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surface.cpp
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surface.cpp
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#include "surface.h"
#include "attractrigidbody.h"
#include <cassert>
namespace PTools
{
void Surface::setUp(int nphi, int ncosth)
{
// dimension csth(ncosth),snth(ncosth),phgh(nphi)
const dbl pi= 3.141592654;
// precalculate costh,sinth and phigh for different ncosth...
for (uint ik=0; ik < (uint) ncosth; ik++)
{
csth.push_back ( -1.0 + ( ( (dbl) ik+1) - 0.5 ) * (2.0 / (dbl) ncosth ) ) ;
snth.push_back ( sqrt(1.0 -csth[ik]*csth[ik] ) );
}
for ( int ik=0; ik<nphi; ik++)
{
cos_phgh.push_back ( cos(2.0 * pi * ((dbl)ik-1.0)/(dbl) nphi )) ;
sin_phgh.push_back ( sin(2.0 * pi * ((dbl)ik-1.0)/(dbl) nphi )) ;
}
}
void Surface::surfpointParams(int max, dbl shift)
{
m_numneh = max;
m_sradshift = shift;
m_init=true;
}
void Surface::readsolvparam(const std::string& file)
{
std::string line ;
//int count = 0;
radi.clear();
std::ifstream sfile(file.c_str());
if (! sfile)
{
// the file cannot be opened
std::string msg = " Cannot Locate file ";
msg.append(file.c_str());
msg.append("\n");
std::cerr << msg ;
throw msg;
}
while (std::getline(sfile, line))
{
//count++ ; // count number of line (unused at the moment)
//int size_line = line.size(); // count line length (unused at the moment)
//dbl data1=atof(line.substr(1,6).c_str()); // read first column - atom type id (unused at the moment)
dbl data2=atof(line.substr(7,13).c_str()); // read second column - radius (unused at the moment)
//dbl data3=atof(line.substr(14,20).c_str()); // read third column - solvation parameters (unused at the moment)
//std::string data4=line.substr(21,size_line).c_str(); // read last column (unused at the moment)
radi.push_back(data2);
}
}
Rigidbody Surface::surfpoint(const Rigidbody & rigid, dbl srad)
{
Rigidbody rigidsurf;
int size_rigid = rigid.Size();
std::vector<int> neigh;
radius.clear();
// fix neighbours parameters if not initialized
if (!m_init)
{
m_numneh = 2000;
m_sradshift = 0.0;
}
// read radius
AttractRigidbody rigid_tmp(rigid);
m_atomtypenumber.resize(size_rigid);
for (uint i=0; i< rigid_tmp.Size(); i++)
{ m_atomtypenumber[i] = rigid_tmp.getAtomTypeNumber(i);}
for (int i=0; i<size_rigid; i++)
{
Atom m_atom = rigid_tmp.CopyAtom(i);
radius.push_back(radi[m_atomtypenumber[i]]);
}
// generate grid points
for (int i=0; i<size_rigid; i++)
if ( radius[i] != 0.0 )
{
Coord3D coord1 = rigid.GetCoords(i);
int numneh = 0;
neigh.clear();
for (int j=0; j<size_rigid; j++) // generate neighbor list
if (i!=j)
{
Coord3D coord2 = rigid.GetCoords(j);
dbl ccdist = Norm2(coord1 - coord2);
dbl rr = (radius[i]+radius[j]+2.0*srad) * (radius[i]+radius[j]+2.0*srad);
if (ccdist <= rr)
{ neigh.push_back(j);
numneh+=1;
if ( numneh > m_numneh )
{
std::string msg = " ERROR: Atom has too many neighbors \n" ;
std::cout << msg;
throw msg;
}
}
}
numneh = numneh - 1;
for (int j=0; j<m_ncosth; j++) // generate points around each atoms
{
dbl costh = csth[j];
dbl sinth = snth[j];
for (int k=0; k<m_nphi; k++)
{
dbl cphigh = cos_phgh[k];
dbl sphigh = sin_phgh[k];
Coord3D coord4;
coord4.x = (radius[i]+srad+m_sradshift)*sinth*cphigh;
coord4.y = (radius[i]+srad+m_sradshift)*sinth*sphigh;
coord4.z = (radius[i]+srad+m_sradshift)*costh;
int l = 0;
bool coverd = false;
while ((!coverd) && (l <= numneh))
{
Coord3D coord5 = rigid.GetCoords(neigh[l]);
dbl ddd = Norm2(coord1 + coord4 - coord5);
if (ddd < (radius[neigh[l]] + srad+m_sradshift)*(radius[neigh[l]] + srad+m_sradshift))
{ coverd = true; }
l+=1;
}
if (!coverd)
{
Atom m_atom2 = rigid.CopyAtom(i);
m_atom2.SetCoords(coord1 + coord4);
rigidsurf.AddAtom(m_atom2);
}
}
}
// fill the top and bottom positions
dbl costh = -1;
while (costh<=1.0)
{
Coord3D coord4;
coord4.x = 0.0;
coord4.y = 0.0;
coord4.z = (radius[i]+srad+m_sradshift)*costh;
int l = 0;
bool coverd = false;
while ((!coverd) && (l <= numneh))
{
Coord3D coord5 = rigid.GetCoords(neigh[l]);
dbl ddd = Norm2(coord1 + coord4 - coord5);
if (ddd < (radius[neigh[l]] + srad+m_sradshift)*(radius[neigh[l]] + srad+m_sradshift))
{ coverd = true; }
l+=1;
}
if (!coverd)
{
Atom m_atom2 = rigid.CopyAtom(i);
m_atom2.SetCoords(coord1 + coord4);
rigidsurf.AddAtom(m_atom2);
}
costh+=2;
}
}
return rigidsurf;
}
Rigidbody Surface::outergrid(const Rigidbody & rigid1, const Rigidbody & rigid2, dbl srad)
{
int size1 = rigid1.Size();
int size2 = rigid2.Size();
Rigidbody rigid3;
for (int i=0; i<size1; i++)
{
Coord3D xyz1 = rigid1.GetCoords(i);
bool select = true;
for (int j=0; j<size2; j++)
{
Coord3D xyz2 = rigid2.GetCoords(j);
dbl dist=Norm2(xyz1-xyz2);
if (dist < srad) { select = false; }
}
if (select) { rigid3.AddAtom(rigid1.CopyAtom(i)); }
}
return rigid3;
}
Rigidbody Surface::removeclosest(const Rigidbody & rigid, dbl srad)
{
std::vector<bool> list,list2;
int size=rigid.Size();
Rigidbody rigid2;
list.clear();
srad=srad*srad;
for (int i=0; i<size; i++) { list.push_back(true); }
for (int i=0; i<size; i++)
{
Coord3D xyz1 = rigid.GetCoords(i);
for (int j=0; j<size; j++)
if ((list[i]) && (i!=j))
{
Coord3D xyz2 = rigid.GetCoords(j);
dbl dist=Norm2(xyz1 - xyz2);
if (dist < srad) { list[j] = false; }
}
}
for (int i=0; i<size; i++)
if (list[i]) { rigid2.AddAtom(rigid.CopyAtom(i)); }
return rigid2;
}
}//namespace PTools