Module to skim the PDB for similar unit cells
LatticeSearch
(lattice_db_fname, model_dir)[source]¶Bases: object
A class to do a search for PDB entries with similar unit cell dimensions
calculate_niggli_cell
(unit_cell, space_group)[source]¶Calculate the parameters of the Niggli cell
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Returns: | The Niggli cell parameters |
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calculate_penalty
(query, reference)[source]¶Calculate the linear cell variation between unit cells
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calculate_probability
(penalty_score)[source]¶Calculate the probability that a penalty score will give a solution
Parameters: | penalty_score (float) – The total penalty score calculate for a search result |
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Returns: | Probability score |
Return type: | float |
calculate_volume_difference
(query, reference)[source]¶Calculate the difference in volume between the query unit cell and the reference unit cell
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Returns: | The absolute difference in cell volumes |
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cell_within_tolerance
(query, reference, tolerance)[source]¶Compare two cells and determine if query
is within reference
cell parameter tolerance
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copy_results
(source, destination)[source]¶Copy the results from a local copy of the PDB
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download_results
(destination)[source]¶Download the results directly from the PDB
Parameters: | destination (str) – The path to save results to |
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lattice_db_fname
¶The path to the lattice database
model_dir
¶The path to the model directory
pdb_in_results
(pdb_code, results)[source]¶Check to see if a pdb_code has already been appended to the results
search
(space_group, unit_cell, tolerance=0.05, max_to_keep=50, max_penalty=12)[source]¶Search for similar Niggli cells
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