distgeom.h

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/**********************************************************************
distgeom.h - Distance Geometry generation and sampling

 Copyright (C) 2011 by Tim Vandermeersch
 Copyright (C) 2012 by Geoffrey 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.
***********************************************************************/

#ifndef OB_DISTGEOM_H
#define OB_DISTGEOM_H

#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>

#ifndef OBAPI
 #define OBAPI
#endif

#ifdef HAVE_EIGEN

#include <Eigen/Core>

namespace OpenBabel {

 class DistanceGeometryPrivate;
 class OBCisTransStereo;

 class OBAPI OBDistanceGeometry {
 public:
 OBDistanceGeometry();
 OBDistanceGeometry(const OBMol &mol, bool useCurrentGeometry);
 ~OBDistanceGeometry();

 bool Setup(const OBMol &mol, bool useCurrentGeom = false);

 void AddConformer();
 void GetConformers(OBMol &mol);

 bool GetGeometry(OBMol &mol, bool useCurrentGeom = false);

 Eigen::MatrixXf GetBoundsMatrix();
 bool SetBoundsMatrix(const Eigen::MatrixXf bounds);

 private:
 OBMol _mol;
 DistanceGeometryPrivate *_d; 

 void SetUpperBounds();
 void Set12Bounds(bool useCurrentGeom);
 void Set13Bounds(bool useCurrentGeom);
 void SetAromaticRingBounds();
 void Set14Bounds();
 void Set15Bounds();
 int AreInSameRing(OBAtom *a, OBAtom *b);
 void TriangleSmooth(int iterations = 8);
 void SetLowerBounds();

 OBCisTransStereo *GetCisTransStereo(OBBond *bond);

 void CorrectStereoConstraints(double scale = 1.0);
 bool CheckStereoConstraints();

 bool CheckBounds();
 };


}

#endif

#endif