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/*
$Id: printEnergies.cc,v 1.23 2014/06/12 01:44:07 mp Exp $
AutoDock
Copyright (C) 2009 The Scripps Research Institute. All rights reserved.
AutoDock is a Trade Mark of The Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "printEnergies.h"
#include "constants.h"
static inline void print1000(FILE *file, ConstReal x) {
pr(file, ((fabs((x)) >= 0.0) && ((fabs(x)) <= 1000.)) ? "%+7.2f" : "%+11.2e" , (x));
}
static inline void print1000_no_sign(FILE *const file, const double x) {
pr(file, ((fabs((x)) >= 0.01) && ((fabs(x)) <= 1000.)) ? "%7.2f" : "%11.2e" , (x));
}
void print_molar(FILE *const file, const double x) {
// 1e-3 <= x < 1 mM millimolar
// 1e-6 <= x < 1e-3 uM micromolar
// 1e-9 <= x < 1e-6 nM nanomolar
// 1e-12 <= x < 1e-9 pM picomolar
// 1e-15 <= x < 1e-12 fM femtomolar
// 1e-18 <= x < 1e-15 aM attomolar
// 1e-21 <= x < 1e-18 zM zeptomolar
// 1e-24 <= x < 1e-21 yM yottomolar
// x < 1e-24 sub-yottomolar
if ((fabs((x)) > 1e-3) && ((fabs(x)) <= 1.)) {
pr(file, "%7.2f mM (millimolar)", x*1e3);
} else if ((fabs((x)) > 1e-6) && ((fabs(x)) <= 1e-3)) {
pr(file, "%7.2f uM (micromolar)", x*1e6);
} else if ((fabs((x)) > 1e-9) && ((fabs(x)) <= 1e-6)) {
pr(file, "%7.2f nM (nanomolar)", x*1e9);
} else if ((fabs((x)) > 1e-12) && ((fabs(x)) <= 1e-9)) {
pr(file, "%7.2f pM (picomolar)", x*1e12);
} else if ((fabs((x)) > 1e-15) && ((fabs(x)) <= 1e-12)) {
pr(file, "%7.2f fM (femtomolar)", x*1e15);
} else if ((fabs((x)) > 1e-18) && ((fabs(x)) <= 1e-15)) {
pr(file, "%7.2f aM (attomolar)", x*1e18);
} else if ((fabs((x)) > 1e-21) && ((fabs(x)) <= 1e-18)) {
pr(file, "%7.2f zM (zeptomolar)", x*1e21);
} else if ((fabs((x)) > 1e-24) && ((fabs(x)) <= 1e-21)) {
pr(file, "%7.2f yM (yottomolar)", x*1e24);
} else {
pr(file, "%11.2e M (molar)", x);
}
}
void printEnergies( const EnergyBreakdown *const eb,
const char *const prefixString,
const int ligand_is_inhibitor,
ConstReal emap_total,
ConstReal elec_total,
const Boole B_have_flexible_residues,
ConstReal emap_flexres_total,
ConstReal elec_flexres_total,
const Unbound_Model ad4_unbound_model,
int outlev, FILE *logFile
)
{
Real Ki = 1.0;
// equilibrium: E + I <=> EI
// binding: E + I -> EI K(binding), Kb
// dissociation: EI -> E + I K(dissociation), Kd
//
// 1
// K(binding) = ---------------
// K(dissociation)
// so:
// ln K(binding) = -ln K(dissociation)
// ln Kb = -ln Kd
// Ki = dissociation constant of the enzyme-inhibitor complex = Kd
// [E][I]
// Ki = ------
// [EI]
// so:
// ln Kb = -ln Ki
// deltaG(binding) = -R*T*ln Kb
// deltaG(inhibition) = R*T*ln Ki
//
// Binding and Inhibition occur in opposite directions, so we
// lose the minus-sign: deltaG = R*T*lnKi, _not_ -R*T*lnKi
// => deltaG/(R*T) = lnKi
// => Ki = exp(deltaG/(R*T))
if (eb->deltaG < 0.0) {
Ki = exp((eb->deltaG*1000.)/(Rcal*TK));
}
if (strncmp(prefixString, "UNBOUND", 7) != 0 ) {
pr( logFile, "%sEstimated Free Energy of Binding = ", prefixString);
print1000(logFile, eb->deltaG);
pr( logFile, " kcal/mol [=(1)+(2)+(3)-(4)]\n");
if (eb->deltaG < 0.0) {
if (ligand_is_inhibitor == 1) {
pr( logFile, "%sEstimated Inhibition Constant, Ki = ", prefixString);
} else {
pr( logFile, "%sEstimated Dissociation Constant, Kd = ", prefixString);
}
// print1000_no_sign(logFile, Ki);
print_molar(logFile, Ki);
pr( logFile, " [Temperature = %.2f K]\n", TK);
}
pr( logFile, "%s\n", prefixString);
}
