or O == None or N == None:
str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.resName, atom.resNumb, "addAmdHydrogen()")
print(str)
@@ -189,20 +191,20 @@ def addAmdHydrogen(residue):
H1.name = "HN1"
H2 = protonateAverageDirection([N, C, O])
H2.name = "HN2"
return
def addBackBoneHydrogen(residue, O, C):
"""
Adds hydrogen backbone atoms to residues according to the old way; dR is wrong for the N-terminus
Adds hydrogen backbone atoms to residues according to the old way; dR is wrong for the N-terminus
(i.e. first residue) but it doesn't affect anything at the moment. Could be improved, but works
for now.
"""
new_C = None
new_O = None
N = None
for atom in residue:
if atom.name == "N":
@@ -211,20 +213,20 @@ def addBackBoneHydrogen(residue, O, C):
new_C = atom
if atom.name == "O":
new_O = atom
if None in [C,O,N]:
return [new_O,new_C]
if N.resName == "PRO":
""" PRO doesn't have an H-atom; do nothing """
else:
H = protonateDirection([N, O, C])
H.name = "H"
return [new_O,new_C]
@@ -247,7 +249,7 @@ def protonateDirection(list):
y = X1.y + dY/length
z = X1.z + dZ/length
H = make_new_H(X1,x,y,z)
H.name = "H"
@@ -277,7 +279,7 @@ def protonateAverageDirection(list):
H = make_new_H(X1,x,y,z)
H.name = "H"
return H
@@ -290,7 +292,7 @@ def protonateSP2(list):
X1 = list[0]
X2 = list[1]
X3 = list[2]
dX = (X1.x + X3.x)*0.5 - X2.x
dY = (X1.y + X3.y)*0.5 - X2.y
dZ = (X1.z + X3.z)*0.5 - X2.z
@@ -301,16 +303,16 @@ def protonateSP2(list):
H = make_new_H(X2,x,y,z)
H.name = "H"
return H
def make_new_H(atom, x,y,z):
new_H = Source.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
new_H = propka.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
chainID = atom.chainID,
resNumb = atom.resNumb,
x = x,
@@ -329,7 +331,7 @@ def make_new_H(atom, x,y,z):
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
atom.bonded_atoms.append(new_H)
atom.conformation_container.add_atom(new_H)
atom.conformation_container.add_atom(new_H)
return new_H
@@ -356,7 +358,7 @@ def radial_volume_desolvation(parameters, group):
# ignore atoms in the same residue
if atom.resNumb == group.atom.resNumb and atom.chainID == group.atom.chainID:
continue
sq_dist = squared_distance(group, atom)
# desolvation
@@ -375,7 +377,7 @@ def radial_volume_desolvation(parameters, group):
# buried
if sq_dist < parameters.buried_cutoff_squared:
group.Nmass += 1
group.buried = calculate_weight(parameters, group.Nmass)
scale_factor = calculate_scale_factor(parameters, group.buried)
volume_after_allowance = max(0.00, volume-parameters.desolvationAllowance)
@@ -385,9 +387,9 @@ def radial_volume_desolvation(parameters, group):
# Elocl, Nlocl -> reorganisation energy (count backbone hydorgen bond acceptors, C=O)
#print('%s %5.2f %5.2f %4d'%(group, group.buried, group.Emass, group.Nmass))
return
return
@@ -395,7 +397,7 @@ def contactDesolvation(parameters, group):
"""
calculates the desolvation according to the Contact Model, the old default
"""
local_radius = {'ASP': 4.5,
'GLU': 4.5,
'HIS': 4.5,
@@ -405,7 +407,7 @@ def contactDesolvation(parameters, group):
'ARG': 5.0,
'C-': 4.5,
'N+': 4.5}
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
if residue.resName in version.desolvationRadii:
local_cutoff = version.desolvationRadii[residue.resName]
@@ -434,7 +436,7 @@ def contactDesolvation(parameters, group):
# Note, there will be an unforseen problem: e.g. if one residue has Nmass > Nmax and
# the other Nmass < Nmax, the Npair will not be Nmass1 + Nmass2!
residue.buried = calculateWeight(residue.Nmass)
return 0.00, 0.00, 0.00, 0.00
@@ -455,10 +457,10 @@ def calculate_weight(parameters, Nmass):
weight = float(Nmass - parameters.Nmin)/float(parameters.Nmax - parameters.Nmin)
weight = min(1.0, weight)
weight = max(0.0, weight)
return weight
def squared_distance(atom1, atom2):
# if atom1 in atom2.squared_distances:
@@ -518,9 +520,9 @@ def HydrogenBondEnergy(distance, dpka_max, cutoff, f_angle=1.0):
value = 0.00
else:
value = 1.0-(distance-cutoff[0])/(cutoff[1]-cutoff[0])
dpKa = dpka_max*value*f_angle
return abs(dpKa)
@@ -535,13 +537,13 @@ def AngleFactorX(atom1=None, atom2=None, atom3=None, center=None):
dX_32 = atom2.x - atom3.x
dY_32 = atom2.y - atom3.y
dZ_32 = atom2.z - atom3.z
distance_23 = math.sqrt( dX_32*dX_32 + dY_32*dY_32 + dZ_32*dZ_32 )
dX_32 = dX_32/distance_23
dY_32 = dY_32/distance_23
dZ_32 = dZ_32/distance_23
if atom1 == None:
dX_21 = center[0] - atom2.x
dY_21 = center[1] - atom2.y
@@ -550,13 +552,13 @@ def AngleFactorX(atom1=None, atom2=None, atom3=None, center=None):
dX_21 = atom1.x - atom2.x
dY_21 = atom1.y - atom2.y
dZ_21 = atom1.z - atom2.z
distance_12 = math.sqrt( dX_21*dX_21 + dY_21*dY_21 + dZ_21*dZ_21 )
dX_21 = dX_21/distance_12
dY_21 = dY_21/distance_12
dZ_21 = dZ_21/distance_12
f_angle = dX_21*dX_32 + dY_21*dY_32 + dZ_21*dZ_32
@@ -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))
@@ -577,20 +579,20 @@ def hydrogen_bond_interaction(group1, group2, version):
# get the parameters
[dpka_max, cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,closest_atom2)
if dpka_max==None or None in cutoff:
return None
# check that the closest atoms are close enough
if distance >= cutoff[1]:
return None
# check that bond distance criteria is met
bond_distance_too_short = group1.atom.is_atom_within_bond_distance(group2.atom,
bond_distance_too_short = group1.atom.is_atom_within_bond_distance(group2.atom,
version.parameters.min_bond_distance_for_hydrogen_bonds,1)
if bond_distance_too_short:
return None
# set the angle factor
#
# ---closest_atom1/2
@@ -602,18 +604,18 @@ 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
# to 0
f_angle = 0.0
elif group1.type in version.parameters.angular_dependent_sidechain_interactions:
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
@@ -621,7 +623,7 @@ def hydrogen_bond_interaction(group1, group2, version):
f_angle = 0.0
weight = version.calculatePairWeight(group1.Nmass, group2.Nmass)
exception, value = version.checkExceptions(group1, group2)
#exception = False # circumventing exception
if exception == True:
@@ -629,7 +631,7 @@ def hydrogen_bond_interaction(group1, group2, version):
#print(" exception for %s %s %6.2lf" % (group1.label, group2.label, value))
else:
value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
# print('distance',distance)
# print('dpka_max',dpka_max)
# print('cutoff',cutoff)
@@ -654,7 +656,7 @@ def HydrogenBondEnergy(distance, dpka_max, cutoff, f_angle=1.0):
value = 1.0-(distance-cutoff[0])/(cutoff[1]-cutoff[0])
dpKa = dpka_max*value*f_angle
return abs(dpKa)
@@ -678,15 +680,15 @@ def checkCoulombPair(parameters, group1, group2, distance):
"""
Npair = group1.Nmass + group2.Nmass
do_coulomb = True
# check if both groups are titratable (ions are taken care of in determinants::setIonDeterminants)
if not (group1.titratable and group2.titratable):
do_coulomb = False
# check if the distance is not too big
if distance > parameters.coulomb_cutoff2:
do_coulomb = False
# check that desolvation is ok
if Npair < parameters.Nmin:
do_coulomb = False
@@ -725,8 +727,8 @@ def BackBoneReorganization(parameters, conformation):
dpKa = 0.00
for BBC_group in BBC_groups:
center = [titratable_group.x, titratable_group.y, titratable_group.z]
distance, f_angle, nada = AngleFactorX(atom2=BBC_group.get_interaction_atoms(titratable_group)[0],
atom3=BBC_group.atom,
distance, f_angle, nada = AngleFactorX(atom2=BBC_group.get_interaction_atoms(titratable_group)[0],
atom3=BBC_group.atom,
center=center)
if distance < 6.0 and f_angle > 0.001:
value = 1.0-(distance-3.0)/(6.0-3.0)
@@ -767,7 +769,7 @@ def checkExceptions(version, group1, group2):
else:
# do nothing, no exception for this pair
exception = False; value = None
return exception, value
@@ -780,7 +782,7 @@ def checkCooArgException(group_coo, group_arg, version):
str = "xxx"
exception = True
value_tot = 0.00
#dpka_max = parameters.sidechain_interaction.get_value(group_coo.type,group_arg.type)
#cutoff = parameters.sidechain_cutoffs.get_value(group_coo.type,group_arg.type)
@@ -801,7 +803,7 @@ def checkCooArgException(group_coo, group_arg, version):
if group_arg.type in version.parameters.angular_dependent_sidechain_interactions:
atom3 = closest_arg_atom.bonded_atoms[0]
distance, f_angle, nada = AngleFactorX(closest_coo_atom, closest_arg_atom, atom3)
value = HydrogenBondEnergy(distance, dpka_max, cutoff, f_angle)
#print(iter, closest_coo_atom, closest_arg_atom,distance,value)
value_tot += value
@@ -809,7 +811,7 @@ def checkCooArgException(group_coo, group_arg, version):
atoms_coo.remove(closest_coo_atom)
atoms_arg.remove(closest_arg_atom)
return exception, value_tot
@@ -820,7 +822,7 @@ def checkCooCooException(group1, group2, version):
exception = True
[closest_atom1, distance, closest_atom2] = get_smallest_distance(group1.get_interaction_atoms(group2),
group2.get_interaction_atoms(group1))
#dpka_max = parameters.sidechain_interaction.get_value(group1.type,group2.type)
#cutoff = parameters.sidechain_cutoffs.get_value(group1.type,group2.type)
[dpka_max, cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,closest_atom2)
@@ -863,7 +865,7 @@ def checkCysHisException(group1, group2, version):
if checkBuried(group1.Nmass, group2.Nmass):
exception = True
return exception, version.parameters.CYS_HIS_exception
return exception, version.parameters.CYS_HIS_exception
def checkCysCysException(group1, group2, version):

