[7d5fcd] | 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2013 University of Bonn. All rights reserved.
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[5aaa43] | 5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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[7d5fcd] | 6 | *
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| 7 | *
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| 8 | * This file is part of MoleCuilder.
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| 9 | *
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| 10 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 11 | * it under the terms of the GNU General Public License as published by
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| 12 | * the Free Software Foundation, either version 2 of the License, or
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| 13 | * (at your option) any later version.
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| 14 | *
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| 15 | * MoleCuilder is distributed in the hope that it will be useful,
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| 16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 18 | * GNU General Public License for more details.
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| 19 | *
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| 20 | * You should have received a copy of the GNU General Public License
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| 21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 22 | */
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| 23 |
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| 24 | /*
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| 25 | * SaturatedFragment.cpp
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| 26 | *
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| 27 | * Created on: Mar 3, 2013
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| 28 | * Author: heber
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| 29 | */
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| 30 |
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| 31 | // include config.h
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| 32 | #ifdef HAVE_CONFIG_H
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| 33 | #include <config.h>
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| 34 | #endif
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| 35 |
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| 36 | #include "CodePatterns/MemDebug.hpp"
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| 37 |
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| 38 | #include "SaturatedFragment.hpp"
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| 39 |
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[c39675] | 40 | #include <cmath>
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| 41 | #include <iostream>
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| 42 |
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[7d5fcd] | 43 | #include "CodePatterns/Assert.hpp"
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[c39675] | 44 | #include "CodePatterns/Log.hpp"
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| 45 |
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| 46 | #include "LinearAlgebra/Exceptions.hpp"
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| 47 | #include "LinearAlgebra/Plane.hpp"
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| 48 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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| 49 | #include "LinearAlgebra/Vector.hpp"
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[7d5fcd] | 50 |
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[c39675] | 51 | #include "Atom/atom.hpp"
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| 52 | #include "Bond/bond.hpp"
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| 53 | #include "config.hpp"
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| 54 | #include "Descriptors/AtomIdDescriptor.hpp"
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[7d5fcd] | 55 | #include "Fragmentation/Exporters/HydrogenPool.hpp"
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[c39675] | 56 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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| 57 | #include "Graph/BondGraph.hpp"
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| 58 | #include "World.hpp"
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[7d5fcd] | 59 |
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| 60 | SaturatedFragment::SaturatedFragment(
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| 61 | const KeySet &_set,
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| 62 | KeySetsInUse_t &_container,
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[c39675] | 63 | HydrogenPool &_hydrogens,
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| 64 | const enum HydrogenTreatment _treatment,
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| 65 | const enum HydrogenSaturation _saturation) :
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[7d5fcd] | 66 | container(_container),
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| 67 | set(_set),
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| 68 | hydrogens(_hydrogens),
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[c39675] | 69 | FullMolecule(set),
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| 70 | treatment(_treatment),
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| 71 | saturation(_saturation)
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[7d5fcd] | 72 | {
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| 73 | // add to in-use container
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| 74 | ASSERT( container.find(set) == container.end(),
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| 75 | "SaturatedFragment::SaturatedFragment() - the set "
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| 76 | +toString(set)+" is already marked as in use.");
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| 77 | container.insert(set);
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| 78 |
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[c39675] | 79 | // prepare saturation hydrogens
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| 80 | saturate();
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[7d5fcd] | 81 | }
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| 82 |
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| 83 | SaturatedFragment::~SaturatedFragment()
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| 84 | {
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| 85 | // release all saturation hydrogens if present
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| 86 | for (KeySet::iterator iter = SaturationHydrogens.begin();
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| 87 | !SaturationHydrogens.empty();
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| 88 | iter = SaturationHydrogens.begin()) {
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| 89 | hydrogens.releaseHydrogen(*iter);
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| 90 | SaturationHydrogens.erase(iter);
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| 91 | }
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| 92 |
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| 93 | // remove ourselves from in-use container
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| 94 | KeySetsInUse_t::iterator iter = container.find(set);
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| 95 | ASSERT( container.find(set) != container.end(),
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| 96 | "SaturatedFragment::SaturatedFragment() - the set "
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| 97 | +toString(set)+" is not marked as in use.");
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| 98 | container.erase(iter);
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| 99 | }
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[c39675] | 100 |
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| 101 | void SaturatedFragment::saturate()
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| 102 | {
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[9d3264] | 103 | // so far, we just have a set of keys. Hence, convert to atom refs
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| 104 | // and gather all atoms in a vector
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[c39675] | 105 | std::vector<atom *> atoms;
