columnarStructureX.py
Inheritance class of ColumnarStructure
ColumnarStructureX(structure, firstModelOnly=True)[source]¶Bases: mmtfPyspark.utils.columnarStructure.ColumnarStructure
Inheritance of class ColumnarStructure with additional functions
Attributes
| structure | (mmtfStructure)) mmtf structure |
| firstModelOnly | (bool) flag to use only the first model of the structure |
Methods
get_alt_loc_list() |
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get_atom_names() |
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get_atom_to_chain_indices() |
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get_atom_to_group_indices() |
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get_b_factors() |
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get_calpha_atom_indices() |
Get the indices of Calpha atoms |
get_calpha_coordinates() |
Get the coordinates for Calpha atoms |
get_chain_ids() |
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get_chain_names() |
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get_chain_to_atom_indices() |
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get_chain_to_entity_index() |
Returns an array that maps a chain index to an entity index |
get_chain_to_group_indices() |
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get_chem_comp_types() |
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get_clamped_normalized_b_factors() |
Returns a normalized B-factors that are clamped to the [-1,1] interval using the method of Liu et at. |
get_elements() |
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get_entity_indices() |
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get_entity_types() |
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get_group_names() |
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get_group_numbers() |
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get_group_to_atom_indices() |
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get_group_types() |
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get_indices() |
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get_normalized_b_factors() |
Returns z-scores for B-factors (normalized B-factors). |
get_num_atoms() |
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get_num_chains() |
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get_num_groups() |
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get_num_models() |
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get_occupancies() |
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get_sequence_positions() |
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get_x_coords() |
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get_y_coords() |
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get_z_coords() |
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is_polymer() |
get_clamped_normalized_b_factors()[source]¶Returns a normalized B-factors that are clamped to the [-1,1] interval using the method of Liu et at. B-factors are normalized and scaled the 90% Confidenceinterval of the B-factors to [-1,1]. Any value outside of the 90% confidence interval is set to either -1 or 1, whichever is closer.
References