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molgroups.cc
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molgroups.cc
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/*
* molgroups.cc
* Gauss
*
* Created by Frank Heinrich on 27/10/08.
* updated July-2013
* Copyright 2008 __MyCompanyName__. All rights reserved.
*
*/
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "math.h"
#include "molgroups.h"
//------------------------------------------------------------------------------------------------------
//Parent Object Implementation
nSLDObj::nSLDObj()
{
bWrapping=true;
bConvolution=false;
bProtonExchange=false;
dSigmaConvolution=1;
iNumberOfConvPoints=7;
absorb=0;
};
nSLDObj::~nSLDObj(){};
double nSLDObj::fnGetAbsorb(double z){return absorb;};
// returns a n-point gaussian interpolation of the area within 4 sigma
// all area calculatioins are routed through this function, whether they use convolution or not
// convolution works only for objects with fixed nSLD. Broadening an nSLD profile is not as direct as
// broadening a nSL profile. For reason, however, objects report a nSLD(z) and not a nSL(z)
// if it becomes necessary to broaden profiles with variable nSLD, structural changes to the code
// have to be implemented.
double nSLDObj::fnGetConvolutedArea(double dz)
{
int i;
double dgauss, dnormsum, dsum, dd;
if (bConvolution==true) {
dnormsum=0; dsum=0;
for (i=0; i<iNumberOfConvPoints; i++) {
dd=8/(double)iNumberOfConvPoints*(double)i-4;
dgauss=exp((-0.5)*dd*dd); //(sigma_convolution)^2/(sigma_convolution)^2 cancels
dnormsum+=dgauss;
dsum+=fnGetArea(dz+dd*dSigmaConvolution)*dgauss;
}
if (dnormsum!=0) {
return dsum/dnormsum;
}
else return 0;
}
else {
return fnGetArea(dz);
}
}
void nSLDObj::fnSetConvolution(double _sigma_convolution, int _iNumberOfConvPoints)
{
bConvolution=true;
dSigmaConvolution=_sigma_convolution;
iNumberOfConvPoints=_iNumberOfConvPoints;
}
void nSLDObj::fnWriteData2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
double dLowerLimit, dUpperLimit, d, dmirror, dAreaInc, dnSLDInc;
int i;
fprintf(fp, "z%s a%s nsl%s \n",cName, cName, cName);
dLowerLimit=fnGetLowerLimit();
dUpperLimit=fnGetUpperLimit();
d=floor(dLowerLimit/stepsize+0.5)*stepsize;
for (i=0; i<dimension; i++)
{
d=double(i)*stepsize;
dmirror=d-float(2*i)*stepsize;
if ((bWrapping==true) && (dmirror>=dLowerLimit))
{
dAreaInc=fnGetConvolutedArea(d)+fnGetConvolutedArea(dmirror);
dnSLDInc=(fnGetnSLD(d)*fnGetConvolutedArea(d)+fnGetnSLD(dmirror)*fnGetConvolutedArea(dmirror))/(fnGetConvolutedArea(d)+fnGetConvolutedArea(dmirror));
//printf("Bin %i Area %f nSLD %e nSL %e \n", i, dAreaInc, fnGetnSLD(d), fnGetnSLD(d)*dAreaInc*stepsize);
}
else
{
dAreaInc=fnGetConvolutedArea(d);
dnSLDInc=fnGetnSLD(d);
//printf("Bin %i z %g Area %f nSLD %e nSL %e \n", i, d, dAreaInc, fnGetnSLD(d), fnGetnSLD(d)*dAreaInc*stepsize);
}
fprintf(fp, "%lf %lf %e \n", d, dAreaInc, dnSLDInc*dAreaInc*stepsize);
};
fprintf(fp, "\n");
}
//does a Catmull-Rom Interpolation on an equal distance grid
// 0<t<=1 is the relative position on the interval between p0 and p1
// p-1 and p2 are needed for derivative calculation
double nSLDObj::CatmullInterpolate(double t, double pm1, double p0, double p1, double p2){
double m0, m1, t_2, t_3, h00, h10, h01, h11;
m0=(p1-pm1)/2;
m1=(p2-p0) /2;
t_2=t*t;
t_3=t_2*t;
h00= 2*t_3-3*t_2+1;
h10= t_3-2*t_2+t;
h01=(-2)*t_3+3*t_2;
h11= t_3-t_2;
return h00*p0+h10*m0+h01*p1+h11*m1;
};
double nSLDObj::fnTriCubicCatmullInterpolate(double p[4][4][4],double t[3]){
double dFirstStage[4][4];
double dSecondStage[4];
int i,j;
for (i=0; i<4; i++){
for (j=0; j<4; j++){
dFirstStage[i][j]=CatmullInterpolate(t[0],p[0][i][j],p[1][i][j],p[2][i][j],p[3][i][j]);
}
}
for (i=0; i<4; i++){
dSecondStage[i]=CatmullInterpolate(t[1],dFirstStage[0][i],dFirstStage[1][i],dFirstStage[2][i],dFirstStage[3][i]);
}
return CatmullInterpolate(t[2],dSecondStage[0],dSecondStage[1],dSecondStage[2],dSecondStage[3]);
};
//Philosophy for this first method: You simply add more and more volume and nSLD to the
//volume and nSLD array. After all objects have filled up those arrays the maximal area is
//determined which is the area per molecule and unfilled volume is filled with bulk solvent.