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| 106 | for (KeySet::const_iterator iter = FullMolecule.begin();
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| 107 | iter != FullMolecule.end();
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| 108 | ++iter) {
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| 109 | atom * const Walker = World::getInstance().getAtom(AtomById(*iter));
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| 110 | ASSERT( Walker != NULL,
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| 111 | "SaturatedFragment::OutputConfig() - id "
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| 112 | +toString(*iter)+" is unknown to World.");
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| 113 | atoms.push_back(Walker);
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| 114 | }
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| 115 |
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| 116 | // bool LonelyFlag = false;
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[9d3264] | 117 | // go through each atom of the fragment and gather all cut bonds in list
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| 118 | typedef std::map<atom *, BondList > CutBonds_t;
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| 119 | CutBonds_t CutBonds;
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[c39675] | 120 | for (std::vector<atom *>::const_iterator iter = atoms.begin();
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| 121 | iter != atoms.end();
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| 122 | ++iter) {
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| 123 | atom * const Walker = *iter;
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| 124 |
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| 125 | // go through all bonds
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| 126 | const BondList& ListOfBonds = Walker->getListOfBonds();
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| 127 | for (BondList::const_iterator BondRunner = ListOfBonds.begin();
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| 128 | BondRunner != ListOfBonds.end();
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| 129 | ++BondRunner) {
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| 130 | atom * const OtherWalker = (*BondRunner)->GetOtherAtom(Walker);
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[9d3264] | 131 | // if other atom is in key set
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[c39675] | 132 | if (set.find(OtherWalker->getId()) != set.end()) {
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| 133 | LOG(4, "DEBUG: Walker " << *Walker << " is bound to " << *OtherWalker << ".");
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| 134 | // if (OtherWalker->getId() > Walker->getId()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
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| 135 | //// std::stringstream output;
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| 136 | //// output << "ACCEPT: Adding Bond: "
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[1f693d] | 137 | // output << Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
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[c39675] | 138 | //// LOG(3, output.str());
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| 139 | // //NumBonds[(*iter)->getNr()]++;
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| 140 | // } else {
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| 141 | //// LOG(3, "REJECY: Not adding bond, labels in wrong order.");
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| 142 | // }
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| 143 | // LonelyFlag = false;
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| 144 | } else {
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| 145 | LOG(4, "DEBUG: Walker " << *Walker << " is bound to "
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| 146 | << *OtherWalker << ", who is not in this fragment molecule.");
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| 147 | if (saturation == DoSaturate) {
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| 148 | // LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
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[9d3264] | 149 | if (CutBonds.count(Walker) == 0)
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| 150 | CutBonds.insert( std::make_pair(Walker, BondList() ));
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| 151 | CutBonds[Walker].push_back(*BondRunner);
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[c39675] | 152 | }
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| 153 | // } else if ((treatment == ExcludeHydrogen) && (OtherWalker->getElementNo() == (atomicNumber_t)1)) {
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| 154 | // // just copy the atom if it's a hydrogen
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| 155 | // atom * const OtherWalker = Leaf->AddCopyAtom(OtherWalker);
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[1f693d] | 156 | // Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
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[c39675] | 157 | // }
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[1f693d] | 158 | //NumBonds[(*iter)->getNr()] += Binder->getDegree();
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[c39675] | 159 | }
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| 160 | }
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| 161 | }
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[9d3264] | 162 |
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| 163 | // go through all cut bonds and replace with a hydrogen
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| 164 | for (CutBonds_t::const_iterator atomiter = CutBonds.begin();
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| 165 | atomiter != CutBonds.end(); ++atomiter) {
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| 166 | atom * const Walker = atomiter->first;
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| 167 | // go through each bond and replace
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| 168 | for (BondList::const_iterator bonditer = atomiter->second.begin();
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| 169 | bonditer != atomiter->second.end(); ++bonditer) {
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| 170 | atom * const OtherWalker = (*bonditer)->GetOtherAtom(Walker);
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| 171 | if (!AddHydrogenReplacementAtom(
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| 172 | (*bonditer),
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| 173 | Walker,
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| 174 | OtherWalker,
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| 175 | World::getInstance().getConfig()->IsAngstroem == 1))
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| 176 | exit(1);
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| 177 | }
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| 178 | }
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[c39675] | 179 | }
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| 180 |
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| 181 | bool SaturatedFragment::OutputConfig(
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| 182 | std::ostream &out,
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| 183 | const ParserTypes _type) const
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| 184 | {
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| 185 | // gather all atoms in a vector
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| 186 | std::vector<atom *> atoms;
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| 187 | for (KeySet::const_iterator iter = FullMolecule.begin();
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| 188 | iter != FullMolecule.end();
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| 189 | ++iter) {
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| 190 | atom * const Walker = World::getInstance().getAtom(AtomById(*iter));
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| 191 | ASSERT( Walker != NULL,
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| 192 | "SaturatedFragment::OutputConfig() - id "
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| 193 | +toString(*iter)+" is unknown to World.");
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| 194 | atoms.push_back(Walker);
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| 195 | }
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| 196 |
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| 197 | // TODO: ScanForPeriodicCorrection() is missing so far!