93
Source/conformation_container.py → propka/conformation_container.py
View File

@@ -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):
@@ -13,10 +16,10 @@ class Conformation_container:
self.groups = []
self.chains = []
self.current_iter_item = 0
self.marvin_pkas_calculated = False
self.non_covalently_coupled_groups = False
return
@@ -28,21 +31,21 @@ 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))
# 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
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:
self.validate_group(atom.group)
return
return
def additional_setup_when_reading_input_file(self):
# if a group is coupled and we are reading a .propka_input file,
# if a group is coupled and we are reading a .propka_input file,
# 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)
@@ -50,11 +53,11 @@ class Conformation_container:
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
self.set_common_charge_centres()
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
@@ -82,19 +85,19 @@ class Conformation_container:
continue
if cg.atom.sybyl_type == group.atom.sybyl_type:
group.couple_covalently(cg)
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
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)
print(map)
return
@@ -102,8 +105,8 @@ class Conformation_container:
# check if non-covalent coupling has already been set up in an input file
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:
@@ -157,26 +160,26 @@ class Conformation_container:
def calculate_pka(self, version, options):
print('\nCalculating pKas for',self)
# calculate desolvation
for group in self.get_titratable_groups()+self.get_ions():
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()
# take coupling effects into account
penalised_labels = self.coupling_effects()
@@ -195,20 +198,20 @@ class Conformation_container:
def coupling_effects(self):
#
# Bases: The group with the highest pKa (the most stable one in the
# charged form) will be the first one to adopt a proton as pH
# Bases: The group with the highest pKa (the most stable one in the
# charged form) will be the first one to adopt a proton as pH
# is lowered and this group is allowed to titrate.
# The remaining groups are penalised
#
# Acids: The group with the highest pKa (the least stable one in the
# charged form) will be the last group to loose the proton as
# charged form) will be the last group to loose the proton as
# pH is raised and will be penalised.
# The remaining groups are allowed to titrate.
#
penalised_labels = []
for all_groups in self.get_coupled_systems(self.get_covalently_coupled_groups(),
Source.group.Group.get_covalently_coupled_groups):
for all_groups in self.get_coupled_systems(self.get_covalently_coupled_groups(),
propka.group.Group.get_covalently_coupled_groups):
# check if we should share determinants
if self.parameters.shared_determinants:
@@ -227,14 +230,14 @@ class Conformation_container:
for a in all_groups:
if a == first_group:
continue # group with the highest pKa is allowed to titrate...
a.coupled_titrating_group = first_group
a.coupled_titrating_group = first_group
penalised_labels.append(a.label) #... and the rest is penalised
return penalised_labels
def share_determinants(self, groups):
# make a list of the determinants to share
types = ['sidechain','backbone','coulomb']
for type in types:
@@ -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)
@@ -260,7 +263,7 @@ class Conformation_container:
def get_coupled_systems(self, groups, get_coupled_groups):
""" This generator will yield one covalently coupled system at the time """
groups = set(groups)
groups = set(groups)
while len(groups)>0:
# extract a system of coupled groups ...
system = set()
@@ -272,7 +275,7 @@ class Conformation_container:
return
def get_a_coupled_system_of_groups(self, new_group, coupled_groups, get_coupled_groups):
coupled_groups.add(new_group)
[self.get_a_coupled_system_of_groups(c, coupled_groups, get_coupled_groups) for c in get_coupled_groups(new_group) if c not in coupled_groups]
@@ -311,7 +314,7 @@ class Conformation_container:
""" returns all sidechain groups needed for the pKa calculations """
return [group for group in self.groups if ('BB' not in group.type\
and not group.atom.cysteine_bridge)]
def get_covalently_coupled_groups(self):
return [g for g in self.groups if len(g.covalently_coupled_groups)>0]
@@ -331,7 +334,7 @@ class Conformation_container:
def get_titratable_groups(self):
return [group for group in self.groups if group.titratable]
def get_titratable_groups_and_cysteine_bridges(self):
return [group for group in self.groups if group.titratable or group.residue_type == 'CYS']
@@ -367,19 +370,19 @@ class Conformation_container:
atom.conformation_container = self
if not atom.molecular_container:
atom.molecular_container = self.molecular_container
# store chain id for bookkeeping
if not atom.chainID in self.chains:
self.chains.append(atom.chainID)
return
return
def copy_atom(self, atom):
new_atom = atom.makeCopy()
self.atoms.append(new_atom)
new_atom.conformation_container = self
return
return
def get_non_hydrogen_atoms(self):
return [atom for atom in self.atoms if atom.element!='H']
@@ -391,7 +394,7 @@ class Conformation_container:
if not self.have_atom(atom):
self.copy_atom(atom)
return
def have_atom(self, atom):
res = False
for a in self.atoms:
@@ -407,12 +410,12 @@ class Conformation_container:
return g
return False
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
def __str__(self):
@@ -431,7 +434,7 @@ class Conformation_container:
return
def sort_atoms_key(self, atom):
key = ord(atom.chainID)*1e7
key = ord(atom.chainID)*1e7
key += atom.resNumb*1000
if len(atom.name) > len(atom.element):
key += ord(atom.name[len(atom.element)])

