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139 lines
3.8 KiB
C++
139 lines
3.8 KiB
C++
//
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// Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#ifndef _RD_CONFORMER_H
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#define _RD_CONFORMER_H
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#include <Geometry/point.h>
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#include <RDGeneral/types.h>
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#include <boost/smart_ptr.hpp>
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namespace RDKit {
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class ROMol;
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//! used to indicate errors from incorrect confomer access
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class ConformerException : public std::exception {
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public:
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//! construct with an error message
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ConformerException(const char *msg) : _msg(msg) {};
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//! construct with an error message
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ConformerException(const std::string msg) : _msg(msg) {};
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//! get the error message
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const char *message () const { return _msg.c_str(); };
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~ConformerException () throw () {};
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private:
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std::string _msg;
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};
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//! The class for representing 2D or 3D conformation of a molecule
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/*!
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This class contains
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- a pointer to the owing molecule
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- a vector of 3D points (positions of atoms)
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*/
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class Conformer {
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public:
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friend class ROMol;
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//! Constructor
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Conformer() : df_is3D(true), d_id(0), dp_mol(NULL) {
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d_positions.clear();
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};
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//! Constructor with number of atoms specified ID specification
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Conformer(unsigned int numAtoms) : df_is3D(true), d_id(0), dp_mol(NULL) {
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if(numAtoms){
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d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
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} else {
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d_positions.resize(0);
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d_positions.clear();
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}
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};
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//! Copy Constructor: initialize from a second conformation.
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Conformer(const Conformer &other);
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//! Destructor
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~Conformer() {};
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//! Resize the conformer so that more atoms location can be added.
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//! Useful, for e.g., when adding hydrogens
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void resize(unsigned int size) {
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d_positions.resize(size);
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}
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//! Reserve more space for atom position
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void reserve(unsigned int size) {
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d_positions.reserve(size);
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}
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//! Get the molecule that oqns this conformation
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ROMol &getOwningMol() const {return *dp_mol;}
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//! Get a const reference to the vector of atom positions
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const RDGeom::POINT3D_VECT &getPositions() const;
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//! Get a reference to the atom positions
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RDGeom::POINT3D_VECT &getPositions();
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//! Get the position of the specified atom
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const RDGeom::Point3D &getAtomPos(unsigned int atomId) const;
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//! Get the position of the specified atom
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RDGeom::Point3D &getAtomPos(unsigned int atomId);
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//! Set the position of the specified atom
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inline void setAtomPos(unsigned int atomId, const RDGeom::Point3D &position) {
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//RANGE_CHECK(0,atomId,d_positions.size()-1);
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if (atomId >= d_positions.size()) {
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d_positions.resize(atomId+1, RDGeom::Point3D(0.0, 0.0, 0.0));
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}
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d_positions[atomId] = position;
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}
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//! get the ID of this conformer
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inline unsigned int getId() const {return d_id;}
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//! set the ID of this conformer
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inline void setId(unsigned int id) {
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d_id = id;
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}
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//! Get the number of atoms
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inline unsigned int getNumAtoms() const {
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return d_positions.size();
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}
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inline bool is3D() const {
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return df_is3D;
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}
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inline void set3D(bool v) {
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df_is3D=v;
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}
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protected:
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//! Set owning moelcule
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void setOwningMol(ROMol *mol);
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//! Set owning moelcule
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void setOwningMol(ROMol &mol);
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private:
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bool df_is3D; // is this a 3D conformation?
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unsigned int d_id; // id is the conformation
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ROMol *dp_mol; // owning molecule
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RDGeom::POINT3D_VECT d_positions; // positions of the atoms
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};
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typedef boost::shared_ptr<Conformer> CONFORMER_SPTR;
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}
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#endif
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