# **************************************************************************
# *
# * Authors:
# * J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# * Slavica Jonic (slavica.jonic@upmc.fr)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program 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 2 of the License, or
# * (at your option) any later version.
# *
# * This program 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 this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import os
from collections import OrderedDict
from pwem.emlib import (MDL_NMA_MODEFILE, MDL_NMA_COLLECTIVITY, MDL_NMA_SCORE, MDL_NMA_EIGENVAL,
MDL_ORDER)
from pyworkflow.utils import Environ
from pwem.objects import NormalMode
from xmipp3.convert import rowToObject, objectToRow
from xmipp3.constants import NMA_HOME
import numpy as np
import math
MODE_DICT = OrderedDict([
("_modeFile", MDL_NMA_MODEFILE),
("_collectivity", MDL_NMA_COLLECTIVITY),
("_score", MDL_NMA_SCORE),
#("_eigenvalue", MDL_NMA_EIGENVAL),
])
[docs]def rowToMode(row):
""" Set properties of a NormalMode object from a Metadata row. """
mode = NormalMode()
rowToObject(row, mode, MODE_DICT)
mode.setObjId(row.getValue(MDL_ORDER))
return mode
[docs]def modeToRow(mode, row):
""" Write the MetaData row from a given NormalMode object. """
row.setValue(MDL_ORDER, int(mode.getObjId()))
objectToRow(mode, row, MODE_DICT)
[docs]def getNMAEnviron():
""" Create the needed environment for NMA programs. """
from xmipp3 import Plugin
environ = Plugin.getEnviron()
environ.update({'PATH': Plugin.getVar(NMA_HOME)}, position=Environ.BEGIN)
return environ
[docs]def eulerAngles2matrix(alpha, beta, gamma, shiftx, shifty, shiftz):
A = np.empty([4,4])
A.fill(2)
A[3,3] = 1
A[3,0:3] = 0
A[0,3] = float(shiftx)
A[1,3] = float(shifty)
A[2,3] = float(shiftz)
alpha = float(alpha)
beta = float(beta)
gamma = float(gamma)
sa = np.sin(np.deg2rad(alpha))
ca = np.cos(np.deg2rad(alpha))
sb = np.sin(np.deg2rad(beta))
cb = np.cos(np.deg2rad(beta))
sg = np.sin(np.deg2rad(gamma))
cg = np.cos(np.deg2rad(gamma))
cc = cb * ca
cs = cb * sa
sc = sb * ca
ss = sb * sa
A[0,0] = cg * cc - sg * sa
A[0,1] = cg * cs + sg * ca
A[0,2] = -cg * sb
A[1,0] = -sg * cc - cg * sa
A[1,1] = -sg * cs + cg * ca
A[1,2] = sg * sb
A[2,0] = sc
A[2,1] = ss
A[2,2] = cb
return A
[docs]def matrix2eulerAngles(A):
abs_sb = np.sqrt(A[0, 2] * A[0, 2] + A[1, 2] * A[1, 2])
if (abs_sb > 16*np.exp(-5)):
gamma = math.atan2(A[1, 2], -A[0, 2])
alpha = math.atan2(A[2, 1], A[2, 0])
if (abs(np.sin(gamma)) < np.exp(-5)):
sign_sb = np.sign(-A[0, 2] / np.cos(gamma))
else:
if np.sin(gamma) > 0:
sign_sb = np.sign(A[1, 2])
else:
sign_sb = -np.sign(A[1, 2])
beta = math.atan2(sign_sb * abs_sb, A[2, 2])
else:
if (np.sign(A[2, 2]) > 0):
alpha = 0
beta = 0
gamma = math.atan2(-A[1, 0], A[0, 0])
else:
alpha = 0
beta = np.pi
gamma = math.atan2(A[1, 0], -A[0, 0])
gamma = np.rad2deg(gamma)
beta = np.rad2deg(beta)
alpha = np.rad2deg(alpha)
return alpha, beta, gamma, A[0,3], A[1,3], A[2,3]
[docs]def l2(Vec1, Vec2):
Vec1 = np.array(Vec1)
Vec2 = np.array(Vec2)
value = np.inner(Vec1-Vec2, Vec1-Vec2)
return np.sqrt(value)