In the file pseudocode is the pseudocode for the lifetime.py script
SCRIPT NAME: lifetime.py
DATA FILES: testfiles.zip
REQUIRED MODULES: the script lifetime.py uses the python 3 modules statistics and argparse
USES OF THE SCRIPT
The script lifetime.py calculates the lifetime for bridging water contacts between protein residues and dna residues (Protres-WAT-Dnares). The script reads contact files of the type bridge_x_y.dat (x=proteinres number; y=dna nucleotide number), where the rows in the files corresponds to frame number, and each fame has either the number 1 (contact is present) or 0 (contact is not present).
To run the script use for example one of:
python3 lifetime.py bridge*.dat --dtime 10 --lib residuelibrary.txt --out lifetimetable.txt
python3 lifetime.py bridge*.dat -dt 10 -l residuelibrary.txt -o lifetimetable.txt
Required inputs:
bridge*.dat: specifies that the script should read all files that start with bridge and ends with the prefix .dat
Optional inputs:
--dtime: converts frame number into time in ps. Default value is 1. If dt=10, then the timeinterval between each frame is 10 ps.
--lib: takes a residuelibrary file that will be used to give the contacts correct names of the type Protres-WAT-Dnares. The file is composed of two columns: col1=residue number (x or y in bridge_x_y.dat) and col2=correct residue name. If this file is not included the contacts mantain the filename as name.
--out: allows one to chose the name of the output.
The script provides a table:
Contactname (name of the contact)
Occupancy % (the fraction of the trajectory where the contact is present)
LifetimeMean (average lifetime in ps)
stdev (standard deviation of the lifetime)
MinVal (min lifetime)
MaxVal (max lifetime)
To test the script one can unzip use the files stored in testfiles.zip (includes bridge_x_y.dat files and residuelibary.txt).