[7d5fcd] | 1 | /*
|
---|
| 2 | * SaturatedFragment.hpp
|
---|
| 3 | *
|
---|
| 4 | * Created on: Mar 3, 2013
|
---|
| 5 | * Author: heber
|
---|
| 6 | */
|
---|
| 7 |
|
---|
| 8 | #ifndef SATURATEDFRAGMENT_HPP_
|
---|
| 9 | #define SATURATEDFRAGMENT_HPP_
|
---|
| 10 |
|
---|
| 11 | // include config.h
|
---|
| 12 | #ifdef HAVE_CONFIG_H
|
---|
| 13 | #include <config.h>
|
---|
| 14 | #endif
|
---|
| 15 |
|
---|
[c39675] | 16 | #include <iosfwd>
|
---|
[7d5fcd] | 17 | #include <set>
|
---|
[c39675] | 18 | #include <string>
|
---|
[7d5fcd] | 19 |
|
---|
[de2cbf] | 20 | #include "Atom/atom_bondedparticleinfo.hpp"
|
---|
[c39675] | 21 | #include "Bond/bond.hpp"
|
---|
[7d5fcd] | 22 | #include "Fragmentation/KeySet.hpp"
|
---|
[c39675] | 23 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
|
---|
| 24 | #include "Parser/FormatParserStorage.hpp"
|
---|
[7d5fcd] | 25 |
|
---|
[98a293b] | 26 | #include "LinearAlgebra/Vector.hpp"
|
---|
| 27 |
|
---|
[c39675] | 28 | class atom;
|
---|
[7d5fcd] | 29 | class HydrogenPool;
|
---|
| 30 |
|
---|
| 31 | /** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
|
---|
| 32 | * of saturation hydrogens.
|
---|
| 33 | *
|
---|
| 34 | * This SaturatedFragment along with a currently leased set of hydrogens from the
|
---|
| 35 | * HydrogenPool is all that is required to create a fully storable molecular
|
---|
| 36 | * fragment from a given Keyset.
|
---|
| 37 | *
|
---|
| 38 | * The instance notes down its existence in an external container.
|
---|
| 39 | *
|
---|
| 40 | */
|
---|
| 41 | class SaturatedFragment
|
---|
| 42 | {
|
---|
| 43 | public:
|
---|
| 44 | //!> typedef to a container to mark keysets that are in use
|
---|
| 45 | typedef std::set<KeySet> KeySetsInUse_t;
|
---|
| 46 |
|
---|
[98a293b] | 47 | //!> List of points giving saturation positions for a single bond neighbor
|
---|
| 48 | typedef std::list<Vector> SaturationsPositions_t;
|
---|
| 49 | //!> map for one atom, containing the saturation points for all its neighbors
|
---|
| 50 | typedef std::map<int, SaturationsPositions_t> SaturationsPositionsPerNeighbor_t;
|
---|
| 51 | //!> containing the saturation points over all desired atoms required
|
---|
| 52 | typedef std::map<int, SaturationsPositionsPerNeighbor_t> GlobalSaturationPositions_t;
|
---|
| 53 |
|
---|
[7d5fcd] | 54 | /** Constructor of SaturatedFragment requires \a set which we are tightly
|
---|
| 55 | * associated.
|
---|
| 56 | *
|
---|
| 57 | * \param _set KeySet which this instance is associated with
|
---|
| 58 | * \param _container container to add KeySet as in-use
|
---|
| 59 | * \param _hydrogens pool with hydrogens for saturation
|
---|
[98a293b] | 60 | * \param _globalsaturationpositions saturation positions to be used
|
---|
[7d5fcd] | 61 | */
|
---|
| 62 | SaturatedFragment(
|
---|
| 63 | const KeySet &_set,
|
---|
| 64 | KeySetsInUse_t &_container,
|
---|
[c39675] | 65 | HydrogenPool &_hydrogens,
|
---|
| 66 | const enum HydrogenTreatment _treatment,
|
---|
[98a293b] | 67 | const enum HydrogenSaturation saturation,
|
---|
| 68 | const GlobalSaturationPositions_t &_globalsaturationpositions);
|
---|
[7d5fcd] | 69 |
|
---|
| 70 | /** Destructor of class SaturatedFragment.
