README

This is my directory for python/bash script development:

Inventory with description (Almost guaranteed to be out of date)

2Dbinning.py -f <data_file> -o <output_file> {-bins <NUMxNUM>} {-binrange <NUM-NUM> <NUM-NUM>} 
   This script will take a data file with 2 columns and bin that data. Do not put any whitespace
   inside NUMxNUM or NUM-NUM. The bin number will be chosen based on the standard deviation and
   the binrange will be chosen based on the range of your data.
   Witten in python by Jason

AA_decomp.py <prmtop>
   This script will break down the composition of amino acids in a given topology file.
   It may be extended to prmtops later if the need arises. It returns the number of each
   kind of amino acid, and it recognizes all names for each residue AMBER uses.
   Written in Python by Jason

analyzeConvergence.py <mdout> <mdcrd> <prmtop> {<gnuplot_script_prefix>}
   This script will take an mdout and mdcrd file and create gnuplot scripts to graph the various
   metrics of an equilibrated system (i.e. total energy, volume, pressure, density, RMS)
   Written in python by Jason

AvgCol.py <file1> <file2> <file3> ... <file n> <column>
   This script calculates the average of the specified column across all files.
   Written in python by Jason

calcpka.f90 <cpin> <cpout1> <cpout2> ... <cpoutN> -o <output_file> -t <dump_interval> -ao <dump_file>
   Does the same thing as calcpka.pl, but does it much faster and also dumps out
   cumulative and "chunk" pKa values for a given time interval.
   Written in Fortran90 by Jason

checkCharges.py cpin1 cpin2
   This script checks to make sure that the charge arrays between 2 cpins are the same.
   Written in python by Jason

cntrl.py
   Object with dictionary of cntrl namelists for sander and pmemd pre-loaded with defaults. For use
   with mdin.py.
   Written in Python by Jason and Ben

cpinutil.py -p <prmtop> -igb <2 or 5> -resname <resname list> -notresname <resname list>           \
            -resnum <residue numbers> -notresnum <residue numbers> -minpKa <value> -maxpKa <value> \
            -states <list of states> -system <system name> {--ignore-warnings}
   This script will take a prmtop and igb value and it will create a CPIN file for use with
   sander's constant pH implementation with the given options.
   Written in python by Jason

energyvectors.sh
   This script will print out all of the energy "vectors" in a given run of MMPBSA.py. Edit the head
   of the file to add further flexibility to the script.
   Written in sh by Jason

ewald.py
   Object with dictionary of ewald namelist variables for sander and pmemd pre-loaded with defaults.
   For use with mdin.py
   Written in Python by Jason and Ben

FindSaltbridge.py -p <prmtop> -y <mdcrd1> <mdcrd2> ... -o <output_list>
   This script will locate salt bridges in a (set of) trajectory/ies.  It will print an
   output file that has the salt bridges that are more than 25% populated (along with the
   fraction population).
   Written in python by Jason

gaussjobs.py <gaussian_input> {<job_name>}
   This is a python script that will automatically submit a job according to ~/.pbsdefaults
   to the queue.  It should work for any system with a .pbsdefaults set up.
   Written in python by Jason

GetEnergy.py -igb <igb> -pka <pka> -resname <residue_name> -maxcyc <number_iterations> \
             -ns <nano-s of simulation per rep> -cpin <cpin name> -reps <repetitions>
   This script will tweak the statene values until a 50/50 protonation population is 
   reached, and it will return the final state energy and population.
   Written in python by Jason

getResidue.py <prmtop> <atom #>
   Returns which residue the given atom number is in in a given prmtop file.
   Written in Python by Jason.

gnuplotnxy.py <datafile> {<script to write>}
   This script very quickly makes a gnuplot script that will graph data in a file
   exactly the same way that using the command 'xmgrace -nxy' would.
   Written in python by Jason

heatmap.py [-b NUM | --binsize=NUM] [-e | --free-energy] [-t NUM | --temperature=NUM]
   [--no-normalise] [--x-tick-spacing=NUM] [--x-max=NUM] [--x-min=NUM] [--x-label=STRING]
   [--y-tick-spacing=NUM] [--y-max=NUM] [--y-min=NUM] [--y-label=STRING] <data_file>
   This script will bin data containing two equally long columns of integer or floating-
   point numbers, and plot the resulting histogram using matplotlib. Optionally, a free
   energy plot (instead of a frequency plot) can be generated using the -e option. If this
   is done, a temperature must also be provided using the -t option.
   Written in python by Ben

integrateRama.py -i <Ramachandran_datafile> -phi <NxN> -psi <NxN>
   This script will integrate a Ramachandran data file inside the defined range and return
   just that number. It should be used with phipsigen.py.
   Written in python by Jason