//Hopefully the fit algorithm finds a physically meaningful solution. There has to be a global
//hydration paramter for the bilayer.
//Returns maximum area
double nSLDObj::fnWriteProfile(double aArea[], double anSL[], int dimension, double stepsize, double dMaxArea)
{
double dLowerLimit, dUpperLimit, d, dAreaInc, dprefactor;
int i;
dLowerLimit=fnGetLowerLimit();
dUpperLimit=fnGetUpperLimit();
if (dUpperLimit==0)
{
dUpperLimit=double(dimension)*stepsize;
}
d=floor(dLowerLimit/stepsize+0.5)*stepsize;
while (d<=dUpperLimit)
{
i=int(d/stepsize);
dprefactor=1;
if ((i<0) && (bWrapping==true)) {i=-1*i;};
if ((i==0) && (bWrapping==true)) {dprefactor=2;} //avoid too low filling when mirroring
if ((i>=0) && (i<dimension))
{
dAreaInc=fnGetConvolutedArea(d);
aArea[i]=aArea[i]+dAreaInc*dprefactor;
if (aArea[i]>dMaxArea) {dMaxArea=aArea[i];};
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
//printf("Bin %i AreaInc %g total %g MaxArea %g nSL %f total %f \n", i, dAreaInc, aArea[i], dMaxArea, fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
}
d=d+stepsize;
};
return dMaxArea;
};
double nSLDObj::fnWriteProfile(double aArea[], double anSL[], double aAbsorb[], int dimension, double stepsize, double dMaxArea)
{
double dLowerLimit, dUpperLimit, d, dAreaInc, dprefactor;
int i;
dLowerLimit=fnGetLowerLimit();
dUpperLimit=fnGetUpperLimit();
if (dUpperLimit==0)
{
dUpperLimit=double(dimension)*stepsize;
}
d=floor(dLowerLimit/stepsize+0.5)*stepsize;
while (d<=dUpperLimit)
{
i=int(d/stepsize);
dprefactor=1;
//printf("Here we are %i, dimension %i \n", i, dimension);
if ((i<0) && (bWrapping==true)) {i=-1*i;};
if ((i==0) && (bWrapping==true)) {dprefactor=2;} //avoid too low filling when mirroring
if ((i>=0) && (i<dimension))
{
//printf("Bin %i Areainc %f area now %f nSLD %g Absorbinc %g Absorb now %g nSLinc %g nSL now %g \n", i, dAreaInc, aArea[i], fnGetnSLD(d), aAbsorb[i], fnGetAbsorb(d)*dAreaInc*stepsize, fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
dAreaInc=fnGetConvolutedArea(d);
aArea[i]=aArea[i]+dAreaInc*dprefactor;
if (aArea[i]>dMaxArea) {dMaxArea=aArea[i];};
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
aAbsorb[i]=aAbsorb[i]+fnGetAbsorb(d)*dAreaInc*stepsize*dprefactor;
//printf("Bin %i Area %f total %f nSL %f total %f \n", i, dAreaInc, aArea[i], fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
}
d=d+stepsize;
};
return dMaxArea;
};
void nSLDObj::fnOverlayProfile(double aArea[], double anSL[], int dimension, double stepsize, double dMaxArea)
{
double dLowerLimit, dUpperLimit, d, dAreaInc, dprefactor, temparea;
int i;
dLowerLimit=fnGetLowerLimit();
dUpperLimit=fnGetUpperLimit();
if (dUpperLimit==0)
{
dUpperLimit=double(dimension)*stepsize;
}
d=floor(dLowerLimit/stepsize+0.5)*stepsize;
while (d<=dUpperLimit)
{
i=int(d/stepsize);
dprefactor=1;
if ((i<0) && (bWrapping==true)) {i=-1*i;};
if ((i==0) && (bWrapping==true)) {dprefactor=2;} //avoid too low filling when mirroring
if ((i>=0) && (i<dimension))
{
dAreaInc=fnGetConvolutedArea(d);
temparea=dAreaInc*dprefactor+aArea[i];
if (temparea<=dMaxArea) {
aArea[i]=aArea[i]+dAreaInc*dprefactor;