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| 198 | // note however that this is not straight-forward for the following reasons:
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| 199 | // - we do not copy all atoms anymore, hence we are forced to shift the real
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| 200 | // atoms hither and back again
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| 201 | // - we use a long-range potential that supports periodic boundary conditions.
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| 202 | // Hence, there we would like the original configuration (split through the
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| 203 | // the periodic boundaries). Otherwise, we would have to shift (and probably
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| 204 | // interpolate) the potential with OBCs applying.
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| 205 |
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| 206 | // list atoms in fragment for debugging
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| 207 | {
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| 208 | std::stringstream output;
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| 209 | output << "INFO: Contained atoms: ";
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| 210 | for (std::vector<atom *>::const_iterator iter = atoms.begin();
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| 211 | iter != atoms.end(); ++iter) {
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| 212 | output << (*iter)->getName() << " ";
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| 213 | }
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| 214 | LOG(3, output.str());
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| 215 | }
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| 216 |
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| 217 | // store to stream via FragmentParser
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| 218 | const bool intermediateResult =
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| 219 | FormatParserStorage::getInstance().save(
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| 220 | out,
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| 221 | FormatParserStorage::getInstance().getSuffixFromType(_type),
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| 222 | atoms);
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| 223 |
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| 224 | return intermediateResult;
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| 225 | }
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| 226 |
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| 227 | atom * const SaturatedFragment::getHydrogenReplacement(atom * const replacement)
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| 228 | {
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| 229 | atom * const _atom = hydrogens.leaseHydrogen(); // new atom
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| 230 | _atom->setAtomicVelocity(replacement->getAtomicVelocity()); // copy velocity
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| 231 | _atom->setFixedIon(replacement->getFixedIon());
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| 232 | // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
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| 233 | _atom->father = replacement;
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| 234 | SaturationHydrogens.insert(_atom->getId());
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| 235 | return _atom;
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| 236 | }
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| 237 |
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| 238 | bool SaturatedFragment::AddHydrogenReplacementAtom(
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| 239 | bond::ptr TopBond,
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| 240 | atom *Origin,
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| 241 | atom *Replacement,
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| 242 | bool IsAngstroem)
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| 243 | {
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| 244 | // Info info(__func__);
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| 245 | bool AllWentWell = true; // flag gathering the boolean return value of molecule::AddAtom and other functions, as return value on exit
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| 246 | double bondlength; // bond length of the bond to be replaced/cut
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| 247 | double bondangle; // bond angle of the bond to be replaced/cut
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| 248 | double BondRescale; // rescale value for the hydrogen bond length
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| 249 | bond::ptr FirstBond;
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| 250 | bond::ptr SecondBond; // Other bonds in double bond case to determine "other" plane
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| 251 | atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
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| 252 | double b,l,d,f,g, alpha, factors[NDIM]; // hold temporary values in triple bond case for coordination determination
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| 253 | Vector Orthovector1, Orthovector2; // temporary vectors in coordination construction
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| 254 | Vector InBondvector; // vector in direction of *Bond
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| 255 | const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
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| 256 | bond::ptr Binder;
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| 257 |
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| 258 | // create vector in direction of bond
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| 259 | InBondvector = Replacement->getPosition() - Origin->getPosition();
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| 260 | bondlength = InBondvector.Norm();
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| 261 |
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| 262 | // is greater than typical bond distance? Then we have to correct periodically
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| 263 | // the problem is not the H being out of the box, but InBondvector have the wrong direction
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| 264 | // due to Replacement or Origin being on the wrong side!
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| 265 | const BondGraph * const BG = World::getInstance().getBondGraph();
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| 266 | const range<double> MinMaxBondDistance(
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| 267 | BG->getMinMaxDistance(Origin,Replacement));
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| 268 | if (!MinMaxBondDistance.isInRange(bondlength)) {
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| 269 | // LOG(4, "InBondvector is: " << InBondvector << ".");
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| 270 | Orthovector1.Zero();
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| 271 | for (int i=NDIM;i--;) {
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| 272 | l = Replacement->at(i) - Origin->at(i);
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| 273 | if (fabs(l) > MinMaxBondDistance.last) { // is component greater than bond distance (check against min not useful here)
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| 274 | Orthovector1[i] = (l < 0) ? -1. : +1.;
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| 275 | } // (signs are correct, was tested!)
