continuousflex.protocols.utilities.genesis_utilities module

class continuousflex.protocols.utilities.genesis_utilities.PDBMol(pdb_file)

Bases: object

add_terminal_res()

alias_atom(atomName, atomNew, resName=None)

alias_res(resName, resNew)

allatoms2ca()

atom_res_reorder()

center()

check_res_order()

copy()

get_chain(chainName)

remove_alter_atom()

remove_hydrogens()

save(file)

Save to PDB Format :param file: pdb file path

select_atoms(idx)

select_chain(chainName)

continuousflex.protocols.utilities.genesis_utilities.alignMol(mol1, mol2, idx=None)

continuousflex.protocols.utilities.genesis_utilities.continuousAssign(inputMeta, inputVol, outputMeta)

Make a continuous angular assignment of angles from a volume :param str inputMeta: File name of input Xmipp metadata file with angles to assign :param str inputVol: File name of the input Volume :param str outputMeta: File name of the output Xmipp metadata file with the angles :return str: the Xmipp command to run

continuousflex.protocols.utilities.genesis_utilities.dcd2numpyArr(filename)

continuousflex.protocols.utilities.genesis_utilities.flipAngles(inputMeta, outputMeta)

Flip angles from Xmipp representation to Euler angles :param str inputMeta : File name of input Xmipp metadata file containing the angles to flip :param str outputMeta: file name of the output Xmipp matadata file :return None:

continuousflex.protocols.utilities.genesis_utilities.generateGROTOP(inputPDB, outputPrefix, forcefield, smog_dir, nucleicChoice)

continuousflex.protocols.utilities.genesis_utilities.generatePSF(inputPDB, inputTopo, outputPrefix, nucleicChoice)

continuousflex.protocols.utilities.genesis_utilities.getAngularShiftDist(angle1MetaFile, angle2MetaData, angle2Idx, tmpPrefix, symmetry)

continuousflex.protocols.utilities.genesis_utilities.getRMSD(mol1, mol2, align=False, idx=None)

continuousflex.protocols.utilities.genesis_utilities.lastPDBFromDCD(inputPDB, inputDCD, outputPDB)

continuousflex.protocols.utilities.genesis_utilities.matchPDBatoms(mols, ca_only=False)

continuousflex.protocols.utilities.genesis_utilities.pdb2vol(inputPDB, outputVol, sampling_rate, image_size)

Create a density volume from a pdb :param str inputPDB: input pdb file name :param str outputVol: output vol file name :param float sampling_rate: Sampling rate :param int image_size: Size of the output volume :return str: the Xmipp command to run

continuousflex.protocols.utilities.genesis_utilities.projectMatch(inputImage, inputProj, outputMeta)

Projection matching of an input experimental image with a set of projections :param str inputImage: File name of the input experimental image :param str inputProj: File name of the input set of projections :param str outputMeta: File name of the output Xmipp metadata file with the angles of the matching :return str: the Xmipp command to run

continuousflex.protocols.utilities.genesis_utilities.projectVol(inputVol, outputProj, expImage, sampling_rate=5.0, angular_distance=- 1, compute_neighbors=True)

Create a set of projections from an input volume :param str inputVol: Input volume file name :param str outputProj: Output set of proj file name :param str expImage: Experimental image to project in the neighborhood :param float sampling_rate: Samplign rate :param float angular_distance: Do not search a distance larger than… :param bool compute_neighbors: Compute projection nearby the experimental image :return str: the Xmipp command to run

continuousflex.protocols.utilities.genesis_utilities.readLogFile(log_file)

continuousflex.protocols.utilities.genesis_utilities.rmsdFromDCD(outputPrefix, inputPDB, targetPDB, idx, align=False)

continuousflex.protocols.utilities.genesis_utilities.runParallelJobs(commands, env=None, numberOfThreads=1, numberOfMpi=1, hostConfig=None)

Run multiple commands in parallel. Wait until all commands returned :param list commands: list of commands to run in parallel :param dict env: Running environement of subprocesses :param numberOfThreads: Number of openMP threads :param numberOfMpi: Number of MPI cores :return None:

continuousflex.protocols.utilities.genesis_utilities.save_dcd(mol, coords_list, prefix)

continuousflex.protocols.utilities.genesis_utilities.waveletAssignement(inputImage, inputProj, outputMeta)

Make a discrete angular assignment of angles from a set of projections :param str inputImage: File name of input experimental image :param str inputProj: File name of the input set of projections :param str outputMeta: File name of the output Xmipp metadata file with the angles assigned :return str: the Xmipp command to run