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
}
else {
if ((temparea-dMaxArea)<=aArea[i]) //overfill is not larger than existing area
{
anSL[i]=anSL[i]*(1-((temparea-dMaxArea)/aArea[i])); //eliminate the overfilled portion using original content
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
aArea[i]=dMaxArea;
//printf("Replace: Bin %i temparea %g Areainc %g area now %g dMaxArea %g nSLD %g nSLinc %g nSL now %g \n", i, temparea, dAreaInc, aArea[i], dMaxArea, fnGetnSLD(d), fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
}
else //overfill is larger!!, this is non-physical
{
anSL[i]=fnGetnSLD(d)*dMaxArea*stepsize;
aArea[i]=dMaxArea;
};
}
}
d=d+stepsize;
}
};
void nSLDObj::fnOverlayProfile(double aArea[], double anSL[], double aAbsorb[], int dimension, double stepsize, double dMaxArea)
{
double dLowerLimit, dUpperLimit, d, dAreaInc, dprefactor, temparea;
int i;
dLowerLimit=fnGetLowerLimit();
dUpperLimit=fnGetUpperLimit();
if (dUpperLimit==0)
{
dUpperLimit=double(dimension)*stepsize;
}
d=floor(dLowerLimit/stepsize+0.5)*stepsize;
while (d<=dUpperLimit)
{
i=int(d/stepsize);
dprefactor=1;
//printf("Here we are %i, dimension %i, maxarea %f \n", i, dimension, dMaxArea);
if ((i<0) && (bWrapping==true)) {i=-1*i;};
if ((i==0) && (bWrapping==true)) {dprefactor=2;} //avoid too low filling when mirroring
if ((i>=0) && (i<dimension))
{
dAreaInc=fnGetConvolutedArea(d);
temparea=dAreaInc*dprefactor+aArea[i];
if (temparea>dMaxArea) {
//printf("Bin %i Areainc %f area now %f nSLD %g Absorbinc %g Absorb now %g nSLinc %g nSL now %g \n", i, dAreaInc, aArea[i], fnGetnSLD(d), aAbsorb[i], fnGetAbsorb(d)*dAreaInc*stepsize, fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
anSL[i]=anSL[i]*(1-((temparea-dMaxArea)/aArea[i])); //eliminate the overfilled portion using original content
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
aAbsorb[i]=aAbsorb[i]*(1-((temparea-dMaxArea)/aArea[i])); //eliminate the overfilled portion using original content
aAbsorb[i]=aAbsorb[i]+fnGetAbsorb(d)*dAreaInc*stepsize*dprefactor;
aArea[i]=dMaxArea;
}
else {
//printf("Bin %i Areainc %f area now %f nSLD %g Absorbinc %g Absorb now %g nSLinc %g nSL now %g \n", i, dAreaInc, aArea[i], fnGetnSLD(d), aAbsorb[i], fnGetAbsorb(d)*dAreaInc*stepsize, fnGetnSLD(d)*dAreaInc*stepsize, anSL[i]);
aArea[i]=aArea[i]+dAreaInc*dprefactor;
anSL[i]=anSL[i]+fnGetnSLD(d)*dAreaInc*stepsize*dprefactor;
aAbsorb[i]=aAbsorb[i]+fnGetAbsorb(d)*dAreaInc*stepsize*dprefactor;
}
}
d=d+stepsize;
};
};
//------------------------------------------------------------------------------------------------------
//Function Object Implementation
//------------------------------------------------------------------------------------------------------
BoxErr::BoxErr(double dz, double dsigma, double dlength, double dvolume, double dnSL, double dnumberfraction=1)
{
z=dz; sigma=dsigma; l=dlength, vol=dvolume, nSL=dnSL, nf=dnumberfraction;
};
BoxErr::~BoxErr(){};
//Gaussian function definition, integral is volume, return value is area at position z
double BoxErr::fnGetArea(double dz) {
return (vol/l)*0.5*(erf((dz-z+0.5*l)/sqrt(2)/sigma)-erf((dz-z-0.5*l)/sqrt(2)/sigma))*nf;
