Source code for relion.protocols.protocol_export_coords

# **************************************************************************
# *
# * Authors:     Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology, MRC-LMB
# *
# * 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 3 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

import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pyworkflow.constants import VERSION_3_0

import relion.convert as convert
from .protocol_base import ProtRelionBase


[docs]class ProtRelionExportCoordinates(ProtRelionBase): """ Export coordinates from Relion to be used outside Scipion. """ _lastUpdateVersion = VERSION_3_0 _label = 'export coordinates' # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputCoordinates', params.PointerParam, pointerClass='SetOfCoordinates', important=True, label="Input coordinates", help='Select the SetOfCoordinates ') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): objId = self.inputCoordinates.get().getObjId() self._insertFunctionStep("exportCoordsStep", objId) # --------------------------- STEPS functions -----------------------------
[docs] def exportCoordsStep(self, coordsId): """ Create the input file in STAR format as expected by Relion. If the input particles comes from Relion, just link the file. """ pwutils.cleanPath(self._getExportPath()) pwutils.makePath(self._getExportPath()) convert.writeSetOfCoordinates(self._getExportPath(), self.getCoords(), self._getMicPos)
# --------------------------- INFO functions ------------------------------ def _validate(self): validateMsgs = [] return validateMsgs def _summary(self): summary = [] summary.append("Output is written to: \n%s\n" % os.path.abspath(self._getExportPath())) return summary # --------------------------- UTILS functions ----------------------------- def _getMicPos(self, mic): fileName = pwutils.removeBaseExt(mic.getFileName()) + "_coords.star" return fileName
[docs] def getCoords(self): return self.inputCoordinates.get()
def _getExportPath(self, *paths): return os.path.join(self._getPath('Export'), *paths)