Integrate_Trap.py <data_file>
   This script calculates the integral numerically using the trapezoid approximation for a data file.
   Written in python by Jason

makeParm.py <options>
   This script will create a prmtop and topology file based on the options passed on the command
   line. It currently will take PDB files as inputs.
   Written in python by Jason

mass.py <prmtop>
   This script calculates the total mass of all atoms in a given prmtop.
   Written in python by Jason

maxmin.py -f <file> -n <column>
   This script will take a data file and will return the maximum and minimum of the data file
   corresponding to the given column (which defaults to 1)
   Written in python by Jason

mdin.py
   This is a python object that calls objects for each of the input namelists.  It aids in the
   setting of variables, checking of parameters, and writing of amber input files.
   Written in Python by Jason and Ben

natom.py <prmtop>
   Returns the number of atoms defined by a prmtop file.
   Written in python by Jason (NOTE: Hard link of nres.py)

nres.py <prmtop>
   Returns the number of residues defined by a prmtop file.
   Written in python by Jason (NOTE: Hard link of natom.py)

pbsjob.py
   This is a python module that contains the PBSjob class.  This is designed to make job 
   submissions on PBS systems easier.  The pbsjob.README file has more information about
   this module.
   Writen in python by Jason

phipsigen.py -i <inputfile> -o <output_prefix> -p <prmtop> -y <mdcrd1> <mdcrd2> ... <mdcrdN> {-nobin} -gnuplot (DEFAULT) || -origin
   This script will create Ramachandran plot files for specified residues in data files
   suitable for viewing and creating graphs in gnuplot.
   Written in Python by Jason.

pkachunks.py <interval> <prefix> <cpin> <cpout1> <cpout2> ... <cpoutN>
   This script will dump pKas as a function of time in chunks based on interval.  It will truncate
   the "chunks" at each <interval> full record. The prefix will be the base of each file name, and
   the suffix will be the number of the chunk.

readparm.py
   This is a python module that contains the amberParm class.  This allows you to instantiate
   a prmtop object, modify the data, and rewrite a new topology file.  It currently only has 
   writeParm() that's typically called outside (rdparm is called upon instantiation).  This 
   will be built on later, but you can still alter the data and write a new topology file.
   Written in python by Jason

redjobs.py {<job_name>}
   This is a python script that will automatically submit a job according to ~/.pbsdefaults
   to the queue for RED.  It should work for any system with a .pbsdefaults set up.
   Written in python by Jason

_sasa_res.tcl
   This script will, when loaded into VMD, calculate SASAs for each residue in a protein. The usage is
   explained inside the script itself. usage: getAllResSASA "selection" probe_radius <startframe <endframe>>
   First, source it in the VMD tclsh, then use the command above where "selection" is a VMD selection
   you would otherwise choose.
   Written in tcl by Lubos Vrbka (Taken from VMD mailing list archives)

scan.sh
   This script must be edited for your specific system, but it takes a prmtop
   and inpcrd and 4 atoms that define a dihedral and produces a potential energy
   profile for that dihedral using sander. Result file is profile.dat
   Written in bash by Jason

SMDprep.sh
   This script prepares a bunch of files (sander jar output) to be used by the
   jarzynski program. Read the header for a description of use.
   Written in bash by Jason

SMD_to_FE.f90
   This program asks simple questions about your system and takes a file prepared
   by SMDprep.sh and calculates a free energy profile from them.
   Written in Fortran90 (need ifort or gfortran to compile) by Jason.

splitNMR_PDB.py <PDB>
   This script will split an NMR structure that has many models into separate, numbered PDBs with the
   same name in the same directory.  One PDB for each model.  I don't know how general it is, but it
   worked well for the one file I threw it at (and designed it for).
   Written in Python by Jason

sum.py <file1> <file2> <file3> ... <file n> <column>
   This script calculates the sum of the specified column across all files.
   Written in python by Jason

utilities.py
   This is the accompanying python script for just about every python script in
   here perhaps.  Hopefully an inventory of its functions has been kept up-to-
   date in its description. Feel free to add to it.
   Written in python (primarily thus far) by Jason

validateCpinData.py
   This utility imports cpin_data.py and checks through all of the defined residues for consistency.
   It checks, among other things, that each state for each residue has integral charge (the residual charge
   can't be greater than or equal to 0.0001, which is the full precision that is set in cpin_data),
   and that the difference between the charge and the proton count is constant for each state in a
   given residue (i.e., adding a proton increases the net charge by 1).  It alerts the user to any
   problem it finds.  It takes no arguments.
   Written in Python by Jason

mdout.py
   This utility supplies the AmberMdout class and MdoutError class (for when exceptions are
   raised during the course of mdout parsing). It exposes all of the data _except_ decomp
   data and A V E R A G E S / R M S  F L U C T U A T I O N S (which is really only applicable
   if ntave != 0, but these sections are just skipped). Data are available in numpy arrays
   referenced by

   mdout_object.data['DATA KEY']

   where 'DATA KEY' is the energy term in front of the '=' on each line. So for instance, common
   keys will be "EPtot", "VDWAALS", and "1-4 EEL".  Spaces between words in the terms are
   preserved (but there are no spaces before or after the words).

   To concatenate mdout files, use IN PLACE ADDITION ONLY (regular addition will NOT give you
   this desired effect).  That is, use 
   
   mdout_object += AmberMdout('next.mdout')

   Regular addition has no defined behavior (nor does subtraction or in-place subtraction)
   Written in Python by Jason Swails

collect_pH_stats.py
   This utility will analyze the output of calcpka (and calcpka.pl, I think) and it will arrange
   the desired data in a CSV file easily imported into a spreadsheet.

   Written in Python by Jason