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/**********************************************************************
obxyz - Open Babel XYZ transformations
Copyright (C) 2001-2006 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
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 version 2 of the License.
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.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/math/matrix3x3.h>
#include <openbabel/obconversion.h>
using namespace std;
using namespace OpenBabel;
int main(int argc,char **argv)
{
char c;
int transX, transY, transZ, centerIdx;
transX = transY = transZ = centerIdx = -1;
char *FileIn = NULL;
char *program_name = argv[0];
// char *iext;
OBConversion conv(&cin,&cout);
OBFormat *pFormat = conv.FindFormat("smi"); // default format is SMILES
// Still need to add:
// rotate X, Y, or Z by set angle
// translate X, Y, or Z by set amount
// Parse options
while ((c = getopt(argc, argv, "x:y:z:c:")) != -1)
{
switch (c)
{
case 'c': /// atom to be centered
c = sscanf(optarg, "%d", ¢erIdx);
if (c != 1 )
{
cerr << program_name << ": unable to parse -c option" << endl;
exit (-1);
}
break;
case 'x': /// atom to be centered
c = sscanf(optarg, "%d", &transX);
if (c != 1 )
{
cerr << program_name << ": unable to parse -x option" << endl;
exit (-1);
}
break;
case 'y': /// atom to y-axis
c = sscanf(optarg, "%d", &transY);
if (c != 1 )
{
cerr << program_name << ": unable to parse -y option" << endl;
exit (-1);
}
break;
case 'z': /// atom to z-axis
c = sscanf(optarg, "%d", &transZ);
if (c != 1 )
{
cerr << program_name << ": unable to parse -z option" << endl;
exit (-1);
}
break;
}
}
ifstream ifs;
FileIn = argv[optind];
if (FileIn != NULL)
{
// Read the file
ifs.open(FileIn);
if (!ifs)
{
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
conv.SetInStream(&ifs);
// Find Input filetype
pFormat = conv.FormatFromExt(FileIn);
if (pFormat == NULL)
{
cerr << program_name << ": cannot read input format!" << endl;
return (-1);
}
}
if (! conv.SetInAndOutFormats(pFormat, pFormat))
{
cerr << program_name << ": cannot read or write to this file format" << endl;
return (-1);
}
OBMol mol;
mol.Clear();
conv.Read(&mol);
if (mol.Empty())
return(1);
vector3 v;
if (centerIdx != -1)
{
v = (mol.GetAtom(centerIdx))->GetVector();
mol.Translate(-1.0f*v);
}
double alpha, beta, gamma;
alpha = beta = gamma = 0.0f;
if (transX != -1)
{
v = (mol.GetAtom(transX))->GetVector();
// angle to rotate vector into XZ plane
// (i.e., angle between x and y components)
gamma = M_PI/2.0 - atan(v.x() / v.y());
// angle to rotate vector from XZ plane to X axis
// (by rotation along Y-axis)
beta = atan(v.z() / sqrt(v.y()*v.y() + v.x()*v.x()) );
}
else if (transY != -1)
{
v = (mol.GetAtom(transY))->GetVector();
// angle to rotate vector into YZ plane
// (i.e., angle between x and y components)
gamma = -1.0 * atan(v.x() / v.y());
// angle to rotate vector from YZ plane to Y axis
// (by rotation along X-axis)
alpha = -1.0 * atan(v.z() / sqrt(v.y()*v.y() + v.x()*v.x()) );
}
else if (transZ != -1)
{
v = (mol.GetAtom(transZ))->GetVector();
// angle to rotate vector into YZ plane
// (i.e., angle between x and y components)
gamma = -1.0 * atan(v.x() / v.y());
// angle to rotate vector from YZ plane to Z axis
// (by rotation along X axis)
alpha = M_PI/2.0f - atan(v.z() / sqrt(v.y()*v.y() + v.x()*v.x()) );
}
if ( !IsNearZero(alpha) ||
!IsNearZero(beta) ||
!IsNearZero(gamma) )
{
matrix3x3 mat;
mat.SetupRotMat(alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG);
double array[9];
mat.GetArray(array);
mol.Rotate(array);
}
conv.Write(&mol, &cout);
return(0);
}
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