- 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
- 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. to download structures).
- 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). This is
eg. useful to superimpose crystal structures. QCP stands for
Quaternion Characteristic Polynomial, which is used in the algorithm.
- 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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