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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| dependencies: | ||
| - conda-forge::arpack | ||
| - conda-forge::lapack | ||
| # - conda-forge::openmpi | ||
| # - anaconda::gcc_impl_linux-64=8.4.0 | ||
| # - anaconda::gcc_linux-64=8.4.0 | ||
| # - anaconda::gxx_impl_linux-64=8.4.0 | ||
| # - anaconda::gxx_linux-64=8.4.0 | ||
| # - anaconda::make | ||
| # - gfortran_impl_linux-64=7.5.0 | ||
| - pip | ||
| - python=3.8 | ||
| - pip: | ||
| - umap-learn | ||
| - scipion-em | ||
| - setuptools==63.4.3 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,261 @@ | ||
| # * Authors: Mohamad Harastani (mohamad.harastani@igbmc.fr) | ||
| # * Rémi Vuillemot (remi.vuillemot@upmc.fr) | ||
| # * | ||
| # * IMPMC, UPMC Sorbonne University | ||
| # * | ||
| # * 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 | ||
| import time | ||
|
|
||
| import pwem.emlib.metadata as md | ||
| import pyworkflow.protocol.params as params | ||
| from pwem.protocols import ProtAnalysis3D | ||
| from pyworkflow.protocol.params import NumericRangeParam | ||
| from pyworkflow.utils import getListFromRangeString | ||
| from pyworkflow.utils import replaceExt | ||
| import numpy as np | ||
| from math import cos, sin, pi | ||
| from pwem.objects import AtomStruct | ||
|
|
||
| from continuousflex.protocols.utilities.pdb_handler import ContinuousFlexPDBHandler | ||
|
|
||
| MODE_RELATION_LINEAR = 0 | ||
| MODE_RELATION_3CLUSTERS = 1 | ||
| MODE_RELATION_MESH = 2 | ||
| MODE_RELATION_RANDOM = 3 | ||
| MODE_RELATION_PARABOLA = 4 | ||
|
|
||
|
|
||
| class FlexProtSynthesizePDBs(ProtAnalysis3D): | ||
| """ Protocol for synthesizing flexible PDBs using Normal Mode Analysis. """ | ||
| _label = 'synthesize PDBs' | ||
|
|
||
| # --------------------------- DEFINE param functions -------------------------------------------- | ||
| def _defineParams(self, form): | ||
| form.addSection('Input') | ||
| form.addParam('inputModes', params.PointerParam, | ||
| pointerClass='SetOfNormalModes', | ||
| label="Normal modes", | ||
| help='Set of modes computed by normal mode analysis.') | ||
| form.addParam('modeList', NumericRangeParam, | ||
| label="Modes selection", | ||
| allowsNull=True, | ||
| default='7-8', | ||
| help='Select the normal modes that will be used for PDB synthesis.' | ||
| 'It is usually two modes that should be selected, unless if the relationship is linear or ' | ||
| 'random.\n ' | ||
| 'You have several ways to specify the modes.\n' | ||
| 'Examples:\n' | ||
| ' "7,8-10" -> [7,8,9,10]\n' | ||
| ' "8, 10, 12" -> [8,10,12]\n' | ||
| ' "8 9, 10-12" -> [8,9,10,11,12])\n') | ||
| form.addParam('modeRelationChoice', params.EnumParam, default=MODE_RELATION_LINEAR, | ||
| choices=['Linear relationship', '3 clusters', 'Grid', 'Random', 'Parabolic'], | ||
| label='Relationship between the modes', | ||
| help='linear relationship: all the selected modes will have equal amplitudes. \n' | ||
| '3 clusters: the volumes will be divided exactly into three classes.\n' | ||
| 'Grid: the amplitudes will be in a grid shape (grid size is square of what grid step).\n' | ||
| 'Random: all the amplitudes will be random in the given range.\n' | ||
| 'Parabolic: The relationship between two modes will resembles an upper half circle.') | ||
| form.addParam('centerPoint', params.IntParam, default=100, | ||
| condition='modeRelationChoice==%d' % MODE_RELATION_3CLUSTERS, | ||
| label='Center point', | ||
| help='This number will be used to determine the distance between the clusters' | ||
| 'center1 = (-center_point, 0)' | ||
| 'center2 = (center_point, 0)' | ||
| 'center3 = (0, center_point)') | ||
| form.addParam('modesAmplitudeRange', params.IntParam, default=150, | ||