// convenience function:
#define item(label, term) pr(logFile, "%s%s", prefixString, label),\
print1000(logFile, term),\
pr(logFile, " kcal/mol\n")
item("(1) Final Intermolecular Energy = ", eb->e_inter);
if(B_have_flexible_residues) {
item(" Moving Ligand-Fixed Receptor = ", eb->e_inter_moving_fixed);
item(" vdW + Hbond + desolv Energy = ", emap_total);
item(" Electrostatic Energy = ", elec_total);
item(" Moving Ligand-Moving Receptor = ", eb->e_inter_moving_moving);
item(" vdW + Hbond + desolv Energy = ", emap_flexres_total);
item(" Electrostatic Energy = ", elec_flexres_total);
} else {
item(" vdW + Hbond + desolv Energy = ", emap_total);
item(" Electrostatic Energy = ", elec_total);
}
item("(2) Final Total Internal Energy = ", eb->e_intra);
if(B_have_flexible_residues) {
item(" Internal Energy Ligand = ", eb->e_intra_lig);
item(" Internal Moving-Fixed Receptor = ", eb->e_intra_moving_fixed_rec);
item(" Internal Moving-Moving Receptor = ", eb->e_intra_moving_moving_rec);
}
item("(3) Torsional Free Energy = ", eb->e_torsFreeEnergy);
switch(ad4_unbound_model){
// in AutoDock 4.2, the default unbound model is "unbound is same as bound"
case Unbound_Default:
case Unbound_Same_As_Bound:
default:
item("(4) Unbound System's Energy [=(2)] = ", eb->e_unbound_internal_FE);
break;
case User:
case Extended:
case Compact:
item("(4) Unbound System's Energy = ", eb->e_unbound_internal_FE);
break;
}
pr( logFile, "%s\n", prefixString);
pr( logFile, "%s\n", prefixString);
}
#undef item
void printStateEnergies( const EnergyBreakdown *const eb,
const char *const prefixString, const int ligand_is_inhibitor,
int outlev, FILE *stateFile)
{
// Real deltaG = 0.0;
Real Ki = 1.0;
// Real RJ = 8.31441; // in J/K/mol, Gas Constant, Atkins Phys.Chem., 2/e
Real Rcal = 1.9871917; // in cal/K/mol, Gas Constant, RJ/4.184
Real TK = 298.15; // Room temperature, in K
// equilibrium: E + I <=> EI
// binding: E + I -> EI K(binding), Kb
// dissociation: EI -> E + I K(dissociation), Kd
//
// 1
// K(binding) = ---------------
// K(dissociation)
// so:
// ln K(binding) = -ln K(dissociation)
// ln Kb = -ln Kd
// Ki = dissociation constant of the enzyme-inhibitor complex = Kd
// [E][I]
// Ki = ------
// [EI]
// so:
// ln Kb = -ln Ki
// deltaG(binding) = -R*T*ln Kb
// deltaG(inhibition) = R*T*ln Ki
//
// Binding and Inhibition occur in opposite directions, so we
// lose the minus-sign: deltaG = R*T*lnKi, _not_ -R*T*lnKi
// => deltaG/(R*T) = lnKi
// => Ki = exp(deltaG/(R*T))
if (eb->deltaG < 0.0) {
Ki = exp((eb->deltaG*1000.)/(Rcal*TK));
}
pr(stateFile, "\t\t<free_NRG_binding>");
print1000(stateFile, eb->deltaG);
pr(stateFile, "</free_NRG_binding>\n");
if (eb->deltaG < 0.0) {
if (ligand_is_inhibitor == 1) {
pr(stateFile, "\t\t<Ki>");
print1000_no_sign(stateFile, Ki);
pr(stateFile, "</Ki>\n");
} else {
pr(stateFile, "\t\t<Kd>");
print1000_no_sign(stateFile, Ki);
pr(stateFile, "</Kd>\n");
}
pr(stateFile, "\t\t<Temp>%.2f</Temp>\n", TK); //temperature in K
}
pr(stateFile, "\t\t<final_intermol_NRG>");
print1000(stateFile, eb->e_inter);
pr(stateFile, "</final_intermol_NRG>\n");
pr(stateFile, "\t\t<internal_ligand_NRG>");
print1000(stateFile, eb->e_intra);
pr(stateFile, "</internal_ligand_NRG>\n");
pr(stateFile, "\t\t<torsonial_free_NRG>");
print1000(stateFile, eb->e_torsFreeEnergy);
pr(stateFile, "</torsonial_free_NRG>\n");
}
// EOF
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