55
Source/coupled_groups.py → propka/coupled_groups.py
View File

@@ -1,12 +1,15 @@
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:
def __init__(self):
self.parameters = None
# self.do_intrinsic = False
# self.do_pair_wise = False
self.do_prot_stat = True
@@ -18,10 +21,10 @@ class non_covalently_couple_groups:
# Methods for finding coupled groups
#
def is_coupled_protonation_state_probability(self, group1, group2, energy_method, return_on_fail=True):
# check if the interaction energy is high enough
interaction_energy = max(self.get_interaction(group1,group2), self.get_interaction(group2,group1))
if interaction_energy<=self.parameters.min_interaction_energy and return_on_fail:
return {'coupling_factor':-1.0}
@@ -29,7 +32,7 @@ class non_covalently_couple_groups:
for group in [group1, group2]:
if not hasattr(group, 'intrinsic_pKa'):
group.calculate_intrinsic_pka()
use_pH = self.parameters.pH
if self.parameters.pH == 'variable':
use_pH = min(group1.pka_value, group2.pka_value)
@@ -61,7 +64,7 @@ class non_covalently_couple_groups:
self.swap_interactions([group1], [group2])
group1.calculate_total_pka()
group2.calculate_total_pka()
# check difference in free energy
if abs(default_energy - swapped_energy) > self.parameters.max_free_energy_diff and return_on_fail:
return {'coupling_factor':-1.0}
@@ -80,21 +83,21 @@ class non_covalently_couple_groups:
self.get_interaction_factor(interaction_energy)
return {'coupling_factor':factor,
'default_energy':default_energy,
'swapped_energy':swapped_energy,
'default_energy':default_energy,
'swapped_energy':swapped_energy,
'interaction_energy':interaction_energy,
'swapped_pka1':swapped_pka1,
'swapped_pka1':swapped_pka1,
'swapped_pka2':swapped_pka2,
'pka_shift1':pka_shift1,
'pka_shift2':pka_shift2,
'pH':use_pH}
#
# Methods for calculating the coupling factor
#
#
def get_pka_diff_factor(self, pka1, pka2):
intrinsic_pka_diff = abs(pka1-pka2)
res = 0.0
@@ -120,10 +123,10 @@ class non_covalently_couple_groups:
def identify_non_covalently_coupled_groups(self, conformation, verbose=True):
""" Finds coupled residues in protein """
self.parameters = conformation.parameters
if verbose:
print('')
@@ -156,19 +159,19 @@ class non_covalently_couple_groups:
data = self.is_coupled_protonation_state_probability(g1, g2,conformation.calculate_folding_energy)
if data['coupling_factor'] >0.0:
g1.couple_non_covalently(g2)
if verbose:
self.print_out_swaps(conformation)
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 = ''
@@ -199,7 +202,7 @@ class non_covalently_couple_groups:
for interaction in combination:
swap_info += ' %s %s\n'%(interaction[0].label, interaction[1].label)
# swap...
# swap...
for interaction in combination:
self.swap_interactions([interaction[0]],[interaction[1]])
@@ -213,13 +216,13 @@ class non_covalently_couple_groups:
return
#
# Interaction and swapping methods
#
#
def get_interaction(self, group1, group2, include_side_chain_hbs = True):
determinants = group1.determinants['coulomb']
if include_side_chain_hbs:
determinants = group1.determinants['sidechain'] + group1.determinants['coulomb']
interaction_energy = 0.0
for det in determinants:
if group2 == det.group:
@@ -234,7 +237,7 @@ class non_covalently_couple_groups:
s = ' '+'-'*113+'\n'
for group in system:
s += self.tagged_print(' %-8s|'%tag,group.getDeterminantString(), all_labels)
return s+'\n'
def swap_interactions(self, groups1, groups2, include_side_chain_hbs = True):
@@ -242,7 +245,7 @@ class non_covalently_couple_groups:
for i in range(len(groups1)):
group1 = groups1[i]
group2 = groups2[i]
# swap the interactions!
self.transfer_determinant(group1.determinants['coulomb'], group2.determinants['coulomb'], group1.label, group2.label)
if include_side_chain_hbs:
@@ -266,7 +269,7 @@ class non_covalently_couple_groups:
for det in determinants2:
if det.label == label1:
from2to1.append(det)
# ...and transfer it!
for det in from1to2:
det.label = label1
@@ -280,7 +283,7 @@ class non_covalently_couple_groups:
return
#
#
# Output methods
#
@@ -295,7 +298,7 @@ class non_covalently_couple_groups:
def make_data_to_string(self, data, group1, group2):
s = """ %s and %s coupled (prot.state): %5.2f
Energy levels: %6.2f, %6.2f (difference: %6.2f) at pH %6.2f
Interaction energy: %6.2f
Interaction energy: %6.2f
Intrinsic pka's: %6.2f, %6.2f (difference: %6.2f)
Swapped pKa's: %6.2f, %6.2f (difference: %6.2f, %6.2f)"""%(group1.label,
group2.label,

3
Source/determinant.py → propka/determinant.py
View File

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

54
Source/determinants.py → propka/determinants.py
View File

@@ -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 Source.calculations
from Source.determinant import Determinant
import propka.iterative, propka.lib, propka.vector_algebra
import propka.calculations
from propka.determinant import Determinant
def setDeterminants(propka_groups, version=None, options=None):
@@ -19,19 +23,19 @@ def setDeterminants(propka_groups, version=None, options=None):
# do not calculate interactions for coupled groups
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):
@@ -52,11 +56,11 @@ def addSidechainDeterminants(group1, group2, version=None):
adding side-chain determinants/perturbations
Note, resNumb1 > resNumb2
"""
hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
if hbond_interaction:
if group1.charge == group2.charge:
# acid pair or base pair
if group1.model_pka < group2.model_pka:
@@ -78,7 +82,7 @@ def addCoulombDeterminants(group1, group2, distance, version):
"""
adding NonIterative Coulomb determinants/perturbations
"""
coulomb_interaction = version.electrostatic_interaction(group1, group2, distance)
if coulomb_interaction:
@@ -104,7 +108,7 @@ def addCoulombAcidPair(object1, object2, value):
Adding the Coulomb interaction (an acid pair):
the higher pKa is raised
"""
if object1.model_pka > object2.model_pka:
newDeterminant = Determinant(object2, value)
object1.determinants['coulomb'].append(newDeterminant)
@@ -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)
@@ -162,16 +166,16 @@ def setIonDeterminants(conformation_container, version):
return
def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
for titratable_group in titratable_groups:
# find out which backbone groups this titratable is interacting with
for backbone_group in backbone_groups:
# find the interacting atoms
backbone_interaction_atoms = backbone_group.get_interaction_atoms(titratable_group)
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)
@@ -186,7 +190,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
# for BBC groups, the hydrogen is on the titratable group
#
# Titra.
# /
# /
# H
# .
# O
@@ -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:
@@ -226,13 +230,13 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
# the titratable atom than the hydrogen. In either case we set the angle factor
# to 0
f_angle = 0.0
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)
return

