forcefield.py 文件源码

python
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项目:Moleidoscope 作者: kbsezginel 项目源码 文件源码
def read_ff_parameters(excel_file_path=ff_par, ff_selection='uff'):
    """
    Read force field parameters from an excel file according to force field selection
    """
    # Read Excel File
    force_field_data = xlrd.open_workbook(excel_file_path)
    # Read columns to acquire force field parameters
    atom_names = force_field_data.sheets()[0].col_values(0)[2:]
    uff_sigma = force_field_data.sheets()[0].col_values(1)[2:]
    uff_epsilon = force_field_data.sheets()[0].col_values(2)[2:]
    dre_sigma = force_field_data.sheets()[0].col_values(3)[2:]
    dre_epsilon = force_field_data.sheets()[0].col_values(4)[2:]

    uff = {'atom': atom_names, 'sigma': uff_sigma, 'epsilon': uff_epsilon}
    dre = {'atom': atom_names, 'sigma': dre_sigma, 'epsilon': dre_epsilon}

    if ff_selection == 'uff':
        return uff
    if ff_selection == 'dre':
        return dre
    else:
        print('No such force field')
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