};
//constant nSLD
double BoxErr::fnGetnSLD(double dz) {return nSL/vol;};
//Gaussians are cut off below and above 3 sigma
double BoxErr::fnGetLowerLimit() {return z-0.5*l-3*sigma;};
double BoxErr::fnGetUpperLimit() {return z+0.5*l+3*sigma;};
void BoxErr::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
fprintf(fp, "BoxErr %s z %lf sigma %lf l %lf vol %lf nSL %e nf %lf \n",cName, z, sigma, l, vol, nSL, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
}
//------------------------------------------------------------------------------------------------------
Box2Err::Box2Err(double dz, double dsigma1, double dsigma2, double dlength, double dvolume, double dnSL, double dnumberfraction=1)
{
z=dz; sigma1=dsigma1; sigma2=dsigma2; l=dlength, vol=dvolume, nSL=dnSL, nf=dnumberfraction;
nsldbulk_store=0;
};
Box2Err::~Box2Err(){};
//Gaussian function definition, integral is volume, return value is area at position z
double Box2Err::fnGetArea(double dz) {
if ((l!=0) && (sigma1!=0) && (sigma2!=0)) {
return (vol/l)*0.5*(erf((dz-z+0.5*l)/sqrt(2)/sigma1)-erf((dz-z-0.5*l)/sqrt(2)/sigma2))*nf;
}
else {
return 0;
}
};
double Box2Err::fnGetnSL(double bulknsld) {
if (bProtonExchange) {
if (vol!=0) {
return ((bulknsld+0.56e-6)*nSL2+(6.36e-6-bulknsld)*nSL)/(6.36e-6+0.56e-6);
}
else {
return 0;
}
}
else {
return nSL;
}
};
//constant nSLD
double Box2Err::fnGetnSLD(double dz) {
if (vol!=0) {
if (bProtonExchange) {
return ((nsldbulk_store+0.56e-6)*nSL2+(6.36e-6-nsldbulk_store)*nSL)/(6.36e-6+0.56e-6)/vol;
}
else {
return nSL/vol;
}
}
else {
return 0;
}
}
double Box2Err::fnGetnSLD(double dz, double bulknsld) {
if (bProtonExchange) {
if (vol!=0) {
nsldbulk_store=bulknsld; //store bulk solvent for later plotting purposes
return ((bulknsld+0.56e-6)*nSL2+(6.36e-6-bulknsld)*nSL)/(6.36e-6+0.56e-6)/vol;
}
else {
return 0;
}
}
else {
return fnGetnSLD(dz);
}
};
//Gaussians are cut off below and above 3 sigma
double Box2Err::fnGetLowerLimit() {return z-0.5*l-3*sigma1;};
double Box2Err::fnGetUpperLimit() {return z+0.5*l+3*sigma2;};
void Box2Err::fnSetnSL(double _nSL, double _nSL2)
{
nSL=_nSL;
nSL2=_nSL2;
bProtonExchange=true;
}
void Box2Err::fnSetSigma(double sigma)
{
sigma1=sigma;
sigma2=sigma;
}
void Box2Err::fnSetSigma(double dsigma1, double dsigma2)
{
sigma1=dsigma1;
sigma2=dsigma2;
}
void Box2Err::fnSetZ(double dz)
{
z=dz;
};
void Box2Err::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
fprintf(fp, "Box2Err %s z %lf sigma1 %lf sigma2 %lf l %lf vol %lf nSL %lf nSL2 %e nf %lf \n",cName, z, sigma1, sigma2, l, vol, nSL, nSL2, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
}
//------------------------------------------------------------------------------------------------------
Gaussian::Gaussian(double dz, double dsigma, double dvolume, double dnSL, double dnumberfraction=1)
{
z=dz; sigma=dsigma; vol=dvolume, nSL=dnSL, nf=dnumberfraction;
};
Gaussian::~Gaussian(){};
//Gaussian function definition, integral is volume, return value is area at position z
double Gaussian::fnGetArea(double dz) {return (vol/sqrt(2*3.141592654)/sigma)*exp(-0.5*(z-dz)*(z-dz)/sigma/sigma)*nf;};