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| 276 | }
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| 277 | Orthovector1 *= matrix;
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| 278 | InBondvector -= Orthovector1; // subtract just the additional translation
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| 279 | bondlength = InBondvector.Norm();
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| 280 | // LOG(4, "INFO: Corrected InBondvector is now: " << InBondvector << ".");
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| 281 | } // periodic correction finished
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| 282 |
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| 283 | InBondvector.Normalize();
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| 284 | // get typical bond length and store as scale factor for later
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| 285 | ASSERT(Origin->getType() != NULL,
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| 286 | "SaturatedFragment::AddHydrogenReplacementAtom() - element of Origin is not given.");
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[1f693d] | 287 | BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree()-1);
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[c39675] | 288 | if (BondRescale == -1) {
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[1f693d] | 289 | ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
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[3fbdca] | 290 | BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree());
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| 291 | if (BondRescale == -1) {
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| 292 | ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of any degree!");
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| 293 | return false;
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| 294 | BondRescale = bondlength;
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| 295 | }
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[c39675] | 296 | } else {
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| 297 | if (!IsAngstroem)
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| 298 | BondRescale /= (1.*AtomicLengthToAngstroem);
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| 299 | }
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| 300 |
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| 301 | // discern single, double and triple bonds
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[1f693d] | 302 | switch(TopBond->getDegree()) {
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[c39675] | 303 | case 1:
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| 304 | // check whether replacement has been an excluded hydrogen
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| 305 | if (Replacement->getType()->getAtomicNumber() == HydrogenPool::HYDROGEN) { // neither rescale nor replace if it's already hydrogen
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| 306 | FirstOtherAtom = Replacement;
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| 307 | BondRescale = bondlength;
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| 308 | } else {
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| 309 | FirstOtherAtom = getHydrogenReplacement(Replacement);
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| 310 | InBondvector *= BondRescale; // rescale the distance vector to Hydrogen bond length
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| 311 | FirstOtherAtom->setPosition(Origin->getPosition() + InBondvector); // set coordination to origin and add distance vector to replacement atom
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| 312 | }
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| 313 | FullMolecule.insert(FirstOtherAtom->getId());
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| 314 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
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| 315 | break;
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| 316 | case 2:
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| 317 | {
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| 318 | // determine two other bonds (warning if there are more than two other) plus valence sanity check
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| 319 | const BondList& ListOfBonds = Origin->getListOfBonds();
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| 320 | for (BondList::const_iterator Runner = ListOfBonds.begin();
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| 321 | Runner != ListOfBonds.end();
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| 322 | ++Runner) {
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| 323 | if ((*Runner) != TopBond) {
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| 324 | if (FirstBond == NULL) {
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| 325 | FirstBond = (*Runner);
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| 326 | FirstOtherAtom = (*Runner)->GetOtherAtom(Origin);
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| 327 | } else if (SecondBond == NULL) {
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| 328 | SecondBond = (*Runner);
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| 329 | SecondOtherAtom = (*Runner)->GetOtherAtom(Origin);
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| 330 | } else {
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| 331 | ELOG(2, "Detected more than four bonds for atom " << Origin->getName());
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| 332 | }
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| 333 | }
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| 334 | }
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| 335 | }
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| 336 | if (SecondOtherAtom == NULL) { // then we have an atom with valence four, but only 3 bonds: one to replace and one which is TopBond (third is FirstBond)
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| 337 | SecondBond = TopBond;
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| 338 | SecondOtherAtom = Replacement;
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| 339 | }
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| 340 | if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
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| 341 | // LOG(3, "Regarding the double bond (" << Origin->Name << "<->" << Replacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << Origin->Name << " to determine orthogonal plane.");
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| 342 |
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| 343 | // determine the plane of these two with the *origin
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| 344 | try {
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| 345 | Orthovector1 = Plane(Origin->getPosition(), FirstOtherAtom->getPosition(), SecondOtherAtom->getPosition()).getNormal();
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| 346 | }
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| 347 | catch(LinearDependenceException &excp){
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| 348 | LOG(0, boost::diagnostic_information(excp));
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| 349 | // TODO: figure out what to do with the Orthovector in this case
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| 350 | AllWentWell = false;
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| 351 | }
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| 352 | } else {
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| 353 | Orthovector1.GetOneNormalVector(InBondvector);
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| 354 | }
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| 355 | //LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
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| 356 | // orthogonal vector and bond vector between origin and replacement form the new plane
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| 357 | Orthovector1.MakeNormalTo(InBondvector);
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| 358 | Orthovector1.Normalize();
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| 359 | //LOG(3, "ReScaleCheck: " << Orthovector1.Norm() << " and " << InBondvector.Norm() << ".");
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| 360 |
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| 361 | // create the two Hydrogens ...