|
---|
| 71 | *
|
---|
| 72 | */
|
---|
| 73 | ~SaturatedFragment();
|
---|
| 74 |
|
---|
| 75 | /** Getter for the KeySet this instance is associated with.
|
---|
| 76 | *
|
---|
| 77 | * \return const ref to KeySet
|
---|
| 78 | */
|
---|
| 79 | const KeySet & getKeySet() const
|
---|
| 80 | {
|
---|
| 81 | return set;
|
---|
| 82 | }
|
---|
| 83 |
|
---|
[c39675] | 84 | /** Getter for the FullMolecule this instance is associated with.
|
---|
| 85 | *
|
---|
| 86 | * \return const ref to FullMolecule
|
---|
| 87 | */
|
---|
| 88 | const KeySet & getFullMolecule() const
|
---|
| 89 | {
|
---|
| 90 | return FullMolecule;
|
---|
| 91 | }
|
---|
| 92 |
|
---|
| 93 | /** Getter for the SaturationHydrogens this instance is associated with.
|
---|
| 94 | *
|
---|
| 95 | * \return const ref to SaturationHydrogens
|
---|
| 96 | */
|
---|
| 97 | const KeySet & getSaturationHydrogens() const
|
---|
| 98 | {
|
---|
| 99 | return SaturationHydrogens;
|
---|
| 100 | }
|
---|
| 101 |
|
---|
| 102 | /** Prints the config of the fragment of \a _type to \a out.
|
---|
| 103 | *
|
---|
| 104 | * \param out output stream to write to
|
---|
| 105 | * \param _type parser type to write config
|
---|
| 106 | */
|
---|
| 107 | bool OutputConfig(
|
---|
| 108 | std::ostream &out,
|
---|
| 109 | const ParserTypes _type) const;
|
---|
| 110 |
|
---|
| 111 | private:
|
---|
| 112 | /** Helper function to lease and bring in place saturation hydrogens.
|
---|
[98a293b] | 113 | *
|
---|
| 114 | * Here, we use local information to calculate saturation positions.
|
---|
[c39675] | 115 | *
|
---|
| 116 | */
|
---|
| 117 | void saturate();
|
---|
| 118 |
|
---|
[98a293b] | 119 | /** Helper function to lease and bring in place saturation hydrogens.
|
---|
| 120 | *
|
---|
| 121 | * Here, saturation positions have to be calculated before and are fully
|
---|
| 122 | * stored in \a _globalsaturationpositions.
|
---|
| 123 | *
|
---|
| 124 | * \param_globalsaturationpositions
|
---|
| 125 | */
|
---|
| 126 | void saturate(const GlobalSaturationPositions_t &_globalsaturationpositions);
|
---|
| 127 |
|
---|
[de2cbf] | 128 | /** Replaces all cut bonds with respect to the given atom by hydrogens.
|
---|
| 129 | *
|
---|
| 130 | * \param _atom atom whose cut bonds to saturate
|
---|
| 131 | * \param _cutbonds list of cut bonds for \a _atom
|
---|
| 132 | * \return true - bonds saturated, false - something went wrong
|
---|
| 133 | */
|
---|
| 134 | bool saturateAtom(atom * const _atom, const BondList &_cutbonds);
|
---|
| 135 |
|
---|
[c39675] | 136 | /** Helper function to get a hydrogen replacement for a given \a replacement.
|
---|
| 137 | *
|
---|
| 138 | * \param replacement atom to "replace" with hydrogen in a fragment.
|
---|
| 139 | * \return ref to leased hydrogen atom
|
---|
| 140 | */
|
---|
| 141 | atom * const getHydrogenReplacement(atom * const replacement);
|
---|
| 142 |
|
---|
[98a293b] | 143 | /** Sets a saturation hydrogen at the given position in place of \a _father.
