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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: main.C,v 1.11 2002/12/12 09:53:11 oliver Exp $
#include <iomanip>
#include "global.h"
#include "reading.h"
#include "assignment.h"
#include <BALL/SYSTEM/timer.h>
#include <BALL/STRUCTURE/numericalSAS.h>
#include <BALL/STRUCTURE/analyticalSES.h>
using namespace BALL;
using namespace std;
void usage()
{
Log.error() << "BALL -- Finite Difference Poisson Solver" << endl
<< endl
<< "PB [<options>]" << endl
<<" where <options> is one or more of the following possibilities:" << endl
<< " -P perform a Finite Difference Poisson calculation" << endl
<< " -A calculate the solvent accessible surface and" << endl
<< " volume of the solute" << endl
<< " -E calculate the solvent excluded surface and" << endl
<< " volume of the solute" << endl
<< endl
<< "further options:" << endl
<< " -p <FILE> read <FILE> as a PDB file" << endl
<< " -h <FILE> read <FILE> as a HyperChem file" << endl
<< " -H <FILE> read <FILE> as a HyperChem file but do not assign" << endl
<< " charges" << endl
<< " -o <FILE> read FDPB options from <FILE>" << endl
<< " -c <FILE> read charges from <FILE>" << endl
<< " -r <FILE> read radii from <FILE>" << endl
<< " -t <FILE> read charge and radius rules from <FILE>" << endl
<< " -u <FILE> read charge rules from <FILE>" << endl
<< " -w <FILE> read radius rules from <FILE>" << endl
<< " -0 clear all charges in subsequently read structures" << endl
<< " -s calculate the solvation free energy by performing a " << endl
<< " second FDPB calculation in vacuum" << endl
<< " -n normalize all atom names in subsequently read" << endl
<< " structures" << endl
<< " -b try to build the bonds (e.g. for PDB files)" << endl
<< " -d <FILE> dump the atom charges, radii, and surface fractions" << endl
<< " to <FILE> (for debugging)" << endl
<< " -v verbose output (implies ``verbosity 99'' in the" << endl
<< " option file, print additional results and options)" << endl
<< " -x <RADIUS> the probe sphere radius for solvent accessible and" << endl
<< " solvent excluded surface calculations" << endl
<< " [default = 1.4 A]" << endl
<< " -e <DIEL_CONST> the dielectric constant of the surrounding medium" << endl
<< " [default = 78.0]" << endl
<< " -f <DIEL_CONST> the dielectric constant of interior of the solute" << endl
<< " [default = 2.0]" << endl
<< " -i <IONIC_STRENGTH> the ionic strength which will be used for the" << endl
<< " Boltzmann part of the Poisson-Boltzmann equation" << endl
<< " [default = 0.0 mol/l, i. e. switched off]" << endl
<< endl
<< " By default, charges and radii are taken from data/charges/PARSE.crg" << endl
<< " and data/radii/PARSE.siz." << endl
<< endl
<< " Charge and radius assignment options can be repeated. They are valid for all" << endl
<< " subsequently read structures." << endl
<< endl;
}
int main(int argc, char** argv)
{
// print usage if no argument was given
if (argc == 1)
{
usage();
return 1;
}
// check all command line options
for (int i = 1; i < argc; i++)
{
// retrieve the current option
String option(argv[i]);
// check for leading "-" and length of argument
if ((option[0] != '-') || (option.size() != 2))
{
// print usage hints and an error message, exit
usage();
Log.error() << "Illegal option: " << option << endl;
return 2;
}
// check for another argument for those
// options requiring a filename (-p -h -c -r -o -u -t -w -d -x)
if (String("phcroutwdxefi").has(option[1]) && (i == (argc - 1)))
{
// pring usage hints, an error message, exit
usage();
Log.error() << "Option " << option << " requires an additional argument." << endl;
return 3;
}
// two temporary variables
float ionic_strength;
float dielectric_medium;
float dielectric_solute;
// interpret all command line options
switch (option[1])
{
// check for the 'main' options (FDPB/SAS/SES)
case 'P':
// perform a FDPB calculation
fdpb_calculation = true;
break;
case 'A':
// perform a SAS calculation
sas_calculation = true;
break;
case 'E':
// perform a SES calculation
ses_calculation = true;
break;
// further options
case 'p': // read a PDB file
readPDBFile(argv[++i]);
break;
case 'h': // read a HyperChem file
readHINFile(argv[++i]);
break;
case 'H': // read a HyperChem file but do not assign chargs
readHINFileNoAssignment(argv[++i]);
break;
case 'o': // read an option file
readOptionFile(argv[++i]);
break;
case 'c': // read a charge file
readChargeFile(argv[++i]);
break;
case 'r': // read a radius file
readRadiusFile(argv[++i]);
break;
case 't': // read a rule file
readRuleFile(argv[++i], CHARGES_AND_RADII);
break;
case 'u': // read a rule file
readRuleFile(argv[++i], CHARGES);
break;
case 'w': // read a rule file
readRuleFile(argv[++i], RADII);
break;
case 's': // calculate solvation energy
calculate_solvation_energy = true;
break;
case 'd': // dump the final results
dump_file = argv[++i];
break;
case 'v': // change verbosity
options[FDPB::Option::VERBOSITY] = 99;
verbose = true;
break;
case '0': // clear charges for next files read
// set the clear charges flag (reset by -c)
clear_charges = true;
break;
case 'n': // normalize names for next files read
// set the normalize names flag
normalize_names = true;
break;
case 'b': // build bonds for next files read
