wepy.util.json_top module¶
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wepy.util.json_top.
json_top_chain_fields
(json_topology)[source]¶ Creates a fields dictionary for all of the chains in a topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
chain_cols
- Return type
dict of str: list
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wepy.util.json_top.
json_top_chain_df
(json_topology)[source]¶ Make a pandas dataframe for the chains in the JSON topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
chain_df
- Return type
pandas.DataFrame
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wepy.util.json_top.
json_top_residue_fields
(json_topology)[source]¶ Creates a fields dictionary for all of the residues in a topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
residue_cols
- Return type
dict of str: list
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wepy.util.json_top.
json_top_residue_df
(json_topology)[source]¶ Make a pandas dataframe for the residues in the JSON topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
residue_df
- Return type
pandas.DataFrame
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wepy.util.json_top.
json_top_atom_fields
(json_topology)[source]¶ Creates a fields dictionary for all of the atoms in a topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
atom_cols
- Return type
dict of str: list
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wepy.util.json_top.
json_top_atom_df
(json_topology)[source]¶ Make a pandas dataframe for the atoms in the JSON topology.
- Parameters
json_topology (str) – JSON format topology
- Returns
atoms_df
- Return type
pandas.DataFrame
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wepy.util.json_top.
json_top_atom_count
(json_str)[source]¶ Count the number of atoms in the JSON topology used by wepy HDF5.
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wepy.util.json_top.
json_top_subset
(json_str, atom_idxs)[source]¶ Given a JSON topology and atom indices from that topology returns another JSON topology which is a subset of the first, preserving the topology between remaining atoms. The atoms will be ordered in the order in which the indices are given.