159
Source/group.py → propka/group.py
View File

@@ -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},
@@ -65,7 +68,7 @@ expected_atoms_base_interactions = {
'SH': {'S':1},
'CG': {'N':3},
'C2N':{'N':2},
'OCO':{'O':2},
'OCO':{'O':2},
'N30':{'N':1},
'N31':{'N':1},
'N32':{'N':1},
@@ -86,7 +89,7 @@ class Group:
self.determinants = {'sidechain':[],'backbone':[],'coulomb':[]}
self.pka_value = 0.0
self.model_pka = 0.0
self.Emass = 0.0
self.Nmass = 0.0
self.Elocl = 0.0
@@ -99,18 +102,18 @@ class Group:
self.interaction_atoms_for_acids = []
self.interaction_atoms_for_bases = []
self.model_pka_set = False
# information on covalent and non-covalent coupling
self.non_covalently_coupled_groups = []
self.covalently_coupled_groups = []
self.coupled_titrating_group = None
self.common_charge_centre = False
self.residue_type = self.atom.resName
if self.atom.terminal:
self.residue_type = self.atom.terminal
if self.atom.type=='atom':
self.label = '%-3s%4d%2s'%(self.residue_type, atom.resNumb, atom.chainID)
elif self.atom.resName in ['DA ','DC ','DG ','DT ']:
@@ -119,7 +122,7 @@ class Group:
atom.name.replace('\'','')[-1],
atom.resNumb,
atom.chainID)
# self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.resNumb, atom.chainID)
else:
self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chainID)
@@ -133,28 +136,28 @@ class Group:
#
# Coupling-related methods
#
#
def couple_covalently(self, other):
""" Couple this group with another group """
# do the coupling
if not other in self.covalently_coupled_groups:
self.covalently_coupled_groups.append(other)
if not self in other.covalently_coupled_groups:
other.covalently_coupled_groups.append(self)
return
return
def couple_non_covalently(self, other):
""" Couple this group with another group """
# do the coupling
if not other in self.non_covalently_coupled_groups:
self.non_covalently_coupled_groups.append(other)
if not self in other.non_covalently_coupled_groups:
other.non_covalently_coupled_groups.append(self)
return
return
def get_covalently_coupled_groups(self): return self.covalently_coupled_groups
def get_non_covalently_coupled_groups(self): return self.non_covalently_coupled_groups
@@ -168,12 +171,12 @@ class Group:
continue
for type in ['sidechain','backbone','coulomb']:
for g in other.determinants[type]: self.share_determinant(g,type)
for g in other.determinants[type]: self.share_determinant(g,type)
# recalculate pka values
self.calculate_total_pka()
other.calculate_total_pka()
return
@@ -190,19 +193,19 @@ 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
def make_covalently_coupled_line(self):
# first check if there are any coupled groups at all
if len(self.covalently_coupled_groups) == 0:
return ''
line = 'CCOUPL%5d'%self.atom.numb
# extract and sort numbers of coupled groups
coupled = []
for g in self.covalently_coupled_groups:
@@ -213,7 +216,7 @@ class Group:
for b in coupled:
line += '%5d'%b
line += '\n'
return line
def make_non_covalently_coupled_line(self):
@@ -222,7 +225,7 @@ class Group:
return ''
line = 'NCOUPL%5d'%self.atom.numb
# extract and sort numbers of coupled groups
coupled = []
for g in self.non_covalently_coupled_groups:
@@ -233,7 +236,7 @@ class Group:
for b in coupled:
line += '%5d'%b
line += '\n'
return line
@@ -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
@@ -344,12 +347,12 @@ class Group:
self.charge = self.parameters.charge[self.type]
if self.residue_type in self.parameters.ions.keys():
self.charge = self.parameters.ions[self.residue_type]
#print('ION setup',self,self.residue_type, self.charge)
# find the center and the interaction atoms
self.setup_atoms()
# set the model pka value
self.titratable = False
if self.residue_type in self.parameters.model_pkas.keys():
@@ -365,7 +368,7 @@ class Group:
if self.model_pka_set and not self.atom.cysteine_bridge:
self.titratable = True
return
def setup_atoms(self):
@@ -378,7 +381,7 @@ class Group:
def set_interaction_atoms(self, interaction_atoms_for_acids, interaction_atoms_for_bases):
[a.set_group_type(self.type) for a in interaction_atoms_for_acids+interaction_atoms_for_bases]
self.interaction_atoms_for_acids = interaction_atoms_for_acids
self.interaction_atoms_for_bases = interaction_atoms_for_bases
@@ -400,11 +403,11 @@ class Group:
print(' Expected %d interaction atoms for acids, found:'%Na)
for i in range(len(self.interaction_atoms_for_acids)):
print(' %s'%self.interaction_atoms_for_acids[i])
print(' Expected %d interaction atoms for bases, found:'%Nb)
for i in range(len(self.interaction_atoms_for_bases)):
print(' %s'%self.interaction_atoms_for_bases[i])
#return
@@ -437,7 +440,7 @@ class Group:
number_of_sidechain = len(self.determinants['sidechain'])
number_of_backbone = len(self.determinants['backbone'])
number_of_coulomb = len(self.determinants['coulomb'])
number_of_lines = max(1, number_of_sidechain, number_of_backbone, number_of_coulomb)
str = ""
for line_number in range(number_of_lines):
@@ -458,11 +461,11 @@ class Group:
str += " %6.2lf %4d" % (self.Elocl, self.Nlocl)
else:
str += "%40s" % (" ")
# add the determinants
for type in ['sidechain','backbone','coulomb']:
str += self.get_determinant_for_string(type,line_number)
# adding end-of-line
str += "\n"
@@ -484,7 +487,7 @@ class Group:
if self.atom.cysteine_bridge:
self.pka_value = 99.99
return
self.pka_value = self.model_pka + self.Emass + self.Elocl
@@ -494,12 +497,12 @@ class Group:
return
def calculate_intrinsic_pka(self):
"""
Calculates the intrinsic pKa values from the desolvation determinants, back-bone hydrogen bonds,
Calculates the intrinsic pKa values from the desolvation determinants, back-bone hydrogen bonds,
and side-chain hydrogen bond to non-titratable residues
"""
back_bone = 0.0
@@ -528,18 +531,18 @@ class Group:
ligand_type = ''
if self.atom.type == 'hetatm':
ligand_type = self.type
penalty = ''
if self.coupled_titrating_group:
penalty = ' NB: Discarded due to coupling with %s'%self.coupled_titrating_group.label
str = " %9s %8.2lf %10.2lf %18s %s\n" % (self.label,
self.pka_value,
self.model_pka,ligand_type,
str = " %9s %8.2lf %10.2lf %18s %s\n" % (self.label,
self.pka_value,
self.model_pka,ligand_type,
penalty)
return str
def __str__(self):
return 'Group (%s) for %s'%(self.type,self.atom)
@@ -559,7 +562,7 @@ class Group:
reference = parameters.reference
# If not titratable, the contribution is zero
if not self.titratable:
return 0.00
@@ -571,25 +574,25 @@ class Group:
if determinant.value > 0.00:
pka_prime -= determinant.value
ddG_neutral = -1.36*(pka_prime - self.model_pka)
# calculating the ddG(low-pH --> pH) contribution
# folded
x = pH - self.pka_value
y = 10**x
Q_pro = math.log10(1+y)
# unfolded
x = pH - self.model_pka
y = 10**x
Q_mod = math.log10(1+y)
ddG_low = -1.36*(Q_pro - Q_mod)
ddG = ddG_neutral + ddG_low
return ddG
def calculate_charge(self, parmaeters, pH=7.0, state='folded'):
if state == "unfolded":
x = self.charge * (self.model_pka - pH)
else:
@@ -597,7 +600,7 @@ class Group:
y = 10**x
charge = self.charge*(y/(1.0+y))
return charge
@@ -610,7 +613,7 @@ class COO_group(Group):
def setup_atoms(self):
# Identify the two caroxyl oxygen atoms
the_oxygens = self.atom.get_bonded_elements('O')
# set the center using the two oxygen carboxyl atoms
self.set_center(the_oxygens)
self.set_interaction_atoms(the_oxygens, the_oxygens)
@@ -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)
@@ -634,11 +637,11 @@ class HIS_group(Group):
# set the center using the ring atoms
self.set_center(ring_atoms)
# find the hydrogens on the ring-nitrogens
hydrogens = []
nitrogens = [ra for ra in ring_atoms if ra.element == 'N']
for nitrogen in nitrogens:
hydrogens.extend(nitrogen.get_bonded_elements('H'))
@@ -673,12 +676,12 @@ class ARG_group(Group):
def setup_atoms(self):
# set the center at the position of the main atom
self.set_center([self.atom])
# find all the hydrogens on the nitrogen atoms
nitrogens = self.atom.get_bonded_elements('N')
for n in nitrogens:
my_protonator.protonate_atom(n)
hydrogens = []
for nitrogen in nitrogens:
hydrogens.extend(nitrogen.get_bonded_elements('H'))
@@ -705,19 +708,19 @@ class AMD_group(Group):
def setup_atoms(self):
# Identify the oxygen and nitrogen amide atoms
the_oxygen = self.atom.get_bonded_elements('O')
the_nitrogen = self.atom.get_bonded_elements('N')
# add protons to the nitrogen
the_nitrogen = self.atom.get_bonded_elements('N')
# add protons to the nitrogen
my_protonator.protonate_atom(the_nitrogen[0])
the_hydrogens = the_nitrogen[0].get_bonded_elements('H')
# set the center using the oxygen and nitrogen amide atoms
self.set_center(the_oxygen+the_nitrogen)
self.set_interaction_atoms(the_nitrogen+the_hydrogens,the_oxygen)
return
class TRP_group(Group):
def __init__(self, atom):
@@ -727,7 +730,7 @@ class TRP_group(Group):
def setup_atoms(self):
# set the center at the position of the main atom
self.set_center([self.atom])
# find the hydrogen on the nitrogen atom
my_protonator.protonate_atom(self.atom)
the_hydrogen = self.atom.get_bonded_elements('H')
@@ -751,12 +754,12 @@ class Cterm_group(Group):
the_carbon = self.atom.get_bonded_elements('C')
the_other_oxygen = the_carbon[0].get_bonded_elements('O')
the_other_oxygen.remove(self.atom)
# set the center and interaction atoms
the_oxygens = [self.atom]+ the_other_oxygen
self.set_center(the_oxygens)
self.set_interaction_atoms(the_oxygens, the_oxygens)
return
@@ -802,7 +805,7 @@ class NAR_group(Group):
self.residue_type = 'NAR'
print('Found NAR group:',atom)
return
def setup_atoms(self):
# Identify the hydrogen
@@ -825,7 +828,7 @@ class NAM_group(Group):
self.residue_type = 'NAM'
print('Found NAM group:',atom)
return
def setup_atoms(self):
# Identify the hydrogen
@@ -936,7 +939,7 @@ class CG_group(Group):
# set the center using the nitrogen
self.set_center([self.atom])
the_hydrogens = []
for n in the_nitrogens:
my_protonator.protonate_atom(n)
@@ -1065,7 +1068,7 @@ class NP1_group(Group):
print('Found NP1 group:',atom)
return
def setup_atoms(self):
# Identify the nitrogens
my_protonator.protonate_atom(self.atom)
@@ -1123,16 +1126,16 @@ class titratable_ligand_group(Group):
self.model_pka = atom.marvin_pka
print('Titratable ligand group ',atom, self.model_pka, self.charge)
self.model_pka_set = True
return
def is_group(parameters, atom):
atom.groups_extracted = 1
# check if this atom belongs to a protein group
protein_group = is_protein_group(parameters, atom)
if protein_group: return protein_group
if protein_group: return protein_group
# check if this atom belongs to a ion group
ion_group = is_ion_group(parameters, atom)
@@ -1168,7 +1171,7 @@ def is_protein_group(parameters,atom):
### Backbone
if atom.type == 'atom' and atom.name == 'N':
# ignore proline backbone nitrogens
if atom.resName != 'PRO':
if atom.resName != 'PRO':
return BBN_group(atom)
if atom.type == 'atom' and atom.name == 'C':
# ignore C- carboxyl
@@ -1199,10 +1202,10 @@ def is_ligand_group_by_groups(parameters, atom):
if atom.sybyl_type == 'N.ar':
if len(atom.get_bonded_heavy_atoms())==2:
return NAR_group(atom)
if atom.sybyl_type == 'N.am':
return NAM_group(atom)
if atom.sybyl_type in ['N.3', 'N.4']:
heavy_bonded = atom.get_bonded_heavy_atoms()
if len(heavy_bonded) == 0:
@@ -1218,14 +1221,14 @@ def is_ligand_group_by_groups(parameters, atom):
return N1_group(atom)
if atom.sybyl_type == 'N.pl3':
# make sure that this atom is not part of a guadinium or amidinium group
# make sure that this atom is not part of a guadinium or amidinium group
bonded_carbons = atom.get_bonded_elements('C')
if len(bonded_carbons) == 1:
bonded_nitrogens = bonded_carbons[0].get_bonded_elements('N')
if len(bonded_nitrogens) == 1:
return NP1_group(atom)
if atom.sybyl_type == 'C.2':
# Guadinium and amidinium groups
bonded_nitrogens = atom.get_bonded_elements('N')
@@ -1263,7 +1266,7 @@ def is_ligand_group_by_groups(parameters, atom):
if atom.sybyl_type == 'O.2':
return O2_group(atom)
if atom.sybyl_type == 'S.3':
# sulphide group
@@ -1272,8 +1275,8 @@ def is_ligand_group_by_groups(parameters, atom):
# other SP3 oxygen
#else:
# return S3_group(atom)
return None
@@ -1284,11 +1287,11 @@ 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)
if atom.marvin_pka:
return titratable_ligand_group(atom)