//constant nSLD
double Gaussian::fnGetnSLD(double dz) {return nSL/vol;};
//Gaussians are cut off below and above 3 sigma
double Gaussian::fnGetLowerLimit() {return z-3*sigma;};
double Gaussian::fnGetUpperLimit() {return z+3*sigma;};
void Gaussian::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
fprintf(fp, "Gaussian %s z %lf sigma %lf vol %lf nSL %e nf %lf \n",cName, z, sigma, vol, nSL, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
}
//------------------------------------------------------------------------------------------------------
Parabolic::Parabolic(double dC, double dH, double dn, double dnSLD, double dnumberfraction=1)
{
C=dC; H=dH, n=dn, nSLD=dnSLD, nf=dnumberfraction;
bWrapping=false;
};
Parabolic::~Parabolic(){};
//Gaussian function definition, integral is volume, return value is area at position z
double Parabolic::fnGetArea(double dz) {
if (dz<H) {return C*(1-pow(dz/H,n))*nf;}
else {return 0;}
};
//constant nSLD
double Parabolic::fnGetnSLD(double dz) {return nSLD;};
//Gaussians are cut off below and above 3 sigma
double Parabolic::fnGetLowerLimit() {return 0;};
double Parabolic::fnGetUpperLimit() {return 0;};
void Parabolic::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
fprintf(fp, "Parabolic %s C %lf H %lf n %lf nSLD %e nf %lf \n",cName, C, H, n, nSLD, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
}
//------------------------------------------------------------------------------------------------------
StretchGaussian::StretchGaussian(double dz, double dsigma, double dlength, double dvolume, double dnSL, double dnumberfraction=1)
{
z=dz; sigma=dsigma; l=dlength, vol=dvolume, nSL=dnSL, nf=dnumberfraction;
};
StretchGaussian::~StretchGaussian(){};
//Gaussian function definition, integral is volume, return value is area at position z
double StretchGaussian::fnGetArea(double dz) {
double returnvalue;
double temp, dvgauss;
temp=sqrt(2*3.141592654)*sigma;
dvgauss=vol/(1+l/temp);
if (dz<(z-0.5*l))
{
returnvalue=dvgauss/temp*exp(-0.5*(z-dz-0.5*l)*(z-dz-0.5*l)/sigma*sigma)*nf;
}
else if ((dz>=(z-0.5*l)) && (dz<=(z+0.5*l)))
{
returnvalue=dvgauss/temp*nf;
}
else
{
returnvalue=dvgauss/temp*exp(-0.5*(dz-z-0.5*l)*(dz-z-0.5*l)/sigma*sigma)*nf;
}
return returnvalue;
};
//constant nSLD
double StretchGaussian::fnGetnSLD(double dz) {return nSL/vol;};
//Gaussians are cut off below and above 3 sigma
double StretchGaussian::fnGetLowerLimit() {return z-0.5*l-3*sigma;};
double StretchGaussian::fnGetUpperLimit() {return z+0.5*l+3*sigma;};
void StretchGaussian::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
fprintf(fp, "Gaussian %s z %lf sigma %lf l %lf vol %lf nSL %e nf %lf \n",cName, z, sigma, l, vol, nSL, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
}
//------------------------------------------------------------------------------------------------------
// Combined Object Implementation
//------------------------------------------------------------------------------------------------------
PC::PC()
{
cg = new Box2Err(0,0,0,0,0,0,1);
phosphate = new Box2Err(0,0,0,0,0,0,1);
