pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:
Currently, there are a few issues with reading and writting to the pyMBE dataframe:
We do not directly provide a writing function pmb.write_pmb_df(filename) and instead expect the user to use the native function from pandas pmb_df.to_csv(filename). This creates an asymmetry in the library and makes the writting of the pyMBE_df less intuitive
The function pmb.read_pmb_df(filename) currently reads the pyMBE df but it does not ensure that the quantities stored on it have the same data type as in the original pmb_dataframe. For example, list variables, such as sequence and residue_list become string-like variables when reading the pmb_df from file and need to be parsed. This becomes a source of many issues when one reads the pmb_df and tries to use the rest of pyMBE functions, for example calculate_HH. We need to extend pmb.read_pmb_df(filename) to transform all variables to its original type
Issue migrated from our original remote repository on Gitlab, see here for further discusion on the topic here
Currently, there are a few issues with reading and writting to the pyMBE dataframe:
We do not directly provide a writing function
pmb.write_pmb_df(filename)and instead expect the user to use the native function from pandaspmb_df.to_csv(filename). This creates an asymmetry in the library and makes the writting of the pyMBE_df less intuitiveThe function
pmb.read_pmb_df(filename)currently reads the pyMBE df but it does not ensure that the quantities stored on it have the same data type as in the original pmb_dataframe. For example, list variables, such assequenceandresidue_listbecome string-like variables when reading the pmb_df from file and need to be parsed. This becomes a source of many issues when one reads the pmb_df and tries to use the rest of pyMBE functions, for examplecalculate_HH. We need to extendpmb.read_pmb_df(filename)to transform all variables to its original typeIssue migrated from our original remote repository on Gitlab, see here for further discusion on the topic here