- Bio.PDB.AbstractPropertyMap: Class that maps (chain_id, residue_id) to a residue property.
- Bio.PDB.Atom: Atom class, used in Structure objects.
- Bio.PDB.Chain: Chain class, used in Structure objects.
- Bio.PDB.DSSP
- Bio.PDB.DSSP': Use the DSSP program to calculate secondary structure and accessibility.
- Bio.PDB.Dice
- Bio.PDB.Entity: Base class for Residue, Chain, Model and Structure classes.
- Bio.PDB.FragmentMapper
- Bio.PDB.FragmentMapper': Classify protein backbone structure according to Kolodny et al's fragment
libraries.
- Bio.PDB.HSExposure: Half-sphere exposure and coordination number calculation.
- Bio.PDB.MMCIF2Dict: Turn an mmCIF file into a dictionary.
- Bio.PDB.MMCIFParser
- Bio.PDB.MMCIFParser': mmCIF parsers
- Bio.PDB.Model: Model class, used in Structure objects.
- Bio.PDB.NACCESS: Interface for the program NACCESS.
- Bio.PDB.NeighborSearch: Fast atom neighbor lookup using a KD tree (implemented in C++).
- Bio.PDB.PDBExceptions: Some Bio.PDB-specific exceptions.
- Bio.PDB.PDBIO
- Bio.PDB.PDBIO': Output of PDB files.
- Bio.PDB.PDBList
- Bio.PDB.PDBList': Access the PDB over the internet (e.g.
- Bio.PDB.PDBParser
- Bio.PDB.PDBParser': Parser for PDB files.
- Bio.PDB.PSEA: Wrappers for PSEA, a program for secondary structure assignment.
- Bio.PDB.Polypeptide: Polypeptide-related classes (construction and representation).
- Bio.PDB.QCPSuperimposer: QCPSuperimposer finds the best rotation and translation to put
two point sets on top of each other (minimizing the RMSD).
- Bio.PDB.Residue: Residue class, used by Structure objects.
- Bio.PDB.ResidueDepth
- Bio.PDB.ResidueDepth': Calculation of residue depth using command line tool MSMS.
- Bio.PDB.Selection: Selection of atoms, residues, etc.
- Bio.PDB.Structure: The structure class, representing a macromolecular structure.
- Bio.PDB.StructureAlignment
- Bio.PDB.StructureAlignment': Map the residues of two structures to each other based on a FASTA alignment
file.
- Bio.PDB.StructureBuilder: Consumer class that builds a Structure object.
- Bio.PDB.Superimposer
- Bio.PDB.Superimposer': Superimpose two structures.
- Bio.PDB.Vector
- Bio.PDB.Vector': Vector class, including rotation-related functions.
- Bio.PDB.mmtf
- Bio.PDB.parse_pdb_header
- Bio.PDB.parse_pdb_header': Parse the header of a PDB file.
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