| allowsNull=True, | ||
| condition='modeRelationChoice != %d' % MODE_RELATION_3CLUSTERS, | ||
| label='Amplitude range N --> [-N, N]', | ||
| help='Choose the number N for which the generated normal mode amplitudes are in the range of' | ||
| ' [-N, N]') | ||
| form.addParam('meshRowPoints', params.IntParam, default=6, | ||
| allowsNull=True, | ||
| condition='modeRelationChoice==%d' % MODE_RELATION_MESH, | ||
| label='Grid number of steps', | ||
| help='This number will be the number of points in the row and the column (grid shape will be ' | ||
| 'size*size)') | ||
| form.addParam('numberOfPDBs', params.IntParam, default=36, | ||
| label='Number of PDBs', | ||
| condition='modeRelationChoice!=%d' % MODE_RELATION_MESH, | ||
| help='Number of atomic structures that will be generated') | ||
| form.addParam('seedOption', params.BooleanParam, default=True, | ||
| expertLevel=params.LEVEL_ADVANCED, | ||
| label='Random seed', | ||
| help='Keeping it as True means that different runs will generate different PDBs in terms ' | ||
| 'of conformations. If you set as False, then different runs will ' | ||
| 'have the same conformations and angles ' | ||
| '(setting to False allows you to generate the same conformations and orientations with ' | ||
| 'different noise values).') | ||
|
|
||
| # form.addParallelSection(threads=0, mpi=8) | ||
| # --------------------------- INSERT steps functions -------------------------------------------- | ||
|
|
||
| def _insertAllSteps(self): | ||
| if self.seedOption.get(): | ||
| np.random.seed(int(time.time())) | ||
| else: | ||
| np.random.seed(0) | ||
| self._insertFunctionStep("generateDeformationsStep") | ||
| self._insertFunctionStep("createOutputStep") | ||
|
|
||
| # --------------------------- STEPS functions -------------------------------------------- | ||
| def generateDeformationsStep(self): | ||
| # Find the right PDB file to use for data synthesis | ||
| pdb_name1 = os.path.dirname(self.inputModes.get().getFileName()) + '/atoms.pdb' | ||
| pdb_name2 = os.path.dirname(self.inputModes.get().getFileName()) + '/pseudoatoms.pdb' | ||
| if os.path.exists(pdb_name1): | ||
| fnPDB = pdb_name1 | ||
| else: | ||
| fnPDB = pdb_name2 | ||
| # use the input relationship between the modes to generate normal mode amplitudes metadata | ||
| fnModeList = replaceExt(self.inputModes.get().getFileName(), 'xmd') | ||
| modeAmplitude = self.modesAmplitudeRange.get() | ||
| meshRowPoints = self.meshRowPoints.get() | ||
| numberOfModes = self.inputModes.get().getSize() | ||
| modeSelection = np.array(getListFromRangeString(self.modeList.get())) | ||
| deformationFile = self._getExtraPath('GroundTruth.xmd') | ||
| pdbMD = md.MetaData() | ||
| # these vairables for alternating the generation when 3 clusters are selected | ||
| cluster1 = cluster2 = cluster3 = False | ||
| # these variables for the generaton of a mesh if selected | ||
| XX, YY = np.meshgrid(np.linspace(start=-modeAmplitude, stop=modeAmplitude, num=meshRowPoints), | ||
| np.linspace(start=modeAmplitude, stop=-modeAmplitude, num=meshRowPoints)) | ||
| mode7_samples = XX.reshape(-1) | ||
| mode8_samples = YY.reshape(-1) | ||
|
|
||
| # iterate over the number of outputs (if mesh, this has to be calculated) | ||
| numberOfPDBs = self.getNumberOfPdbs() | ||
|
|
||
| for i in range(numberOfPDBs): | ||
| deformations = np.zeros(numberOfModes) | ||
|
|
||
| if self.modeRelationChoice == MODE_RELATION_LINEAR: | ||
| amplitude = self.modesAmplitudeRange.get() | ||
| deformations[modeSelection - 1] = np.ones(len(modeSelection)) * np.random.uniform(-amplitude, amplitude) | ||
| elif self.modeRelationChoice == MODE_RELATION_3CLUSTERS: | ||
| center_point = self.centerPoint.get() | ||
| center1 = (-center_point, 0) | ||
