dx_analysis.config

# ----------------------------------------
# PARAMETERS
# ----------------------------------------
output_directory = 'example_dx_results'
dx_output_file_name = 'solvent.dx'	# output filename for the 3D histogram of atom_selection positions

# MODULE FILES TO BE READ IN
visualization_functions_file = 'visualization_functions.py'

selection = 'resname HOH'	# String value; specifies your node definition

pdb_list = [['structures/3MJ5_chain_B_aligned_6WX4.pdb', 1.0], ['structures/6XA9_chain_E_aligned_6WX4.pdb', 1.0], ['structures/5KO3_aligned_6WX4.pdb', 1.0], ['structures/6WUU_chain_C_aligned_6WX4.pdb', 1.0], ['structures/6W9C_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6XG3_aligned_6WX4.pdb', 1.0], ['structures/5TL7_chain_B_aligned_6WX4.pdb', 1.0], ['structures/7JIV_aligned_6WX4.pdb', 1.0], ['structures/6XAA_chain_A_aligned_6WX4.pdb', 1.0], ['structures/2FE8_chain_A_aligned_6WX4.pdb', 1.0], ['structures/4REZ_aligned_6WX4.pdb', 1.0], ['structures/3E9S_aligned_6WX4.pdb', 1.0], ['structures/5WFI_chain_B_aligned_6WX4.pdb', 1.0], ['structures/5W8U_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6WRH_aligned_6WX4.pdb', 1.0], ['structures/6XA9_chain_C_aligned_6WX4.pdb', 1.0], ['structures/4RNA_aligned_6WX4.pdb', 1.0], ['structures/6BI8_chain_B_aligned_6WX4.pdb', 1.0], ['structures/7JIW_aligned_6WX4.pdb', 1.0], ['structures/5Y3Q_aligned_6WX4.pdb', 1.0], ['structures/2FE8_chain_C_aligned_6WX4.pdb', 1.0], ['structures/6WZU_aligned_6WX4.pdb', 1.0], ['structures/5W8U_chain_C_aligned_6WX4.pdb', 1.0], ['structures/4OVZ_chain_A_aligned_6WX4.pdb', 1.0], ['structures/7JIR_aligned_6WX4.pdb', 1.0], ['structures/6WUU_chain_B_aligned_6WX4.pdb', 1.0], ['structures/4OW0_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6XA9_chain_A_aligned_6WX4.pdb', 1.0], ['structures/5Y3E_aligned_6WX4.pdb', 1.0], ['structures/4WUR_chain_A_aligned_6WX4.pdb', 1.0], ['structures/4MM3_chain_B_aligned_6WX4.pdb', 1.0], ['structures/4R3D_chain_B_aligned_6WX4.pdb', 1.0], ['structures/4OW0_chain_B_aligned_6WX4.pdb', 1.0], ['structures/5TL6_chain_D_aligned_6WX4.pdb', 1.0], ['structures/5W8T_chain_C_aligned_6WX4.pdb', 1.0], ['structures/7JN2_aligned_6WX4.pdb', 1.0], ['structures/4YPT_aligned_6WX4.pdb', 1.0], ['structures/5V69_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6W9C_chain_B_aligned_6WX4.pdb', 1.0], ['structures/5V6A_chain_A_aligned_6WX4.pdb', 1.0], ['structures/5E6J_chain_D_aligned_6WX4.pdb', 1.0], ['structures/4RF0_chain_A_aligned_6WX4.pdb', 1.0], ['structures/4P16_aligned_6WX4.pdb', 1.0], ['structures/5TL6_chain_B_aligned_6WX4.pdb', 1.0], ['structures/5W8T_chain_A_aligned_6WX4.pdb', 1.0], ['structures/5WFI_chain_A_aligned_6WX4.pdb', 1.0], ['structures/5E6J_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6WUU_chain_A_aligned_6WX4.pdb', 1.0], ['structures/3MJ5_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6WX4_chain_D_aligned_6WX4.pdb', 1.0], ['structures/7JIT_aligned_6WX4.pdb', 1.0], ['structures/2FE8_chain_B_aligned_6WX4.pdb', 1.0], ['structures/6W9C_chain_C_aligned_6WX4.pdb', 1.0], ['structures/6YVA_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6BI8_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6WUU_chain_D_aligned_6WX4.pdb', 1.0], ['structures/4R3D_chain_A_aligned_6WX4.pdb', 1.0], ['structures/4RF1_chain_A_aligned_6WX4.pdb', 1.0], ['structures/6L5T_aligned_6WX4.pdb', 1.0], ['structures/4PT5_aligned_6WX4.pdb', 1.0], ['structures/5TL7_chain_D_aligned_6WX4.pdb', 1.0]]	# list of lists where each element is ['path/to/pdb/file.pdb',float of structure's weight]

# ----------------------------------------
# OPTIONAL PARAMETERS:
# ----------------------------------------
# dx parameter
dx_delta = 1.25	# units: Angstrom; 3D histogram cubic bin dimension

# BOOLEANS
summary_boolean = True		# Boolean value; if True, the script will print out a summary file that breaks down the parameters used in the analysis and how to rerun the same analysis
other_cv = True			# Boolean value; if True, the script will analyze a different, user-defined variable associated with the same atom_selection made above; will output a dx file associated with that parameter.

user_functions_file = 'user_defined_functions.py'	# function file that contains the function used to analyze the structures and outputs the cv results.

cv_type = 'b_factor'
cv_file_name = 'solvent_b_factor_average.dx'