// set the normalize names flag
build_bonds = true;
break;
case 'x': // set the probe sphere radius
probe_radius = atof(argv[++i]);
if (verbose)
{
Log.info() << "probe sphere radius for surface calculations is set to "
<< probe_radius << " Angstrom" << endl;
}
break;
case 'e': // set the dielectric constant of the medium
dielectric_medium = atof(argv[++i]);
options[FDPB::Option::SOLVENT_DC] = dielectric_medium;
if (verbose)
{
Log.info() << "dielectric constant of the medium is set to"
<< dielectric_medium << endl;
}
break;
case 'f': // set the dielectric constant of the solute
dielectric_solute = atof(argv[++i]);
options[FDPB::Option::SOLUTE_DC] = dielectric_solute;
if (verbose)
{
Log.info() << "dielectric constant of the solute is set to"
<< dielectric_solute << endl;
}
break;
case 'i': // set the ionic strength of the medium
ionic_strength = atof(argv[++i]);
options[FDPB::Option::IONIC_STRENGTH] = ionic_strength;
if (verbose)
{
Log.info() << "ionic strength for Boltzmann calculations is set to"
<< ionic_strength << " mol/l" << endl;
}
break;
default: // unknown option
// print usage hints and an error message, exit
usage();
Log.error() << "Illegal option: " << option << endl;
return 2;
}
}
// check whether at least one of the main options
// was given
if (!(fdpb_calculation || ses_calculation || sas_calculation))
{
usage();
Log.error() << "Error: specify at least one of the main options -P, -A, or -E!" << endl;
return 8;
}
// check whether anything was constructed at all
if (S.countAtoms() == 0)
{
usage();
Log.error() << "Error: no atoms given." << endl;
return 6;
}
// setup logging to print the current time in front of each line
Log.setPrefix(cout, "[%T] ");
Log.setPrefix(cerr, "[%T ERROR] ");
// calculate the solvent excluded surface area of the solute
// (used to estimate the non electrostatic contribution
// to the solvation free energy)
if (ses_calculation)
{
total_SES_area = calculateSESArea(S, probe_radius);
total_SES_volume = calculateSESVolume(S, probe_radius);
Log.info() << "Solvent excluded surface : " << total_SES_area << " A^2";
Log.info() << endl;
Log.info() << "Solvent excluded volume : " << total_SES_volume << " A^3";
Log.info() << " (" << probe_radius << " Angstrom probe radius)" << endl;
}
// calculate the solvent accessible surface area of the solute
// (used to estimate the non electrostatic contribution
// to the solvation free energy)
if (sas_calculation)
{
total_SAS_area = calculateSASAtomAreas(S, surface_map, probe_radius);
total_SAS_volume = calculateSASVolume(S, probe_radius);
Log.info() << "Solvent accessible surface : " << total_SAS_area << " A^2";
Log.info() << endl;
Log.info() << "Solvent accessible volume : " << total_SAS_volume << " A^3";
Log.info() << " (" << probe_radius << " Angstrom probe radius)" << endl;
}
// if the option -d was give, dump the positions, charges, and radii to a file
if (dump_file != "")
{
dumpFile();
}
// the part that performs the FDPB calculation
if (fdpb_calculation)
{
// setup the calculation
Timer T;
T.start();
fdpb.setup(S, options);
if (verbose)
{
Log.info() << "FDPB setup CPU time: " << T.getCPUTime() << endl;
}
if (calculate_solvation_energy)
{
Log.info() << "Calculating the solvation free energy." << endl;
Log.info() << "first calculation step: solvent dielectric constant = "
<< fdpb.options[FDPB::Option::SOLVENT_DC] << endl;
}
// solve the PB equation
T.reset();
fdpb.solve();
if (verbose)
{
Log.info() << "FDPB solve CPU time: " << T.getCPUTime() << endl;
// dump the options for documentation purposes
fdpb.options.dump(Log);
}
// print the energies
Log.info() << "total energy: " << fdpb.getEnergy() << " kJ/mol" << endl;
Log.info() << "reaction field energy: " << fdpb.getReactionFieldEnergy() << " kJ/mol" << endl;
if (calculate_solvation_energy)
{
Log.info() << "Calculating the solvation free energy." << endl;
Log.info() << "first calculation step: solvent dielectric constant = "
<< fdpb.options[FDPB::Option::SOLVENT_DC] << endl;
/*
}
T.start();
fdpb.setup(S, options);
if (verbose)
{
Log.info() << "FDPB setup CPU time: " << T.getCPUTime() << endl;
}
if (calculate_solvation_energy)
{
*/
Log.info() << "second calculation step: solvent dielectric constant = 1.0 (vacuum)" << endl;
// store the old energies
double dG = fdpb.getEnergy();
double dG_RF = fdpb.getReactionFieldEnergy();
T.reset();
options[FDPB::Option::SOLVENT_DC] = 1.0;
fdpb.setup(S, options);
if (verbose)
{
Log.info() << "FDPB setup CPU time: " << T.getCPUTime() << endl;
}
// solve the PB equation
T.reset();
fdpb.solve();
if (verbose)
{
Log.info() << "FDPB solve CPU time: " << T.getCPUTime() << endl;
// dump the options for documentation purposes
fdpb.options.dump(Log);
}
// print the energies
Log.info() << "total energy: " << fdpb.getEnergy() << " kJ/mol" << endl;
Log.info() << "reaction field energy: " << fdpb.getReactionFieldEnergy() << " kJ/mol" << endl;
Log.info() << endl;
Log.info() << "Solvation energy as change of the total energy: "
<< dG - fdpb.getEnergy()<< " kJ/mol" << endl;
Log.info() << "Solvation energy as change of the reaction field: "
<< dG_RF - fdpb.getReactionFieldEnergy() << " kJ/mol" << endl;
}
}
// done
return 0;
}
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