| center2 = (center_point, 0) | ||
| center3 = (0, center_point) | ||
| if not (cluster1 or cluster2 or cluster3): | ||
| cluster1 = True | ||
| if cluster3: | ||
| deformations[modeSelection - 1] = center3 | ||
| cluster3 = False | ||
| if cluster2: | ||
| deformations[modeSelection - 1] = center2 | ||
| cluster2 = False | ||
| cluster3 = True | ||
| if cluster1: | ||
| deformations[modeSelection - 1] = center1 | ||
| cluster1 = False | ||
| cluster2 = True | ||
| elif self.modeRelationChoice == MODE_RELATION_RANDOM: | ||
| amplitude = self.modesAmplitudeRange.get() | ||
| deformations[modeSelection - 1] = np.random.uniform(-amplitude, amplitude, len(modeSelection)) | ||
| elif self.modeRelationChoice == MODE_RELATION_PARABOLA: | ||
| amplitude = self.modesAmplitudeRange.get() | ||
| rv = np.random.uniform(0, 1) | ||
| point = (amplitude * cos(rv * pi), amplitude * sin(rv * pi)) | ||
| deformations[modeSelection - 1] = point | ||
|
|
||
| elif self.modeRelationChoice == MODE_RELATION_MESH: | ||
| new_point = (mode7_samples[i], mode8_samples[i]) | ||
| deformations[modeSelection - 1] = new_point | ||
|
|
||
| # we won't keep the first 6 modes | ||
| deformations = deformations[6:] | ||
|
|
||
| self.nma_deform_pdb(fnPDB, fnModeList, self._getExtraPath(str(i + 1).zfill(5) + '_df.pdb'), deformations) | ||
|
|
||
| pdbMD.setValue(md.MDL_IMAGE, self._getExtraPath(str(i + 1).zfill(5) + '_df.pdb'), | ||
| pdbMD.addObject()) | ||
| pdbMD.setValue(md.MDL_NMA, list(deformations), i + 1) | ||
|
|
||
| pdbMD.write(deformationFile) | ||
|
|
||
| def nma_deform_pdb(self, fnPDB, fnModeList, fnOut, deformList): | ||
|
|
||
| def readModes(fnIn): | ||
| modesMD = md.MetaData(fnIn) | ||
| vectors = [] | ||
| for objId in modesMD: | ||
| vecFn = modesMD.getValue(md.MDL_NMA_MODEFILE, objId) | ||
| vec = np.loadtxt(vecFn) | ||
| vectors.append(vec) | ||
| return vectors | ||
|
|
||
| pdb = ContinuousFlexPDBHandler(fnPDB) | ||
| modes = readModes(fnModeList) | ||
| for i in range(len(deformList)): | ||
| pdb.coords += deformList[i] * modes[7 - 1 + i] | ||
| pdb.write_pdb(fnOut) | ||
|
|
||
| def createOutputStep(self): | ||
| pdbset = self._createSetOfPDBs("outputPDBs") | ||
| pdbMD = md.MetaData(self._getExtraPath('GroundTruth.xmd')) | ||
| for objID in pdbMD: | ||
| filename = pdbMD.getValue(md.MDL_IMAGE, objID) | ||
| pdb = AtomStruct(filename=filename) | ||
| pdbset.append(pdb) | ||
|
|
||
| self._defineOutputs(outputPDBs=pdbset) | ||
|
|
||
| def getNumberOfPdbs(self): | ||
| if self.modeRelationChoice.get() is MODE_RELATION_MESH: | ||
| numberOfPDBs = self.meshRowPoints.get() ** 2 | ||
| else: | ||
| numberOfPDBs = self.numberOfPDBs.get() | ||
| return numberOfPDBs | ||
|
|
||
| def getInputPdb(self): | ||
| """ Return the Pdb object associated with the normal modes. """ | ||
| return self.inputModes.get().getPdb() | ||
|
|
||
| # --------------------------- UTILS functions -------------------------------------------- | ||
| def _printWarnings(self, *lines): | ||
| """ Print some warning lines to 'warnings.xmd', | ||
| the function should be called inside the working dir.""" | ||
| fWarn = open("warnings.xmd", 'w') | ||
| for l in lines: | ||
| print >> fWarn, l | ||
| fWarn.close() | ||
|
|
||
| def _getLocalModesFn(self): | ||
| modesFn = self.inputModes.get().getFileName() | ||
| return self._getBasePath(modesFn) | ||
|
|
||
| # --------------------------- INFO functions -------------------------------------------- | ||
| def _summary(self): | ||
| summary = [] | ||
| return summary | ||
|
|
||
| def _validate(self): | ||
| errors = [] | ||
| return errors | ||
|
|
||
| def _citations(self): | ||
| return ['harastani2022continuousflex'] | ||
|
|
||
| def _methods(self): | ||
| pass |