wepy.util.json_top module

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

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

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

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

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

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

wepy.util.json_top.json_top_atom_count(json_str)[source]

Count the number of atoms in the JSON topology used by wepy HDF5.

Parameters:

json_str (str) – A string of valid JSON in the format of JSON used in WepyHDF5 and mdtraj HDF5 format.

Returns:

n_atoms – Number of atoms in the topology.

Return type:

int

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.

Parameters:

  • json_str (str) – A string of valid JSON in the format of JSON used in WepyHDF5 and mdtraj HDF5 format.

  • atom_idxs (list of int) – The atoms for which you want to make a subset of.

Returns:

subset_json_str – JSON string of the subset of atoms. Ordering preserved.

Return type:

str