Test whether the pdbid has electron density maps by querying if the PDBe API has electron density statistics.Ĭlass pdb_eda.densityAnalysis. Parameters:īool whether the operation was successful. Removes PDB entry, ccp4, and mmcif files associated with a PDB id. ccp4DiffDensityFile ( str, io.IOBase, optional) – ccp4 difference density file.ccp4DensityFile ( str, io.IOBase, optional) – ccp4 density file.pdbFile ( str, io.IOBase) – PDB entry file.fromFile ( pdbFile, ccp4DensityFile=None, ccp4DiffDensityFile=None ) ¶Ĭreates pdb_ object given the appropriate PDB and CCP4 files. mmcif ( bool) – Whether to download the mmCif file, defaults to False.downloadFile ( bool) – Whether to save the downloaded ccp4 density, ccp4 difference density, and PDB file, defaults to True.pdbi ( bool) – Whether to generate in default of PDB object, defaults to True.pdbbio ( bool) – Whether to generate in default of bio.PDB object, defaults to True.ccp4diff ( bool) – Whether to generate in default of ccp4 difference density object, defaults to True.ccp4density ( bool) – Whether to generate ccp4 density object, defaults to True.fromPDBid ( pdbid, ccp4density=True, ccp4diff=True, pdbbio=True, pdbi=True, downloadFile=True, mmcif=False ) ¶Ĭreates pdb_ object given the PDB id if the id is validĪnd the structure has electron density file available. Loads and assigns global parameters needed for F000 estimation. Params ( dict) – dictionary of parameters needed for pdb_eda calculations. Typically used for optimizing parameters. This module provides methods for the creation of the pdb_eda.densityAnalysis class given a PDB id,Īlong with methods to analyze its 2Fo-Fc and Fo-Fc electron density maps. PDB Electron Density Analysis (pdb_eda.densityAnalysis) ¶
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