31
Source/iterative.py → propka/iterative.py
View File

@@ -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 Source.calculations
import propka.lib as lib
from propka.determinant import Determinant
import propka.calculations
# Some library functions for the interative pKa determinants
@@ -32,11 +37,11 @@ def addtoDeterminantList(group1, group2, distance, iterative_interactions, versi
def addIterativeAcidPair(object1, object2, interaction):
"""
"""
Adding the Coulomb 'iterative' interaction (an acid pair):
the higher pKa is raised with QQ+HB
the lower pKa is lowered with HB
"""
"""
values = interaction[1]
annihilation = interaction[2]
hbond_value = values[0]
@@ -69,10 +74,10 @@ def addIterativeAcidPair(object1, object2, interaction):
def addIterativeBasePair(object1, object2, interaction):
"""
"""
Adding the Coulomb 'iterative' interaction (a base pair):
the lower pKa is lowered
"""
"""
values = interaction[1]
annihilation = interaction[2]
hbond_value = values[0]
@@ -106,10 +111,10 @@ def addIterativeBasePair(object1, object2, interaction):
def addIterativeIonPair(object1, object2, interaction, version):
"""
"""
Adding the Coulomb 'iterative' interaction (an acid-base pair):
the pKa of the acid is lowered & the pKa of the base is raised
"""
"""
values = interaction[1]
annihilation = interaction[2]
hbond_value = values[0]
@@ -132,7 +137,7 @@ def addIterativeIonPair(object1, object2, interaction, version):
annihilation[0] = 0.00
annihilation[1] = 0.00
if add_term == True:
# Coulomb
@@ -161,9 +166,9 @@ def addIterativeIonPair(object1, object2, interaction, version):
def addDeterminants(iterative_interactions, version, options=None):
"""
"""
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
"""
"""
# --- setup ---
iteratives = []
done_group = []
@@ -270,7 +275,7 @@ def addDeterminants(iterative_interactions, version, options=None):
g = interaction[0]
newDeterminant = Determinant(g, value)
itres.group.determinants[type].append(newDeterminant)
def findIterative(pair, iteratives):

52
Source/lib.py → propka/lib.py Executable file → Normal file
View File

@@ -1,23 +1,27 @@
#!/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 open(filename,'r')
return f
def open_file_for_writing(filename):
res = open(filename,'w')
if not res:
try:
res = open(filename,'w')
except:
raise Exception('Could not open %s'%filename)
return res
#
# bookkeeping etc.
#
@@ -43,7 +47,7 @@ def make_molecule(atom, atoms):
if ba in atoms:
atoms.remove(ba)
res_atoms.extend(make_molecule(ba, atoms))
return res_atoms
@@ -61,7 +65,7 @@ def generate_combinations(interactions):
res.remove([])
return res
def make_combination(combis, interaction):
res = []
@@ -85,37 +89,37 @@ def loadOptions():
parser = OptionParser(usage)
# loading the parser
parser.add_option("-f", "--file", action="append", dest="filenames",
parser.add_option("-f", "--file", action="append", dest="filenames",
help="read data from <filename>, i.e. <filename> is added to arguments")
parser.add_option("-r", "--reference", dest="reference", default="neutral",
parser.add_option("-r", "--reference", dest="reference", default="neutral",
help="setting which reference to use for stability calculations [neutral/low-pH]")
parser.add_option("-c", "--chain", action="append", dest="chains",
parser.add_option("-c", "--chain", action="append", dest="chains",
help="creating the protein with only a specified chain, note, chains without ID are labeled 'A' [all]")
parser.add_option("-t", "--thermophile", action="append", dest="thermophiles",
parser.add_option("-t", "--thermophile", action="append", dest="thermophiles",
help="defining a thermophile filename; usually used in 'alignment-mutations'")
parser.add_option("-a", "--alignment", action="append", dest="alignment",
parser.add_option("-a", "--alignment", action="append", dest="alignment",
help="alignment file connecting <filename> and <thermophile> [<thermophile>.pir]")
parser.add_option("-m", "--mutation", action="append", dest="mutations",
parser.add_option("-m", "--mutation", action="append", dest="mutations",
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",
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",
help="set the parameter file")
parser.add_option("-z", "--verbose", dest="verbose", action="store_true", default=True,
parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
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",
help="sleep during calculations")
parser.add_option("-s", "--silent", dest="verbose", action="store_false",
parser.add_option("-s", "--silent", dest="verbose", action="store_false",
help="not activated yet")
parser.add_option("--verbosity", dest="verbosity", action="store_const",
parser.add_option("--verbosity", dest="verbosity", action="store_const",
help="level of printout - not activated yet")
parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]")
parser.add_option("-w", "--window", dest="window", nargs=3, type="float", default=(0.0, 14.0, 1.0),
help="setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0]")
parser.add_option("-g", "--grid", dest="grid", nargs=3, type="float", default=(0.0, 14.0, 0.1),
help="setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1]")
parser.add_option("--mutator", dest="mutator",
parser.add_option("--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
parser.add_option("--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]")
@@ -156,7 +160,7 @@ def makeTidyAtomLabel(name,element):
"""
Returns a 'tidier' atom label for printing the new pdbfile
"""
if len(name)>4:# if longer than 4, just truncate the name
label=name[0:4]
elif len(name)==4:# if lenght is 4, otherwise use the name as it is

45
Source/ligand.py → propka/ligand.py Executable file → Normal file
View File

@@ -1,7 +1,12 @@
#!/usr/bin/python
import sys, Source.calculations
from Source.vector_algebra import *
from __future__ import division
from __future__ import print_function
import sys
import propka.calculations
from propka.vector_algebra import *
all_sybyl_types = [
@@ -157,7 +162,7 @@ def assign_sybyl_type(atom):
bonded_elements[i]=atom.bonded_atoms[i].element
# Aromatic carbon/nitrogen
if aromatic:
for ra in ring_atoms:
@@ -187,7 +192,7 @@ def assign_sybyl_type(atom):
nitrogens = atom.get_bonded_elements('N')
oxygens = atom.get_bonded_elements('O')
if len(nitrogens)==1 and len(oxygens)==1:
C = atom
C = atom
N = nitrogens[0]
O = oxygens[0]
@@ -199,9 +204,9 @@ def assign_sybyl_type(atom):
set_type(C,'C.2')
set_type(O,'O.2')
return
if atom.element=='C':
if atom.element=='C':
# check for carboxyl
if len(atom.bonded_atoms)==3 and list(bonded_elements.values()).count('O')==2:
i1 = list(bonded_elements.values()).index('O')
@@ -213,11 +218,11 @@ def assign_sybyl_type(atom):
return
# 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:
@@ -232,7 +237,7 @@ def assign_sybyl_type(atom):
if len(b.bonded_atoms)<3 or is_planar(b):
set_type(b,'N.pl3')
return
# sp3 carbon
set_type(atom, 'C.3')
return
@@ -244,11 +249,11 @@ def assign_sybyl_type(atom):
if is_planar(atom.bonded_atoms[0]):
set_type(atom,'N.pl3')
return
if planar:
set_type(atom,'N.pl3')
return
set_type(atom,'N.3')
return
@@ -262,7 +267,7 @@ def assign_sybyl_type(atom):
the_carbon = atom.bonded_atoms[0]
if len(the_carbon.bonded_atoms)==3 and the_carbon.count_bonded_elements('O')==2:
[O1,O2] = the_carbon.get_bonded_elements('O')
if len(O1.bonded_atoms)==1 and len(O2.bonded_atoms)==1:
set_type(O1,'O.co2-')
set_type(O2,'O.co2')
@@ -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')
@@ -287,7 +292,7 @@ def assign_sybyl_type(atom):
set_type(atom.bonded_atoms[i2],'O.2')
set_type(atom,'S.o2')
return
# check for SO4
if list(bonded_elements.values()).count('O')==4:
no_O2 = 0
@@ -297,7 +302,7 @@ def assign_sybyl_type(atom):
no_O2+=1
else:
set_type(atom.bonded_atoms[i],'O.3')
set_type(atom,'S.3')
@@ -315,8 +320,8 @@ def assign_sybyl_type(atom):
# # find oxygens only bonded to current phosphorus
# 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))
# closest_oxygen = min(bonded_oxygens_1,
# key= lambda o:propka.calculations.squared_distance(atom,o))
# # ... and set it to O.2
# set_type(closest_oxygen,'O.2')
@@ -378,20 +383,20 @@ def are_atoms_planar(atoms):
v1 = vector(atom1=atoms[0], atom2=atoms[1])
v2 = vector(atom1=atoms[0], atom2=atoms[2])
n = (v1**v2).rescale(1.0)
margin = 0.20
for b in atoms[3:]:
v = vector(atom1=atoms[0], atom2=b).rescale(1.0)
#print(atoms[0],abs(v*n) )
if abs(v*n)>margin:
return False
return True
def is_aromatic_ring(atoms):
if len(atoms)<5:
return False
for i in range(len(atoms)):
if not are_atoms_planar(atoms[i:]+atoms[:i]):
return False