choline = new Box2Err(0,0,0,0,0,0,1);
cg->l=4.21; phosphate->l=3.86; choline->l=6.34; //from fit to Feller data
cg->sigma1=2.53; cg->sigma2=2.29;
phosphate->sigma1=2.29; phosphate->sigma2=2.02;
choline->sigma1=2.02; choline->sigma2=2.26;
//from fit to Feller data
l=9.575; //group cg phosphate choline
//z 15.00 18.44 19.30
//l 4.21 3.86 6.34
cg->vol=147; phosphate->vol=54; choline->vol=120; //nominal values
cg->nSL=3.7755e-4; phosphate->nSL=2.8350e-4; choline->nSL=-6.0930e-5;
cg->nf=1; phosphate->nf=1; choline->nf=1;
vol=cg->vol+phosphate->vol+choline->vol;
nSL=cg->nSL+phosphate->nSL+choline->nSL;
fnAdjustParameters();
};
PC::~PC(){
delete cg;
delete phosphate;
delete choline;
};
void PC::fnAdjustParameters(){
cg->z=z-0.5*l+0.5*cg->l; phosphate->z=z-0.5*l+cg->l+0.5*phosphate->l;
choline->z=z+0.5*l-0.5*choline->l;
};
//Return value is area at position z
double PC::fnGetArea(double dz) {
return (cg->fnGetArea(dz)+phosphate->fnGetArea(dz)+choline->fnGetArea(dz))*nf;
};
double PC::fnGetTotalnSL(){
return cg->nSL+phosphate->nSL+choline->nSL;
};
//get nSLD from molecular subgroups
double PC::fnGetnSLD(double dz) {
double cgarea, pharea, charea, sum;
cgarea=cg->fnGetArea(dz);
pharea=phosphate->fnGetArea(dz);
charea=choline->fnGetArea(dz);
sum=cgarea+pharea+charea;
if (sum==0) {return 0;}
else {
return (cg->fnGetnSLD(dz)*cgarea+
phosphate->fnGetnSLD(dz)*pharea+
choline->fnGetnSLD(dz)*charea)/sum;
}
};
//Use limits of molecular subgroups
double PC::fnGetLowerLimit() {return cg->fnGetLowerLimit();};
double PC::fnGetUpperLimit() {return choline->fnGetUpperLimit();};
void PC::fnSetSigma(double sigma)
{
cg->sigma1=sigma;
cg->sigma2=sigma;
phosphate->sigma1=sigma;
phosphate->sigma2=sigma;
choline->sigma1=sigma;
choline->sigma2=sigma;
};
void PC::fnSetZ(double dz){
z=dz;
fnAdjustParameters();
};
void PC::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
//char *str = new char[80];
fprintf(fp, "PC %s z %lf l %lf vol %lf nf %lf \n",cName, z, l,cg->vol+phosphate->vol+choline->vol, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
//cg->fnWritePar2File(fp, "cg", dimension, stepsize);
//phosphate->fnWritePar2File(fp, "phosphate", dimension, stepsize);
//choline->fnWritePar2File(fp, "choline", dimension, stepsize);
//delete []str;
}
//------------------------------------------------------------------------------------------------------
PCm::PCm()
{
cg->sigma2=2.53; cg->sigma1=2.29; //from fit to Feller data
phosphate->sigma2=2.29; phosphate->sigma1=2.02;
choline->sigma2=2.02; choline->sigma1=2.26;
fnAdjustParameters();
};
PCm::~PCm() {};
void PCm::fnAdjustParameters(){
cg->z=z+0.5*l-0.5*cg->l; phosphate->z=z+0.5*l-cg->l-0.5*phosphate->l;
choline->z=z-0.5*l+0.5*choline->l;
};
//Use limits of molecular subgroups
double PCm::fnGetLowerLimit() {return cg->fnGetLowerLimit();};
double PCm::fnGetUpperLimit() {return choline->fnGetUpperLimit();};
void PCm::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
//char *str = new char[80];
fprintf(fp, "PCm %s z %lf l %lf vol %lf nf %lf \n",cName, z, l,cg->vol+phosphate->vol+choline->vol, nf);
nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
