#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2015 The ProteinDF development team.
# see also AUTHORS and README if provided.
#
# This file is a part of the ProteinDF software package.
#
# The ProteinDF is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# The ProteinDF is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ProteinDF. If not, see <http://www.gnu.org/licenses/>.
from .aminoacid import AminoAcid
from .atomgroup import AtomGroup
from .position import Position
import logging
logger = logging.getLogger(__name__)
[docs]
class IonPair(object):
def __init__(self, model):
self._model = AtomGroup(model)
[docs]
def get_ion_pairs(self):
ion_pairs = []
(anion_list, cation_list) = self._get_ion_list()
for anion_path, anion_pos_array in anion_list.items():
for (anion_pos, anion_type) in anion_pos_array:
for cation_path, cation_pos_array in cation_list.items():
for (cation_pos, cation_type) in cation_pos_array:
d = anion_pos.distance_from(cation_pos)
if d < 4.0:
logger.info("found ion pair: {}".format(anion_path))
logger.info(" : {}".format(cation_path))
ion_pairs.append((anion_path, cation_path, anion_type, cation_type))
return ion_pairs
def _get_ion_list(self):
anion_list = {}
cation_list = {}
for chain_key, chain in self._model.groups():
for res_key, res in chain.groups():
name = res.name
if name == 'GLU':
anion_list[res.path] = [(self._get_center_GLU(res), 'GLU')]
elif name == 'ASP':
anion_list[res.path] = [(self._get_center_ASP(res), 'ASP')]
elif name == 'LYS':
cation_list[res.path] = [(self._get_center_LYS(res), 'LYS')]
elif name == 'ARG':
cation_list[res.path] = [(self._get_center_ARG(res, 0), 'ARG'),
(self._get_center_ARG(res, 1), 'ARG1'),
(self._get_center_ARG(res, 2), 'ARG2')]
if AminoAcid.is_aminoacid(res):
if res.has_atom('H3'):
cation_list.setdefault(res.path, [])
cation_list[res.path].append((self._get_center_Nterm(res), 'NTM'))
if res.has_atom('OXT'):
anion_list.setdefault(res.path, [])
anion_list[res.path].append((self._get_center_Cterm(res), 'CTM'))
return (anion_list, cation_list)
def _get_center_Nterm(self, res):
"""
Return the coordinates used for N-terminal ion-pair determination.
"""
return res['N'].xyz
def _get_center_Cterm(self, res):
"""
Return the coordinates used for C-terminal ion-pair determination.
"""
ag = AtomGroup()
ag.set_atom('C', res['C'])
ag.set_atom('O1', res['O'])
ag.set_atom('O2', res['OXT'])
return ag.center()
def _get_center_GLU(self, res):
"""
Return the coordinates used for GLU ion-pair determination.
"""
ag = AtomGroup()
ag.set_atom('C', res['CD'])
ag.set_atom('O1', res['OE1'])
ag.set_atom('O2', res['OE2'])
return ag.center()
def _get_center_ASP(self, res):
"""
Return the coordinates used for ASP ion-pair determination.
"""
ag = AtomGroup()
ag.set_atom('C', res['CG'])
ag.set_atom('O1', res['OD1'])
ag.set_atom('O2', res['OD2'])
return ag.center()
def _get_center_LYS(self, res):
"""
Return the coordinates used for LYS ion-pair determination.
"""
xyz = None
if res.has_atom('NZ'):
xyz = res['NZ'].xyz
else:
logger.critical('The LYS has no "NZ" atom.')
raise
return xyz
def _get_center_ARG(self, res, case=0):
"""
case: 0; center
case: 1; NH1 side
case: 2; NH2 side
"""
case = int(case)
answer = Position()
ag = AtomGroup()
if case == 0:
ag.set_atom('NH1', res['NH1'])
ag.set_atom('NH2', res['NH2'])
ag.set_atom('CZ', res['CZ'])
answer = ag.center()
elif case == 1:
answer = res['NH1'].xyz
elif case == 2:
answer = res['NH2'].xyz
else:
logger.warning("unknown case={}".format(case))
return answer
# if __name__ == "__main__":
# main()