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Classes for representing biological macromolecules.
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StructureError Base class of errors raised by Structure objects. |
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ModelOverwrite Raised by Structure.add_model() when a Model added to a Structure has the same model_id of a Model already in the Structure. |
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ChainOverwrite Raised by Structure.add_chain() or by Model.add_chain() when a Chain added to a Structure has the same chain_id of a Chain already in the Structure. |
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FragmentOverwrite Raised by Chain.add_fragment() when a Fragment added to a Chain has the same fragment_id as a Fragment already in the Chain. |
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AtomOverwrite Raised by Structure.add_atom() or Fragment.add_atom() when an Atom added to a Structure or Fragment has the same chain_id, fragment_id, name, and alt_loc as an Atom already in the Structure or Fragment. |
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Structure The Structure object is the parent container object for the entire macromolecular data structure. |
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Model Multiple models support. |
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Segment Segment objects are a container for Fragment objects, but are disassociated with the Structure object hierarch. |
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Chain Chain objects contain an ordered list of Fragment objects. |
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Fragment Fragment objects are a basic unit for organizing small groups of Atoms. |
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Residue A subclass of Fragment representing one residue in a polymer chain. |
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AminoAcidResidue A subclass of Residue representing one amino acid residue in a polypeptide chain. |
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NucleicAcidResidue A subclass of Residue representing one nuclic acid in a strand of DNA or RNA. |
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Altloc Container holding the same atom, but for different conformations and occupancies. |
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Atom Class representing a single atom. |
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Bond Indicates two atoms are bonded together. |
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AlphaHelix Class containing information on a protein alpha helix. |
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Strand One strand of a BetaSheet. |
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BetaSheet Class containing information on a protein beta sheet. |
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Site List of Fragments within a structure involved in a SITE description. |
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FragmentID Stores a fragment_id as integer residue sequence number and a single-character insertion code. |
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AtomList Provides the functionality of a Python list class for containing Atom instances. |
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