Structure#
The structure module represents atomic structures in accordance with the Protein Data Bank (PDB) specification, ensuring standardized handling of molecular data.
Constructor#
Represents atomic structures per the Protein Data Bank (PDB) specification. |
Attributes and underlying data#
Array of record types, e.g., ATOM (n,) |
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Array of serial numbers (n,) |
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Array of atom names (n,) |
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Array of x,y,z atom coordinates (n, d) |
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Array of alternate location indices (n,) |
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Array of residue names (n,) |
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Array of chain identifiers (n,) |
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Array of residue ids (n,) |
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Array of insertion information (n,) |
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Array of occupancy factors (n,) |
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Array of B-factors (n,) |
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Array of segment identifiers (n,) |
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Array of element symbols (n,) |
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Array of charges (n,) |
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Metadata dictionary |
Serialization#
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Writes the |
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Reads an atomic structure file and into a |
Conversion#
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Maps class instance to a volume. |
Subsetting#
Returns a copy of the Structure instance. |
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Return a subset of the structure that contains only atoms belonging to a specific chain. |
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Return a subset of the structure within a specific range of residues. |
Computations#
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Performs a rigid transform of internal structure coordinates. |
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Align |
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Compute root mean square deviation (RMSD) between two structures with the same number of atoms. |
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Calculate the center of mass of the structure. |