Source code for xmipp3.protocols.protocol_extract_asymmetric_unit
# **************************************************************************
# * Authors: Marta Martinez (mmmtnez@cnb.csic.es)
# *
# * 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 pyworkflow import VERSION_3_0
from pwem.objects import Volume
from pwem.constants import (SYM_DIHEDRAL_X,SCIPION_SYM_NAME)
from pwem.objects import Transform
from pwem.convert import Ccp4Header
from pwem.protocols import EMProtocol
from pyworkflow.protocol.params import (PointerParam, FloatParam,
EnumParam, IntParam, GE)
from xmipp3.constants import (XMIPP_SYM_NAME, XMIPP_TO_SCIPION, XMIPP_CYCLIC,
XMIPP_DIHEDRAL_X, XMIPP_TETRAHEDRAL, XMIPP_OCTAHEDRAL,
XMIPP_I222, XMIPP_I222r, XMIPP_In25, XMIPP_In25r)
DEBUG = True
[docs]class XmippProtExtractUnit(EMProtocol):
""" Generates the necessary files for volumes and Fourier Shell Correlation (FSC) curves to submit structural data to the Electron Microscopy Data Bank (EMDB). This protocol ensures proper formatting and data preparation for public deposition.
"""
_label = 'extract asymmetric unit'
_program = ""
_version = VERSION_3_0
def __init__(self, **kwargs):
EMProtocol.__init__(self, **kwargs)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputVolumes', PointerParam, label="Input Volume",
important=True, pointerClass='Volume',
help='This volume will be cropped')
form.addParam('symmetryGroup', EnumParam,
choices=[XMIPP_SYM_NAME[XMIPP_CYCLIC] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_CYCLIC]] + ")",
XMIPP_SYM_NAME[XMIPP_DIHEDRAL_X] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_DIHEDRAL_X]] + ")",
XMIPP_SYM_NAME[XMIPP_TETRAHEDRAL] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_TETRAHEDRAL]] + ")",
XMIPP_SYM_NAME[XMIPP_OCTAHEDRAL] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_OCTAHEDRAL]] + ")",
XMIPP_SYM_NAME[XMIPP_I222] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_I222]] + ")",
XMIPP_SYM_NAME[XMIPP_I222r] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_I222r]] + ")",
XMIPP_SYM_NAME[XMIPP_In25] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_In25]] + ")",
XMIPP_SYM_NAME[XMIPP_In25r] +
" (" + SCIPION_SYM_NAME[XMIPP_TO_SCIPION[XMIPP_In25r]] + ")"],
default=XMIPP_I222,
label="Symmetry",
help="See https://i2pc.github.io/docs/Utils/Conventions/index.html#symmetry"
"Symmetry for a description of the symmetry groups "
"format in Xmipp.\n"
"If no symmetry is present, use _c1_."
)
form.addParam('symmetryOrder', IntParam, default=1,
condition='symmetryGroup<=%d' % SYM_DIHEDRAL_X,
label='Symmetry Order',
help='Order of cyclic symmetry.')
form.addParam('offset', FloatParam, default=0.,
condition='symmetryGroup<=%d' % SYM_DIHEDRAL_X,
label="offset",
help="rotate unit cell around z-axis by offset degrees")
form.addParam('innerRadius', FloatParam, default=0.0,
label="Inner Radius (px)", validators=[GE(0.0)],
help="inner Mask radius")
form.addParam('outerRadius', FloatParam, default=-1,
label="Outer Radius (px)",
help="outer Mask radius, if -1, the radius will be "
"volume_size/2")
form.addParam('expandFactor', FloatParam, default=0.,
label="Expand Factor",
help="Increment cropped region by this factor")
# --------------------------- INSERT steps functions ----------------------
def _insertAllSteps(self):
self._insertFunctionStep(self.extractUnit)
self._insertFunctionStep(self.createOutputStep)
# --------------------------- STEPS functions -----------------------------
[docs] def extractUnit(self):
sym = self.symmetryGroup.get()
if sym == XMIPP_CYCLIC:
sym = "%s%d" % (XMIPP_SYM_NAME[XMIPP_CYCLIC][:1], self.symmetryOrder)
elif sym == XMIPP_DIHEDRAL_X:
sym = "%s%d" % \
(XMIPP_SYM_NAME[XMIPP_DIHEDRAL_X][:1], self.symmetryOrder)
elif sym == XMIPP_TETRAHEDRAL:
sym = "%s" % XMIPP_SYM_NAME[XMIPP_TETRAHEDRAL]
elif sym == XMIPP_OCTAHEDRAL:
sym = "%s" % XMIPP_SYM_NAME[XMIPP_OCTAHEDRAL]
elif sym >= XMIPP_I222 and sym <= XMIPP_In25r :
sym = XMIPP_SYM_NAME[sym]
inFileName = self.inputVolumes.get().getFileName()
if inFileName.endswith('.mrc'):
inFileName = inFileName + ":mrc"
args = "-i %s -o %s" % \
(inFileName, self._getOutputVol())
args += " --unitcell %s " % sym
args += " %f " % self._getInnerRadius()
args += " %f " % self._getOuterRadius()
args += " %f " % self.expandFactor.get()
args += " %f " % self.offset.get()
sampling = self.inputVolumes.get().getSamplingRate()
args += " %f " % sampling
origin = self.inputVolumes.get().getShiftsFromOrigin()
# x origin coordinate (from Angstroms to pixels)
args += " %f " % (origin[0] / (-1. * sampling))
# y origin coordinate (from Angstroms to pixels)
args += " %f " % (origin[1] / (-1. * sampling))
# z origin coordinate (from Angstroms to pixels)
args += " %f " % (origin[2] / (-1. * sampling))
self.runJob("xmipp_transform_window", args)
[docs] def createOutputStep(self):
vol = Volume()
vol.setLocation(self._getOutputVol())
sampling = self.inputVolumes.get().getSamplingRate()
vol.setSamplingRate(sampling)
#
ccp4header = Ccp4Header(self._getOutputVol(), readHeader=True)
t = Transform()
x, y, z = ccp4header.getOrigin() # origin output vol
# coordinates
t.setShifts(x, y, z)
vol.setOrigin(t)
#
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputVolumes, self.outputVolume)
# --------------------------- INFO functions ------------------------------
def _validate(self):
message = []
return message
def _summary(self):
# message = "Data Available at : *%s*"% self.filesPath.get()
message = ""
return [message]
def _methods(self):
return []
# --------------------------- UTILS functions -----------------------------
def _getInnerRadius(self):
return self.innerRadius.get()
def _getOuterRadius(self):
outerRadius = self.outerRadius.get()
if outerRadius < 0:
volume: Volume = self.inputVolumes.get()
dim = volume.getDimensions()
outerRadius = dim[0] / 2
return outerRadius
def _getOutputVol(self):
prefix = os.path.basename(self.inputVolumes.get().getFileName()).split(".")[0]
return self._getExtraPath(prefix + "_output_volume.mrc")