RNADiscrepancy.utilities
Module Contents
Functions
From a list of atoms with their properties, and right nucleotide name, will build the Nucleotide object |
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From a cif file will extract all pairs [(chain1, position1), (chain2, position2), … (chainZ, positionZ)] (chainX, positionX) must both be strings If the position is a base not annotated in reference, it will return NONE |
API
- RNADiscrepancy.utilities.rawdata2nucleotide(nucleotide_name: str, list_atoms_names: [str], list_atoms_elements: [str], list_positions: [[float, float, float]]) RNADiscrepancy.rna.Nucleotide
From a list of atoms with their properties, and right nucleotide name, will build the Nucleotide object
- Args:
nucleotide_name: A, C, G, U list_atoms_names : [str] list_atoms_elements : [str] list_positions : [[float, float, float]]
- Returns:
rna.Nucleotide
- RNADiscrepancy.utilities.cif2nucleotides(path_cif: str, to_find: [str, str], author_chain: bool = False, author_position: bool = False, add_virtual: bool = True) dict[str, str, RNADiscrepancy.rna.Nucleotide | None]
From a cif file will extract all pairs [(chain1, position1), (chain2, position2), … (chainZ, positionZ)] (chainX, positionX) must both be strings If the position is a base not annotated in reference, it will return NONE
- if author_chain or author_position are set to True:
chain will be checked with author_chain
position will be checked with position + PDB_insertion_code (as one string)
add_virtual will complete the Nucleotide object with virtual atoms fitted from the ideal positions to the ones observed
Returns them in a dictio as rna.Nucleotide objects