//cg->fnWritePar2File(fp, "cg_m", dimension, stepsize);
//phosphate->fnWritePar2File(fp, "phosphate_m", dimension, stepsize);
//choline->fnWritePar2File(fp, "choline_m", dimension, stepsize);
//delete []str;
}
//---------------------------------------------------------------------------------------------------------------
PS::PS()
{
cg = new Box2Err(0,0,0,0,0,0,1);
phosphate = new Box2Err(0,0,0,0,0,0,1);
serine = new Box2Err(0,0,0,0,0,0,1);
cg->l=3.6; phosphate->l=2.0; serine->l=3.0; //from fit to Feller data
cg->sigma1=2.53; cg->sigma2=2.29;
phosphate->sigma1=2.29; phosphate->sigma2=2.02;
serine->sigma1=2.02; serine->sigma2=2.26;
//from fit to Feller data
l=8.6; //group cg phosphate choline
//z 15.00 18.44 19.30
//l 4.21 3.86 6.34
cg->vol=147; phosphate->vol=54; serine->vol=80; //nominal values
cg->nSL=3.7755e-4; phosphate->nSL=2.8350e-4; serine->nSL=1.8408E-04;
cg->nf=1; phosphate->nf=1; serine->nf=1;
fnAdjustParameters();
};
PS::~PS(){
delete cg;
delete phosphate;
delete serine;
};
void PS::fnAdjustParameters(){
cg->z=z-0.5*l+0.5*cg->l; phosphate->z=z-0.5*l+cg->l+0.5*phosphate->l;
serine->z=z+0.5*l-0.5*serine->l;
};
//Return value is area at position z
double PS::fnGetArea(double dz) {
return (cg->fnGetArea(dz)+phosphate->fnGetArea(dz)+serine->fnGetArea(dz))*nf;
};
//get nSLD from molecular subgroups
double PS::fnGetnSLD(double dz) {
double cgarea, pharea, searea, sum;
cgarea=cg->fnGetArea(dz);
pharea=phosphate->fnGetArea(dz);
searea=serine->fnGetArea(dz);
sum=cgarea+pharea+searea;
if (sum==0) {return 0;}
else {
return (cg->fnGetnSLD(dz)*cgarea+
phosphate->fnGetnSLD(dz)*pharea+
serine->fnGetnSLD(dz)*searea)/sum;
}
};
//Use limits of molecular subgroups
double PS::fnGetLowerLimit() {return cg->fnGetLowerLimit();};
double PS::fnGetUpperLimit() {return serine->fnGetUpperLimit();};
void PS::fnSetSigma(double sigma)
{
cg->sigma1=sigma;
cg->sigma2=sigma;
phosphate->sigma1=sigma;
phosphate->sigma2=sigma;
serine->sigma1=sigma;
serine->sigma2=sigma;
};
void PS::fnSetZ(double dz){
z=dz;
fnAdjustParameters();
};
void PS::fnSetnSL(double nSL_cg, double nSL_phosphate, double nSL_serine){
//printf("nSL cg %e nSL phosphate %e nSL serine %e \n", nSL_cg, nSL_phosphate, nSL_serine);
cg->nSL=nSL_cg;
phosphate->nSL=nSL_phosphate;
serine->nSL=nSL_serine;
}
void PS::fnWritePar2File(FILE *fp, const char *cName, int dimension, double stepsize)
{
//char *str = new char[80];
//fprintf(fp, "PC %s z %lf l %lf nf %lf \n",cName, z, l, nf);
//nSLDObj::fnWriteData2File(fp, cName, dimension, stepsize);
cg->fnWritePar2File(fp, "cg", dimension, stepsize);
phosphate->fnWritePar2File(fp, "phosphate", dimension, stepsize);
serine->fnWritePar2File(fp, "serine", dimension, stepsize);
//delete []str;
}
//-----------------------------------------------------------------------------------------------------------
//Amino Acids
//-----------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------
//general implementation
//-----------------------------------------------------------------------------------------------------------
//ExchangeRatio is not yet fully implemented
AminoAcid::AminoAcid()