|
---|
| 144 | *
|
---|
| 145 | * \param _OwnerAtom atom "owning" the hydrogen (i.e. the one getting saturated)
|
---|
| 146 | * \param _position new position relative to \a _OwnerAtom
|
---|
| 147 | * \param _distance scale factor to the distance (default 1.)
|
---|
| 148 | * \param _father bond partner of \a _OwnerAtom that is replaced
|
---|
| 149 | */
|
---|
| 150 | const atom& setHydrogenReplacement(
|
---|
| 151 | const atom * const _OwnerAtom,
|
---|
| 152 | const Vector &_position,
|
---|
| 153 | const double _distance,
|
---|
| 154 | atom * const _father);
|
---|
| 155 |
|
---|
[c39675] | 156 | /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
|
---|
| 157 | * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
|
---|
| 158 | * a different scheme when adding \a *replacement atom for the given one.
|
---|
| 159 | * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
|
---|
| 160 | * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
|
---|
| 161 | * *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
|
---|
| 162 | * The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
|
---|
| 163 | * replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
|
---|
| 164 | * element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
|
---|
| 165 | * hydrogens forming this angle with *origin.
|
---|
| 166 | * -# Triple Bond: The idea is to set up a tetraoid (C1-H1-H2-H3) (however the lengths \f$b\f$ of the sides of the base
|
---|
| 167 | * triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
|
---|
| 168 | * determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
|
---|
| 169 | * We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
|
---|
| 170 | * \f[ h = l \cdot \cos{\left (\frac{\alpha}{2} \right )} \qquad b = 2l \cdot \sin{\left (\frac{\alpha}{2} \right)} \quad \rightarrow \quad d = l \cdot \sqrt{\cos^2{\left (\frac{\alpha}{2} \right)}-\frac{1}{3}\cdot\sin^2{\left (\frac{\alpha}{2}\right )}}
|
---|
| 171 | * \f]
|
---|
| 172 | * vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
|
---|
| 173 | * the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
|
---|
| 174 | * The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
|
---|
| 175 | * the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
|
---|
| 176 | * \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
|
---|
| 177 | * \f]
|
---|
| 178 | * as the coordination of all three atoms in the coordinate system of these three vectors:
|
---|
| 179 | * \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
|
---|
| 180 | *
|
---|
| 181 | * \param TopBond pointer to bond between \a *origin and \a *replacement
|
---|
| 182 | * \param Origin atom that is actually contained in the fragment
|
---|
| 183 | * \param Replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
|
---|
| 184 | * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
|
---|
| 185 | * \return number of atoms added, if < bond::BondDegree then something went wrong
|
---|
| 186 | */
|
---|
| 187 | bool AddHydrogenReplacementAtom(
|
---|
| 188 | bond::ptr TopBond,
|
---|
| 189 | atom *Origin,
|
---|
| 190 | atom *Replacement,
|
---|
| 191 | bool IsAngstroem);
|
---|
| 192 |
|
---|
[7d5fcd] | 193 | private:
|
---|
| 194 | //!> container to mark ourselves RAII-style
|
---|
| 195 | KeySetsInUse_t &container;
|
---|
| 196 | //!> key set this fragment is associated with.
|
---|
| 197 | const KeySet &set;
|
---|
| 198 | //!> pool with saturation hydrogens
|
---|
| 199 | HydrogenPool &hydrogens;
|
---|
| 200 | //!> key set containing all atoms used for e.g. storing this to file
|
---|
| 201 | KeySet FullMolecule;
|
---|
| 202 | //!> key set containing the ids of all hydrogens added for saturation
|
---|
| 203 | KeySet SaturationHydrogens;
|
---|
[c39675] | 204 | //!> whether hydrogens are generally contained in set or not
|
---|
| 205 | const enum HydrogenTreatment treatment;
|
---|
| 206 | //!> whether to actually saturate or not
|
---|
| 207 | const enum HydrogenSaturation saturation;
|
---|
[7d5fcd] | 208 | };
|
---|
| 209 |
|
---|
| 210 | #endif /* SATURATEDFRAGMENT_HPP_ */
|
---|