source: src/Fragmentation/Exporters/SaturatedFragment.hpp@ bdd5a8

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since bdd5a8 was de2cbf, checked in by Frederik Heber <heber@…>, 11 years ago

Added SaturateFragment()::saturateAtom() replacing all cut bonds at once.

  • so far, we have just outsourced the loop over each cut bond into this function.
  • Property mode set to 100644
File size: 6.7 KB
Line 
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
16#include <iosfwd>
17#include <set>
18#include <string>
19
20#include "Atom/atom_bondedparticleinfo.hpp"
21#include "Bond/bond.hpp"
22#include "Fragmentation/KeySet.hpp"
23#include "Fragmentation/HydrogenSaturation_enum.hpp"
24#include "Parser/FormatParserStorage.hpp"
25
26class atom;
27class HydrogenPool;
28
29/** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
30 * of saturation hydrogens.
31 *
32 * This SaturatedFragment along with a currently leased set of hydrogens from the
33 * HydrogenPool is all that is required to create a fully storable molecular
34 * fragment from a given Keyset.
35 *
36 * The instance notes down its existence in an external container.
37 *
38 */
39class SaturatedFragment
40{
41public:
42 //!> typedef to a container to mark keysets that are in use
43 typedef std::set<KeySet> KeySetsInUse_t;
44
45 /** Constructor of SaturatedFragment requires \a set which we are tightly
46 * associated.
47 *
48 * \param _set KeySet which this instance is associated with
49 * \param _container container to add KeySet as in-use
50 * \param _hydrogens pool with hydrogens for saturation
51 */
52 SaturatedFragment(
53 const KeySet &_set,
54 KeySetsInUse_t &_container,
55 HydrogenPool &_hydrogens,
56 const enum HydrogenTreatment _treatment,
57 const enum HydrogenSaturation saturation);
58
59 /** Destructor of class SaturatedFragment.
60 *
61 */
62 ~SaturatedFragment();
63
64 /** Getter for the KeySet this instance is associated with.
65 *
66 * \return const ref to KeySet
67 */
68 const KeySet & getKeySet() const
69 {
70 return set;
71 }
72
73 /** Getter for the FullMolecule this instance is associated with.
74 *
75 * \return const ref to FullMolecule
76 */
77 const KeySet & getFullMolecule() const
78 {
79 return FullMolecule;
80 }
81
82 /** Getter for the SaturationHydrogens this instance is associated with.
83 *
84 * \return const ref to SaturationHydrogens
85 */
86 const KeySet & getSaturationHydrogens() const
87 {
88 return SaturationHydrogens;
89 }
90
91 /** Prints the config of the fragment of \a _type to \a out.
92 *
93 * \param out output stream to write to
94 * \param _type parser type to write config
95 */
96 bool OutputConfig(
97 std::ostream &out,
98 const ParserTypes _type) const;
99
100private:
101 /** Helper function to lease and bring in place saturation hydrogens.
102 *
103 */
104 void saturate();
105
106 /** Replaces all cut bonds with respect to the given atom by hydrogens.
107 *
108 * \param _atom atom whose cut bonds to saturate
109 * \param _cutbonds list of cut bonds for \a _atom
110 * \return true - bonds saturated, false - something went wrong
111 */
112 bool saturateAtom(atom * const _atom, const BondList &_cutbonds);
113
114 /** Helper function to get a hydrogen replacement for a given \a replacement.
115 *
116 * \param replacement atom to "replace" with hydrogen in a fragment.
117 * \return ref to leased hydrogen atom
118 */
119 atom * const getHydrogenReplacement(atom * const replacement);
120
121 /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
122 * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
123 * a different scheme when adding \a *replacement atom for the given one.
124 * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
125 * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
126 * *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
127 * The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
128 * replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
129 * element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
130 * hydrogens forming this angle with *origin.
131 * -# 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
132 * triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
133 * determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
134 * We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
135 * \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 )}}
136 * \f]
137 * vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
138 * the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
139 * The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
140 * the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
141 * \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
142 * \f]
143 * as the coordination of all three atoms in the coordinate system of these three vectors:
144 * \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
145 *
146 * \param TopBond pointer to bond between \a *origin and \a *replacement
147 * \param Origin atom that is actually contained in the fragment
148 * \param Replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
149 * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
150 * \return number of atoms added, if < bond::BondDegree then something went wrong
151 */
152 bool AddHydrogenReplacementAtom(
153 bond::ptr TopBond,
154 atom *Origin,
155 atom *Replacement,
156 bool IsAngstroem);
157
158private:
159 //!> container to mark ourselves RAII-style
160 KeySetsInUse_t &container;
161 //!> key set this fragment is associated with.
162 const KeySet &set;
163 //!> pool with saturation hydrogens
164 HydrogenPool &hydrogens;
165 //!> key set containing all atoms used for e.g. storing this to file
166 KeySet FullMolecule;
167 //!> key set containing the ids of all hydrogens added for saturation
168 KeySet SaturationHydrogens;
169 //!> whether hydrogens are generally contained in set or not
170 const enum HydrogenTreatment treatment;
171 //!> whether to actually saturate or not
172 const enum HydrogenSaturation saturation;
173};
174
175#endif /* SATURATEDFRAGMENT_HPP_ */
Note: See TracBrowser for help on using the repository browser.