29
Source/ligand_pka_values.py → propka/ligand_pka_values.py
View File

@@ -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):
@@ -14,14 +17,14 @@ class ligand_pka_values:
print(self.molconvert)
return
def find_in_path(self, program):
path = os.environ.get('PATH').split(os.pathsep)
l = [i for i in filter(lambda loc: os.access(loc, os.F_OK),
map(lambda dir: os.path.join(dir, program),path))]
if len(l) == 0:
print('Error: Could not find %s. Please make sure that it is found in the path.'%program)
sys.exit(-1)
@@ -29,14 +32,14 @@ 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
def get_marvin_pkas_for_molecular_container(self, molecule, no_pkas=10, min_pH =-10, max_pH=20):
for name in molecule.conformation_names:
filename = '%s_%s'%(molecule.name,name)
self.get_marvin_pkas_for_conformation_container(molecule.conformations[name], name=filename, reuse=molecule.options.reuse_ligand_mol2_file,
self.get_marvin_pkas_for_conformation_container(molecule.conformations[name], name=filename, reuse=molecule.options.reuse_ligand_mol2_file,
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)
@@ -61,18 +64,18 @@ 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)
# Marvin
# calculate pKa values
options = 'pka -a %d -b %d --min %f --max %f -d large'%(no_pkas, no_pkas, min_pH, max_pH)
(output,errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
(output,errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
if len(errors)>0:
@@ -86,7 +89,7 @@ class ligand_pka_values:
# extract calculated pkas
indices,pkas,types = self.extract_pkas(output)
# store calculated pka values
for i in range(len(indices)):
atoms[indices[i]].marvin_pka = pkas[i]
@@ -104,10 +107,10 @@ class ligand_pka_values:
values = values.split('\t')
# format values
types = [tags[i][0] for i in range(1,len(tags)-1) if len(values)>i and values[i] != '']
types = [tags[i][0] for i in range(1,len(tags)-1) if len(values)>i and values[i] != '']
indices = [int(a)-1 for a in values[-1].split(',') if a !='']
values = [float(v.replace(',','.')) for v in values[1:-1] if v != '']
if len(indices) != len(values) != len(types):
raise Exception('Lengths of atoms and pka values mismatch')

66
Source/molecular_container.py → propka/molecular_container.py Executable file → Normal file
View File

@@ -1,15 +1,19 @@
#!/usr/bin/python
#
# Molecular container for storing all contents of pdb files
# 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()
@@ -103,15 +107,15 @@ class Molecular_container:
""" Identify the groups needed for pKa calculation """
for name in self.conformation_names:
self.conformations[name].extract_groups()
return
def additional_setup_when_reading_input_file(self):
for name in self.conformation_names:
self.conformations[name].additional_setup_when_reading_input_file()
return
def calculate_pka(self):
# calculate for each conformation
@@ -120,21 +124,21 @@ class Molecular_container:
# find non-covalently coupled groups
self.find_non_covalently_coupled_groups()
# find the average of the conformations
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',
parameters=self.conformations[self.conformation_names[0]].parameters,
avr_conformation = propka.conformation_container.Conformation_container(name='average',
parameters=self.conformations[self.conformation_names[0]].parameters,
molecular_container=self)
for group in self.conformations[self.conformation_names[0]].get_titratable_groups_and_cysteine_bridges():
# new group to hold average values
avr_group = group.clone()
@@ -161,13 +165,13 @@ 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),
# conformation=name,reference=reference,
# propka.output.writePKA(self, self.version.parameters, filename='%s_3.1_%s.pka'%(self.name, name),
# conformation=name,reference=reference,
# direction=direction, options=options)
# write out the average conformation
filename=os.path.join('%s.pka'%(self.name))
# if the display_coupled_residues option is true,
# write the results out to an alternative pka file
if self.options.display_coupled_residues:
@@ -176,8 +180,8 @@ 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,
conformation='AVR',reference=reference,
propka.output.writePKA(self, self.version.parameters, filename=filename,
conformation='AVR',reference=reference,
direction=direction, options=options)
return
@@ -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])
@@ -196,29 +200,29 @@ class Molecular_container:
opt = min(opt, point, key=lambda v:v[1])
# find values within 80 % of optimum
range_80pct = [None, None]
range_80pct = [None, None]
values_within_80pct = [p[0] for p in profile if p[1]< 0.8*opt[1]]
if len(values_within_80pct)>0:
range_80pct = [min(values_within_80pct), max(values_within_80pct)]
# find stability range
stability_range = [None, None]
stable_values = [p[0] for p in profile if p[1]< 0.0]
stable_values = [p[0] for p in profile if p[1]< 0.0]
if len(stable_values)>0:
stability_range = [min(stable_values), max(stable_values)]
return profile, opt, range_80pct, stability_range
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])
return charge_profile
def getPI(self, conformation='AVR', grid=[0., 14., 1], iteration=0):
#print('staring',grid, iteration)
# search
@@ -240,7 +244,7 @@ class Molecular_container:
return pi_folded_value, pi_unfolded_value
if __name__ == '__main__':
input_file = sys.argv[1]

35
Source/output.py → propka/output.py
View File

@@ -1,5 +1,10 @@
from __future__ import division
from __future__ import print_function
import sys
import Source.lib
import propka.lib
def printHeader():
@@ -17,7 +22,7 @@ def writePDB(protein, file=None, filename=None, include_hydrogens=False, options
"""
Write the residue to the new pdbfile
"""
if file == None:
# opening file if not given
if filename == None:
@@ -124,7 +129,7 @@ def getDeterminantSection(protein, conformation, parameters):
# printing determinants
for chain in protein.conformations[conformation].chains:
for residue_type in parameters.write_out_order:
groups = [g for g in protein.conformations[conformation].groups if g.atom.chainID == chain]
groups = [g for g in protein.conformations[conformation].groups if g.atom.chainID == chain]
for group in groups:
if group.residue_type == residue_type:
str += "%s" % ( group.getDeterminantString(parameters.remove_penalised_group) )
@@ -158,8 +163,8 @@ def getFoldingProfileSection(protein, conformation='AVR', direction="folding", r
str += "\n"
str += "Free energy of %9s (kcal/mol) as a function of pH (using %s reference)\n" % (direction, reference)
profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.getFoldingProfile(conformation=conformation,
reference=reference,
profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.getFoldingProfile(conformation=conformation,
reference=reference,
direction=direction, grid=[0., 14., 0.1], options=options)
if profile == None:
str += "Could not determine folding profile\n"
@@ -183,7 +188,7 @@ def getFoldingProfileSection(protein, conformation='AVR', direction="folding", r
str += "Could not determine the pH-range where the free energy is negative\n\n"
else:
str += "The free energy is negative in the range %4.1lf - %4.1lf\n\n" % (pH_min, pH_max)
return str
@@ -209,7 +214,7 @@ def getChargeProfileSection(protein, conformation='AVR', options=None):
str += "Could not determine the pI\n\n"
else:
str += "The pI is %5.2lf (folded) and %5.2lf (unfolded)\n" % (pI_pro, pI_mod)
return str
@@ -300,8 +305,8 @@ def getReferencesHeader():
str += " Journal of Chemical Theory and Computation, 7(2):525-537 (2011)\n"
str += " \n"
str += " Improved Treatment of Ligands and Coupling Effects in Empirical Calculation\n"
str += " and Rationalization of pKa Values\n"
str += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n"
str += " and Rationalization of pKa Values\n"
str += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n"
str += " Journal of Chemical Theory and Computation, (2011)\n"
str += " \n"
str += "-------------------------------------------------------------------------------------------------------\n"
@@ -357,13 +362,13 @@ def getTheLine():
# Interaction maps
def make_interaction_map(name, list, interaction):
""" Print out an interaction map named 'name' of the groups in 'list'
""" Print out an interaction map named 'name' of the groups in 'list'
based on the function 'interaction' """
# return an empty string, if the list is empty
if len(list)==0:
return ''
# for long list, use condensed formatting
if len(list)>10:
res = 'Condensed form:\n'
@@ -377,7 +382,7 @@ def make_interaction_map(name, list, interaction):
res = '%s\n%12s'%(name,'')
for g in list:
res += '%9s | '%g.label
# do the map
for g1 in list:
res += '\n%-12s'%(g1.label)
@@ -386,6 +391,6 @@ def make_interaction_map(name, list, interaction):
if interaction(g1, g2):
tag = ' X '
res += '%10s| '%tag
return res