{
ExchangeRatio=0;
Deuterated=0;
}
double AminoAcid::fnGetnSLD(double z)
{
double temp;
if (Deuterated==1) {temp=1;}
else {temp=0.;}
//correct for deuterated residues
return (nSL-temp*float(nH)*(-3.741e-5)+temp*float(nH)*(6.674e-5))/vol;
}
//-----------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------
//Specific implementations
//-----------------------------------------------------------------------------------------------------------
//-----------------------------------------------------------------------------------------------------------
AA_Lys::AA_Lys()
{
nSL=1.5660e-4;
vol=171.3;
nH=13;
nExch=4;
}
AA_Arg::AA_Arg()
{
nSL=3.4260e-4;
vol=202.1;
nH=13;
nExch=6;
}
AA_His::AA_His()
{
nSL=4.7406e-4;
vol=167.3;
nH=7;
nExch=3;
}
AA_Asn::AA_Asn()
{
nSL=3.4356e-4;
vol=135.2;
nH=6;
nExch=3;
}
AA_Asp::AA_Asp()
{
nSL=3.8343e-4;
vol=124.5;
nH=4;
nExch=1;
}
AA_Cys::AA_Cys()
{
nSL=1.9191e-4;
vol=105.6;
nH=5;
nExch=1;
}
AA_Thr::AA_Thr()
{
nSL=2.1315e-4;
vol=122.1;
nH=7;
nExch=2;
}
AA_Ser::AA_Ser()
{
nSL=2.2149e-4;
vol=99.1;
nH=5;
nExch=2;
}
AA_Gln::AA_Gln()
{
nSL=3.3522e-4;
vol=161.1;
nH=8;
nExch=3;
}
AA_Glu::AA_Glu()
{
nSL=3.7509e-4;
vol=155.1;
nH=6;
nExch=1;
}
AA_Pro::AA_Pro()
{
nSL=2.2158e-4;
vol=129.3;
nH=7;
nExch=0;
}
AA_Gly::AA_Gly()
{
nSL=1.7178e-4;
vol=66.4;
nH=3;
nExch=1;
}
AA_Ala::AA_Ala()
{
nSL=1.6344e-4;
vol=91.5;
nH=5;
nExch=1;
}
AA_Val::AA_Val()
{
nSL=1.4676e-4;
vol=141.7;
nH=9;
nExch=1;
}
AA_Ile::AA_Ile()
{
nSL=1.3842e-4;
vol=168.8;
nH=11;
nExch=1;
}
AA_Leu::AA_Leu()
{
nSL=1.3842e-4;
vol=167.9;
nH=11;
nExch=1;
}
AA_Met::AA_Met()
{
nSL=1.7523e-4;
vol=170.8;
nH=9;
nExch=1;
}
AA_Tyr::AA_Tyr()
{
nSL=4.7073e-4;
vol=203.6;
nH=9;
nExch=2;
}
AA_Phe::AA_Phe()
{
nSL=4.1268e-4;
vol=203.4;
nH=9;
nExch=1;
}
AA_Trp::AA_Trp()
{
nSL=6.0123e-4;
vol=237.6;
nH=10;
nExch=2;
}
//----------------------------------------------------------------------------------------------------------------
// floating lipid bilayer
//----------------------------------------------------------------------------------------------------------------
BLM_quaternary::BLM_quaternary(){
headgroup1 = new PCm(); //mirrored PC head group
lipid1 = new Box2Err();
methyl1 = new Box2Err();
methyl2 = new Box2Err();
lipid2 = new Box2Err();
headgroup2 = new PC(); //PC head group
headgroup1_2= new Box2Err(); //second headgroups
headgroup2_2 = new Box2Err();
headgroup1_3 = new Box2Err();
headgroup2_3 = new Box2Err();
defect_hydrocarbon = new Box2Err();
defect_headgroup = new Box2Err();
volacyllipid=925;
nslacyllipid=-2.67e-4;
volmethyllipid=98.8;
nslmethyllipid=-9.15e-5;
hc_substitution_1=0;
hc_substitution_2=0;
headgroup1_2->vol=330; //was 330
headgroup2_2->vol=330; //was 330
headgroup1_3->vol=330; //was 330
headgroup2_3->vol=330; //was 330
headgroup1_2->nSL=6.0012e-4; // was 6.0122e-4
headgroup2_2->nSL=6.0012e-4; // was 6.0122e-4
headgroup1_3->nSL=6.0012e-4; // was 6.0122e-4
headgroup2_3->nSL=6.0012e-4; // was 6.0122e-4
headgroup1_2->l=9.5;
headgroup2_2->l=9.5;
headgroup1_3->l=9.5;
headgroup2_3->l=9.5;
volacyllipid_2=925;
nslacyllipid_2=-2.67e-4;
volmethyllipid_2=98.8;
nslmethyllipid_2=-9.15e-5;