00001
00002
00003
00004
00005
00006
00007
00008
00009
00010
00011
00012
00013
00014
00015
00016
00017
00018
00019
00020
00021
00022
00023
00024
00025
00026
00027
00028 #ifndef _chemistry_molecule_molecule_h
00029 #define _chemistry_molecule_molecule_h
00030
00031 #ifdef __GNUC__
00032 #pragma interface
00033 #endif
00034
00035 #include <stdio.h>
00036 #include <iostream>
00037 #include <util/class/class.h>
00038 #include <util/state/state.h>
00039 #include <util/keyval/keyval.h>
00040 #include <util/misc/units.h>
00041 #include <math/symmetry/pointgrp.h>
00042 #include <math/scmat/vector3.h>
00043 #include <math/scmat/matrix.h>
00044 #include <chemistry/molecule/atominfo.h>
00045
00046 namespace sc {
00047
00099 class Molecule: public SavableState
00100 {
00101 protected:
00102 int natoms_;
00103 Ref<AtomInfo> atominfo_;
00104 Ref<PointGroup> pg_;
00105 Ref<Units> geometry_units_;
00106 double **r_;
00107 int *Z_;
00108 double *charges_;
00109
00110
00111 int nuniq_;
00112 int *nequiv_;
00113 int **equiv_;
00114 int *atom_to_uniq_;
00115 void init_symmetry_info(double tol=0.5);
00116 void clear_symmetry_info();
00117
00118
00119 double *mass_;
00120 char **labels_;
00121
00122 void clear();
00123 public:
00124 Molecule();
00125 Molecule(const Molecule&);
00126 Molecule(StateIn&);
00128 Molecule(const Ref<KeyVal>&input);
00129
00130 virtual ~Molecule();
00131
00132 Molecule& operator=(const Molecule&);
00133
00135 void add_atom(int Z,double x,double y,double z,
00136 const char * = 0, double mass = 0.0,
00137 int have_charge = 0, double charge = 0.0);
00138
00140 virtual void print(std::ostream& =ExEnv::out0()) const;
00141 virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(),
00142 int print_pg = 1,
00143 int print_unit = 1,
00144 int number_atoms = 1) const;
00145
00147 int natom() const { return natoms_; }
00148
00149 int Z(int atom) const { return Z_[atom]; }
00150 double &r(int atom, int xyz) { return r_[atom][xyz]; }
00151 const double &r(int atom, int xyz) const { return r_[atom][xyz]; }
00152 double *r(int atom) { return r_[atom]; }
00153 const double *r(int atom) const { return r_[atom]; }
00154 double mass(int atom) const;
00157 const char *label(int atom) const;
00158
00161 int atom_at_position(double *, double tol = 0.05) const;
00162
00165 int atom_label_to_index(const char *label) const;
00166
00170 double *charges() const;
00171
00173 double charge(int iatom) const;
00174
00176 double nuclear_charge() const;
00177
00179 void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7);
00181 Ref<PointGroup> point_group() const;
00182
00186 Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const;
00187
00190 int is_axis(SCVector3 &origin,
00191 SCVector3 &udirection, int order, double tol=1.0e-8) const;
00192
00195 int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const;
00196
00198 int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const;
00199
00201 int is_linear(double tolerance = 1.0e-5) const;
00203 int is_planar(double tolerance = 1.0e-5) const;
00206 void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const;
00207
00210 SCVector3 center_of_mass() const;
00211
00213 double nuclear_repulsion_energy();
00214
00217 void nuclear_repulsion_1der(int center, double xyz[3]);
00218
00220 void nuclear_efield(const double *position, double* efield);
00221
00224 void nuclear_charge_efield(const double *charges,
00225 const double *position, double* efield);
00226
00232 void symmetrize(double tol = 0.5);
00233
00235 void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5);
00236
00240 void cleanup_molecule(double tol = 0.1);
00241
00242 void translate(const double *r);
00243 void move_to_com();
00244 void transform_to_principal_axes(int trans_frame=1);
00245 void transform_to_symmetry_frame();
00246 void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const;
00247
00248 void read_pdb(const char *filename);
00249
00252 void principal_moments_of_inertia(double *evals, double **evecs=0) const;
00253
00255 int nunique() const { return nuniq_; }
00257 int unique(int iuniq) const { return equiv_[iuniq][0]; }
00259 int nequivalent(int iuniq) const { return nequiv_[iuniq]; }
00261 int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; }
00264 int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; }
00267 int atom_to_unique_offset(int iatom) const;
00268
00270 int n_core_electrons();
00271
00273 int max_z();
00274
00276 Ref<AtomInfo> atominfo() const { return atominfo_; }
00277
00278 void save_data_state(StateOut&);
00279 };
00280
00281 }
00282
00283 #endif
00284
00285
00286
00287
00288