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lipid_order_parameters.py
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lipid_order_parameters.py
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#------------------------------------------------------------------------------------------------
#This file is part of the ost_pymodules project (https://github.com/njohner/ost_pymodules).
#
#Copyright 2015 Niklaus Johner
#
#ost_pymodules is free software: you can redistribute it and/or modify
#it under the terms of the GNU Lesser General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#ost_pymodules 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 Lesser General Public License for more details.
#
#You should have received a copy of the GNU Lesser General Public License
#along with ost_pymodules. If not, see <http://www.gnu.org/licenses/>.
#------------------------------------------------------------------------------------------------
"""
.. codeauthor:: Niklaus Johner <[email protected]>
This module contains functions to calculate lipid order parameters.
"""
try:
from ost import *
import time
import numpy as npy
import os,math
import entity_alg,trajectory_utilities,surface_alg,file_utilities
except:
print 'could not import at least one of the modules nedded: ost, time, numpy, os, math, entity_alg,trajectory_utilities,surface_alg,file_utilities'
__all__=['AnalyzeMolecularOrderParameters',"CalculateMolecularOrderParameters"]
def _OrderParameter(v1,v2):
a=geom.Angle(v1,v2)
return 0.5*(3.*math.cos(a)**2.0-1)
def CalculateDeuteriumOrderParameter(res,aname1,aname2,n):
"""
This function calculates the deutirium order parameter as the angle between
the bond between two atoms and a vector, typically the membrane normal.
:param res: the residue
:param aname1: First atom name
:param aname2: Second atom name
:param n: Typically the membrane normal
:type res: :class:`~ost.mol.ResidueHandle`
:type aname1: :class:`str`
:type aname2: :class:`str`
:type n: :class:`~ost.geom.Vec3`
"""
a1=res.FindAtom(aname1)
a2=res.FindAtom(aname2)
if not (a1.IsValid() and a2.IsValid()):return
v1=a1.pos-a2.pos
return _OrderParameter(v1,n)
def CalculateMolecularOrderParameter(res,aname1,aname2,aname3):
"""
This function calculates the order parameter for 3 atoms, it is calculated
from the angle between the director vectors between two successive pairs of atoms.
:param res: the residue
:param aname1: First atom name
:param aname2: Second atom name
:param aname3: Third atom name
:type res: :class:`~ost.mol.ResidueHandle`
:type aname1: :class:`str`
:type aname2: :class:`str`
:type aname3: :class:`str`
"""
a1=res.FindAtom(aname1)
a2=res.FindAtom(aname2)
a3=res.FindAtom(aname3)
if not (a1.IsValid() and a2.IsValid() and a3.IsValid()):return
v1=a1.pos-a2.pos
v2=a2.pos-a3.pos
return _OrderParameter(v1,v2)
def CalculateDeuteriumOrderParameters(res,aname_pairs_list,n):
"""
This function calculates the deuterium order parameter for each pair of atoms
for a residue. The order parameter is calculated from the angle
between the bond between the two atoms and a reference vector, typically the membrane normal.
:param res: the residue
:param aname_pairs_list: A list of pairs of atom names
:param n: Typically the membrane normal
:type res: :class:`~ost.mol.ResidueHandle`
:type aname_pairs_list: :class:`list`
:type n: :class:`~ost.geom.Vec3`
"""
return [CalculateDeuteriumOrderParameter(res,aname_pair) for aname_pair in aname_pairs]
def CalculateMolecularOrderParameters(res,aname_list):
"""
This function calculates the order parameter for each successive triplet of atoms
for a residue. The order parameter is calculated from the angle
between the director vectors between two successive pairs of atoms.
:param res: the residue
:param aname_list: An ordered list of atom names. An order parameter is calculated for each successive triple of atoms
:type res: :class:`~ost.mol.ResidueHandle`
:type aname_list: :class:`list`
"""
natoms=len(aname_list)
if natoms<3:return
return [CalculateMolecularOrderParameter(res,*aname_list[i:i+3]) for i in range(natoms-2)]
def AnalyzeDeuteriumOrderParameters(t,lipids,aname_pairs_list,n,return_average=True):
"""
This function calculates the deuterium order parameter for each pair of atoms
for each lipid over a trajectory. The order parameter is calculated from the angle
between the bond between the two atoms and a reference vector, typically the membrane normal.
:param t: The trajectory
:param lipids: Selection of the lipids to be analyzed
:param aname_pairs_list: A list of pairs of atom names
:param n: Typically the membrane normal
:type t: :class:`~ost.mol.CoordGroupHandle`
:type lipids: :class:`~ost.mol.EntityView`
:type aname_pairs_list: :class:`list`
:type n: :class:`~ost.geom.Vec3`
"""
order_parameter_list=[]
for aname1,aname2 in aname_pairs_list:
op=FloatList()
for res in lipids.residues:
a1=res.FindAtom(aname1)
a2=res.FindAtom(aname2)
if not (a1.IsValid() and a2.IsValid()):
print res,'is missing one of',aname1,aname2
continue
pl1=mol.alg.AnalyzeAtomPos(t,a1.handle)
pl2=mol.alg.AnalyzeAtomPos(t,a2.handle)
vl1=pl1-pl2
op.extend([_OrderParameter(v1,n) for v1 in vl1])
order_parameter_list.append(op)
if return_average:return FloatList([npy.average(el) for el in order_parameter_list])
else: return order_parameter_list
def AnalyzeMolecularOrderParameters(t,lipids,aname_list,return_average=True):
"""
This function calculates the order parameter for each successive triplet of atoms
for each lipid over a trajectory. The order parameter is calculated from the angle
between the director vectors between two successive pairs of atoms.
:param t: The trajectory
:param lipids: Selection of the lipids to be analyzed
:param aname_list: An ordered list of atom names. An order parameter is calculated for each successive triple of atoms
:type t: :class:`~ost.mol.CoordGroupHandle`
:type lipids: :class:`~ost.mol.EntityView`
:type aname_list: :class:`list`
"""
atom_triplet_list=[]
order_parameter_list=[]
natoms=len(aname_list)
if natoms<3:return
for i in range(natoms-2):
[aname1,aname2,aname3]=aname_list[i:i+3]
atom_triplet_list.append([aname1,aname2,aname3])
op=FloatList()
for res in lipids.residues:
a1=res.FindAtom(aname1)
a2=res.FindAtom(aname2)
a3=res.FindAtom(aname3)
if not (a1.IsValid() and a2.IsValid() and a3.IsValid()):
print res,'is missing one of',aname1,aname2,aname3
continue
pl1=mol.alg.AnalyzeAtomPos(t,a1.handle)
pl2=mol.alg.AnalyzeAtomPos(t,a2.handle)
pl3=mol.alg.AnalyzeAtomPos(t,a3.handle)
vl1=pl1-pl2
vl2=pl2-pl3
op.extend([_OrderParameter(v1,v2) for v1,v2 in zip(vl1,vl2)])
order_parameter_list.append(op)
if return_average:return atom_triplet_list,FloatList([npy.average(el) for el in order_parameter_list])
else: return atom_triplet_list,order_parameter_list