60
Source/parameters.py → propka/parameters.py
View File

@@ -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']
@@ -45,16 +50,15 @@ class Parameters:
#self.print_interaction_parameters_latex()
#####self.print_interactions_latex()
#sys.exit(0)
return
def read_parameters(self, file):
# try to locate the parameters file
try:
path = os.path.dirname(__file__)
ifile = os.path.join(path,'../'+file)
ifile = pkg_resources.resource_filename(__name__, file)
input = lib.open_file_for_reading(ifile)
except:
input = lib.open_file_for_reading(file)
@@ -94,7 +98,7 @@ class Parameters:
elif len(words)==3 and words[0] in string_dictionaries:
self.parse_to_string_dictionary(words)
#print(words)
return
@@ -226,25 +230,25 @@ class Parameters:
print("""
Titratable:
CG ARG
C2N ARG
C2N ARG
N30 N+/LYS
N31 N+/LYS
N32 N+/LYS
N33 N+/LYS
N33 N+/LYS
NAR HIS
OCO COO
OP TYR/SER?
SH CYS
SH CYS
Non-titratable:
NP1 AMD?
OH ROH
O3 ?
CL
F
NAM
N1
O2
CL
F
NAM
N1
O2
""")
return
@@ -283,7 +287,7 @@ O2
'N1' :[],
'O2' :[]}
s = """
\\begin{longtable}{lllll}
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
@@ -296,11 +300,11 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\
\\toprule
Group1 & Group2 & Interaction & c1 &c2 \\\\
Group1 & Group2 & Interaction & c1 &c2 \\\\
\\midrule
\\endhead
\\midrule
\\midrule
\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\
\\endfoot
@@ -332,7 +336,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
s = """
\\begin{longtable}{%s}
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
@@ -345,11 +349,11 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\
\\toprule
Group1 & Group2 & Interaction & c1 &c2 \\\\
Group1 & Group2 & Interaction & c1 &c2 \\\\
\\midrule
\\endhead
\\midrule
\\midrule
\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\
\\endfoot
@@ -399,14 +403,14 @@ class Interaction_matrix:
self.dictionary[group][new_group] = self.value
self.dictionary[new_group][group] = self.value
return
def get_value(self, item1, item2):
try:
return self.dictionary[item1][item2]
except:
return None
return None
def __getitem__(self, group):
if group not in self.dictionary.keys():
@@ -430,7 +434,7 @@ class Interaction_matrix:
return s
# ks = ['COO', 'SER', 'ARG', 'LYS', 'HIS', 'AMD', 'CYS', 'TRP','ROH','TYR','N+','CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
# p = ''
# n=0
# for i in range(len(ks)):
@@ -442,7 +446,7 @@ class Interaction_matrix:
# print('total',n,len(ks))
# return p
class Pair_wise_matrix:
@@ -451,7 +455,7 @@ class Pair_wise_matrix:
self.dictionary = {}
self.default = [0.0, 0.0]
return
def add(self,words):
# assign the default value
if len(words)==3 and words[0]=='default':
@@ -462,7 +466,7 @@ class Pair_wise_matrix:
g1 = words[0]
g2 = words[1]
v = [float(words[2]), float(words[3])]
self.insert(g1,g2,v)
self.insert(g2,g1,v)
@@ -482,7 +486,7 @@ class Pair_wise_matrix:
return
def get_value(self, item1, item2):
try:
return self.dictionary[item1][item2]
except:
@@ -504,7 +508,7 @@ class Pair_wise_matrix:
s += '%s %s %s\n'%(k1,k2,self[k1][k2])
return s

72
Source/pdb.py → propka/pdb.py
View File

@@ -1,6 +1,12 @@
import string, sys, copy, Source.lib
from Source.atom import Atom
from Source.conformation_container import Conformation_container
from __future__ import division
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,
@@ -35,23 +41,23 @@ 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]
def protein_precheck(conformations, names):
for name in names:
atoms = conformations[name].atoms
res_ids = []
[res_ids.append(resid_from_atom(a)) for a in atoms if not res_ids.count(resid_from_atom(a))]
for res_id in res_ids:
res_atoms = [a for a in atoms if resid_from_atom(a) == res_id and a.element != 'H']
resname = res_atoms[0].resName
residue_label = '%3s%5s'%(resname, res_id)
# ignore ligand residues
if resname not in expected_atom_numbers:
continue
@@ -65,7 +71,7 @@ def protein_precheck(conformations, names):
# check number of atoms in residue
if len(res_atoms) != expected_atom_numbers[resname]:
print('Warning: Unexpected number (%d) of atoms in residue %s in conformation %s'%(len(res_atoms),residue_label, name))
return
def resid_from_atom(a):
@@ -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
@@ -88,7 +94,7 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False,
if tag == 'MODEL ':
model = int(line[6:])
nterm_residue = 'next_residue'
if tag == 'TER ':
nterm_residue = 'next_residue'
@@ -102,21 +108,21 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False,
continue
if chains and line[21] not in chains:
continue
# set the Nterm residue number - nessecary because we may need to
# set the Nterm residue number - nessecary because we may need to
# identify more than one N+ group for structures with alt_conf tags
if nterm_residue == 'next_residue' and tag == 'ATOM ':
# make sure that we reached a new residue - nessecary if OXT is not the last atom in
# the previous residue
# make sure that we reached a new residue - nessecary if OXT is not the last atom in
# the previous residue
if old_residue != residue_number:
nterm_residue = residue_number
old_residue = None
# Identify the configuration
# Identify the configuration
# convert digits to letters
if alt_conf_tag in '123456789':
alt_conf_tag = chr(ord(alt_conf_tag)+16)
alt_conf_tag = chr(ord(alt_conf_tag)+16)
if alt_conf_tag == ' ':
alt_conf_tag = 'A'
conformation = '%d%s'%(model, alt_conf_tag)
@@ -145,10 +151,10 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues = [], keep_protons=False,
def write_pdb(conformation, filename):
write_pdb_for_atoms(conformation.atoms, 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())
@@ -171,7 +177,7 @@ def write_mol2_for_atoms(atoms, filename):
for i in range(len(atoms)):
atoms_section += atoms[i].make_mol2_line(i+1)
bonds_section = '@<TRIPOS>BOND\n'
id = 1
for i in range(len(atoms)):
@@ -180,12 +186,12 @@ def write_mol2_for_atoms(atoms, filename):
type = get_bond_order(atoms[i],atoms[j])
bonds_section += '%7d %7d %7d %7s\n'%(id, i+1, j+1, type)
id+=1
substructure_section = '@<TRIPOS>SUBSTRUCTURE\n\n'
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)
@@ -209,14 +215,14 @@ def get_bond_order(atom1, atom2):
if '.ar' in atom1.sybyl_type and '.ar' in atom2.sybyl_type:
type = 'ar'
return type
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 = {}
@@ -278,7 +284,7 @@ def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']):
atom.is_protonated = True
atoms[atom.numb] = atom
numbers.append(atom.numb)
# found bonding information - apply it
if tag == 'CONECT' and len(line)>14:
conect_numbers = [line[i:i+5] for i in range(6, len(line)-1, 5)]
@@ -301,7 +307,7 @@ def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']):
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_covalently(cg.group)
center_atom.group.couple_covalently(cg.group)
# found info on non-covalent coupling
if tag == 'NCOUPL' and len(line)>14:
@@ -309,8 +315,8 @@ def get_atom_lines_from_input(input_file, tags = ['ATOM ','HETATM']):
center_atom = atoms[int(conect_numbers[0])]
for n in conect_numbers[1:]:
cg = atoms[int(n)]
center_atom.group.couple_non_covalently(cg.group)
center_atom.group.couple_non_covalently(cg.group)
# this conformation is done - yield the atoms
if tag == 'ENDMDL':
for n in numbers:

398
propka/propka.cfg Normal file
View File

@@ -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

0
Source/protein_bonds.dat → propka/protein_bonds.dat
View File

97
Source/protonate.py → propka/protonate.py Executable file → Normal file
View File

@@ -1,11 +1,14 @@
#!/usr/bin/python
from Source.vector_algebra import *
import Source.bonds, Source.pdb, Source.atom
from __future__ import division
from __future__ import print_function
from propka.vector_algebra import *
import propka.bonds, propka.pdb, propka.atom
class Protonate:
""" Protonates atoms using VSEPR theory """
def __init__(self, verbose=False):
self.verbose=verbose
@@ -56,9 +59,9 @@ class Protonate:
'HIS-ND1':1.0,
'LYS-NZ':1.0,
'N+':1.0,
'C-':-1.0}
'C-':-1.0}
self.sybyl_charges = {'N.pl3':+1,
'N.3':+1,
'N.4':+1,
@@ -92,17 +95,17 @@ class Protonate:
self.display('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
# protonate all atoms
for name in molecules.conformation_names:
non_H_atoms = molecules.conformations[name].get_non_hydrogen_atoms()
for atom in non_H_atoms:
self.protonate_atom(atom)
# fix hydrogen names
#self.set_proton_names(non_H_atoms)
return
@@ -110,7 +113,7 @@ class Protonate:
for name in molecular_container.conformation_names:
molecular_container.conformations[name].atoms = molecular_container.conformations[name].get_non_hydrogen_atoms()
return
def set_charge(self, atom):
# atom is a protein atom
@@ -148,11 +151,11 @@ class Protonate:
for heavy_atom in heavy_atoms:
i = 1
for bonded in heavy_atom.bonded_atoms:
if bonded.element == 'H':
bonded.name+='%d'%i
i+=1
return
@@ -160,7 +163,7 @@ class Protonate:
def set_number_of_protons_to_add(self, atom):
self.display('*'*10)
self.display('Setting number of protons to add for',atom)
atom.number_of_protons_to_add = 8
atom.number_of_protons_to_add = 8
self.display(' %4d'%8)
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
self.display('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
@@ -177,7 +180,7 @@ class Protonate:
return
def set_steric_number_and_lone_pairs(self, atom):
# If we already did this, there is no reason to do it again
if atom.steric_number_and_lone_pairs_set:
return
@@ -195,10 +198,10 @@ class Protonate:
atom.steric_number = 0
self.display('%65s: %4d'%('Valence electrons',self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
self.display('%65s: %4d'%('Number of bonds',len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
@@ -216,7 +219,7 @@ class Protonate:
self.display('%65s: %4.1f'%('Charge(-)',atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number/2.0)
atom.number_of_lone_pairs = atom.steric_number - len(atom.bonded_atoms) - atom.number_of_protons_to_add
@@ -240,9 +243,9 @@ class Protonate:
return
def trigonal(self, atom):
self.display('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
self.display('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
c = vector(atom1 = atom)
@@ -250,13 +253,13 @@ class Protonate:
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if atom.bonded_atoms[0].steric_number == 3 and len(atom.bonded_atoms[0].bonded_atoms)>1:
# use other atoms bonded to the neighbour to establish the plane, if possible
@@ -265,21 +268,21 @@ class Protonate:
if atom.bonded_atoms[0].bonded_atoms[i] != atom:
other_atom_indices.append(i)
v1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
v2 = vector(atom1 = atom.bonded_atoms[0],
v2 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[0]])
axis = v1**v2
# this is a trick to make sure that the order of atoms doesn't influence
# the final postions of added protons
if len(other_atom_indices)>1:
v3 = vector(atom1 = atom.bonded_atoms[0],
v3 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[1]])
axis2 = v1**v3
if axis * axis2>0:
axis = axis+axis2
else:
@@ -294,12 +297,12 @@ class Protonate:
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
new_a = -a1 - a2
new_a = self.set_bond_distance(new_a, atom.element)
new_a = -a1 - a2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
@@ -307,20 +310,20 @@ class Protonate:
def tetrahedral(self, atom):
self.display('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
self.display('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(109.5)
# sanity check
# if atom.number_of_protons_to_add + len(atom.bonded_atoms) != 4:
# self.display 'Error: Attempting tetrahedral structure with %d bonds'%(atom.number_of_protons_to_add +
# self.display 'Error: Attempting tetrahedral structure with %d bonds'%(atom.number_of_protons_to_add +
# len(atom.bonded_atoms))
c = vector(atom1 = atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
@@ -332,7 +335,7 @@ class Protonate:
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
@@ -351,16 +354,16 @@ class Protonate:
new_a = -a1-a2-a3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
return
def add_proton(self, atom, position):
# Create the new proton
new_H = Source.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
new_H = propka.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
chainID = atom.chainID,
resNumb = atom.resNumb,
x = round(position.x,3), # round of to three digimal points
@@ -381,19 +384,19 @@ class Protonate:
atom.bonded_atoms.append(new_H)
atom.number_of_protons_to_add -=1
atom.conformation_container.add_atom(new_H)
atom.conformation_container.add_atom(new_H)
# update names of all protons on this atom
new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.resNumb, new_H.chainID)
new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.resNumb, new_H.chainID)
no_protons = atom.count_bonded_elements('H')
if no_protons > 1:
i = 1
for proton in atom.get_bonded_elements('H'):
proton.name = 'H%s%d'%(atom.name[1:],i)
proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.resNumb, proton.chainID)
proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.resNumb, proton.chainID)
i+=1
self.display('added',new_H, 'to',atom)
return
@@ -407,7 +410,7 @@ class Protonate:
a = a.rescale(d)
return a
def display(self,*text):
if self.verbose:
s = ''
@@ -429,11 +432,11 @@ if __name__ == '__main__':
print('Error: Could not find \"%s\"'%filename)
sys.exit(1)
p = Protonate()
pdblist = pdb.readPDB(filename)
my_protein = protein.Protein(pdblist,'test.pdb')
p.remove_all_hydrogen_atoms_from_protein(my_protein)
my_protein.writePDB('before_protonation.pdb')

15
propka/run.py Normal file
View File

@@ -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()

2
Source/vector_algebra.py → propka/vector_algebra.py
View File

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

75
Source/version.py → propka/version.py
View File

@@ -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:
@@ -21,7 +24,7 @@ class version:
def hydrogen_bond_interaction(self, group1, group2):
return self.hydrogen_bond_interaction_model(group1, group2, self)
def calculateSideChainEnergy(self, distance, dpka_max, cutoff, weight, f_angle):
def calculateSideChainEnergy(self, distance, dpka_max, cutoff, weight, f_angle):
return self.sidechain_interaction_model(distance, dpka_max, cutoff, f_angle) # weight is ignored in 3.0 Sep07
# coulomb
@@ -47,38 +50,38 @@ class version:
def setup_bonding(self, molecular_container):
return self.prepare_bonds(self.parameters, molecular_container)
class version_A(version):
def __init__(self, parameters):
# set the calculation rutines used in this version
# set the calculation rutines used in this version
version.__init__(self, parameters)
# atom naming, bonding, and protonation
self.molecular_preparation_method = Source.calculations.setup_bonding_and_protonation
self.prepare_bonds = Source.calculations.setup_bonding
self.molecular_preparation_method = propka.calculations.setup_bonding_and_protonation
self.prepare_bonds = propka.calculations.setup_bonding
# 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.hydrogen_bond_interaction_model = Source.calculations.hydrogen_bond_interaction
self.sidechain_interaction_model = propka.calculations.HydrogenBondEnergy
self.hydrogen_bond_interaction_model = propka.calculations.hydrogen_bond_interaction
# colomb methods
self.electrostatic_interaction_model = Source.calculations.electrostatic_interaction
self.check_coulomb_pair_method = Source.calculations.checkCoulombPair
self.coulomb_interaction_model = Source.calculations.CoulombEnergy
self.electrostatic_interaction_model = propka.calculations.electrostatic_interaction
self.check_coulomb_pair_method = propka.calculations.checkCoulombPair
self.coulomb_interaction_model = propka.calculations.CoulombEnergy
#backbone
self.backbone_interaction_model = Source.calculations.HydrogenBondEnergy
self.backbone_reorganisation_method = Source.calculations.BackBoneReorganization
self.backbone_interaction_model = propka.calculations.HydrogenBondEnergy
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):
@@ -91,7 +94,7 @@ class version_A(version):
if atom.group_type in self.parameters.backbone_CO_hydrogen_bond.keys():
[v,c1,c2] = self.parameters.backbone_CO_hydrogen_bond[atom.group_type]
return [v,[c1,c2]]
if backbone_atom.group_type == 'BBN':
if atom.group_type in self.parameters.backbone_NH_hydrogen_bond.keys():
[v,c1,c2] = self.parameters.backbone_NH_hydrogen_bond[atom.group_type]
@@ -104,7 +107,7 @@ class version_A(version):
class simple_hb(version_A):
def __init__(self, parameters):
# set the calculation rutines used in this version
# set the calculation rutines used in this version
version_A.__init__(self, parameters)
print('Using simple hb model')
return
@@ -116,23 +119,23 @@ class simple_hb(version_A):
def get_backbone_hydrogen_bond_parameters(self, backbone_atom, atom):
return self.parameters.hydrogen_bonds.get_value(backbone_atom.element, atom.element)
class element_based_ligand_interactions(version_A):
def __init__(self, parameters):
# set the calculation rutines used in this version
# set the calculation rutines used in this version
version_A.__init__(self, parameters)
print('Using detailed SC model!')
return
def get_hydrogen_bond_parameters(self, atom1, atom2):
if not 'hetatm' in [atom1.type, atom2.type]:
if not 'hetatm' in [atom1.type, atom2.type]:
# this is a protein-protein interaction
dpka_max = self.parameters.sidechain_interaction.get_value(atom1.group_type, atom2.group_type)
cutoff = self.parameters.sidechain_cutoffs.get_value(atom1.group_type, atom2.group_type)
return [dpka_max, cutoff]
# at least one ligand atom is involved in this interaction
# make sure that we are using the heavy atoms for finding paramters
elements = []
@@ -140,17 +143,17 @@ class element_based_ligand_interactions(version_A):
if a.element == 'H': elements.append(a.bonded_atoms[0].element)
else: elements.append(a.element)
return self.parameters.hydrogen_bonds.get_value(elements[0], elements[1])
return self.parameters.hydrogen_bonds.get_value(elements[0], elements[1])
def get_backbone_hydrogen_bond_parameters(self, backbone_atom, atom):
if atom.type == 'atom':
if atom.type == 'atom':
# this is a backbone-protein interaction
if backbone_atom.group_type == 'BBC' and\
atom.group_type in self.parameters.backbone_CO_hydrogen_bond.keys():
[v,c1,c2] = self.parameters.backbone_CO_hydrogen_bond[atom.group_type]
return [v,[c1,c2]]
if backbone_atom.group_type == 'BBN' and\
atom.group_type in self.parameters.backbone_NH_hydrogen_bond.keys():
[v,c1,c2] = self.parameters.backbone_NH_hydrogen_bond[atom.group_type]
@@ -168,7 +171,7 @@ class element_based_ligand_interactions(version_A):
print('Could not determine backbone interaction parameters for:',
backbone_atom,atom)
return
return
return None
@@ -176,28 +179,28 @@ class element_based_ligand_interactions(version_A):
class propka30(version):
def __init__(self, parameters):
# set the calculation rutines used in this version
# set the calculation rutines used in this 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.coulomb_interaction_model = Source.calculations.CoulombEnergy
self.check_coulomb_pair_method = propka.calculations.checkCoulombPair
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

31
scripts/propka31.py Executable file
View File

@@ -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()

51
setup.py Normal file
View File

@@ -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,
)