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| 362 | FirstOtherAtom = getHydrogenReplacement(Replacement);
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| 363 | SecondOtherAtom = getHydrogenReplacement(Replacement);
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| 364 | FullMolecule.insert(FirstOtherAtom->getId());
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| 365 | FullMolecule.insert(SecondOtherAtom->getId());
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| 366 | bondangle = Origin->getType()->getHBondAngle(1);
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| 367 | if (bondangle == -1) {
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[1f693d] | 368 | ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
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[c39675] | 369 | return false;
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| 370 | bondangle = 0;
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| 371 | }
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| 372 | bondangle *= M_PI/180./2.;
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| 373 | // LOG(3, "INFO: ReScaleCheck: InBondvector " << InBondvector << ", " << Orthovector1 << ".");
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| 374 | // LOG(3, "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle));
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| 375 | FirstOtherAtom->Zero();
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| 376 | SecondOtherAtom->Zero();
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| 377 | for(int i=NDIM;i--;) { // rotate by half the bond angle in both directions (InBondvector is bondangle = 0 direction)
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| 378 | FirstOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (sin(bondangle)));
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| 379 | SecondOtherAtom->set(i, InBondvector[i] * cos(bondangle) + Orthovector1[i] * (-sin(bondangle)));
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| 380 | }
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| 381 | FirstOtherAtom->Scale(BondRescale); // rescale by correct BondDistance
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| 382 | SecondOtherAtom->Scale(BondRescale);
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| 383 | //LOG(3, "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << ".");
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| 384 | *FirstOtherAtom += Origin->getPosition();
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| 385 | *SecondOtherAtom += Origin->getPosition();
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| 386 | // ... and add to molecule
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| 387 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
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| 388 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
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| 389 | break;
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| 390 | case 3:
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| 391 | // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
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| 392 | FirstOtherAtom = getHydrogenReplacement(Replacement);
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| 393 | SecondOtherAtom = getHydrogenReplacement(Replacement);
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| 394 | ThirdOtherAtom = getHydrogenReplacement(Replacement);
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| 395 | FullMolecule.insert(FirstOtherAtom->getId());
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| 396 | FullMolecule.insert(SecondOtherAtom->getId());
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| 397 | FullMolecule.insert(ThirdOtherAtom->getId());
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| 398 |
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| 399 | // we need to vectors orthonormal the InBondvector
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| 400 | AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(InBondvector);
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| 401 | // LOG(3, "INFO: Orthovector1: " << Orthovector1 << ".");
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| 402 | try{
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| 403 | Orthovector2 = Plane(InBondvector, Orthovector1,0).getNormal();
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| 404 | }
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| 405 | catch(LinearDependenceException &excp) {
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| 406 | LOG(0, boost::diagnostic_information(excp));
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| 407 | AllWentWell = false;
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| 408 | }
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| 409 | // LOG(3, "INFO: Orthovector2: " << Orthovector2 << ".")
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| 410 |
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| 411 | // create correct coordination for the three atoms
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| 412 | alpha = (Origin->getType()->getHBondAngle(2))/180.*M_PI/2.; // retrieve triple bond angle from database
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| 413 | l = BondRescale; // desired bond length
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| 414 | b = 2.*l*sin(alpha); // base length of isosceles triangle
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| 415 | d = l*sqrt(cos(alpha)*cos(alpha) - sin(alpha)*sin(alpha)/3.); // length for InBondvector
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| 416 | f = b/sqrt(3.); // length for Orthvector1
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| 417 | g = b/2.; // length for Orthvector2
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| 418 | // LOG(3, "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", ");
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| 419 | // LOG(3, "The three Bond lengths: " << sqrt(d*d+f*f) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g));
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| 420 | factors[0] = d;
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| 421 | factors[1] = f;
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| 422 | factors[2] = 0.;
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| 423 | FirstOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
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| 424 | factors[1] = -0.5*f;
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| 425 | factors[2] = g;
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| 426 | SecondOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
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| 427 | factors[2] = -g;
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| 428 | ThirdOtherAtom->LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
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| 429 |
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| 430 | // rescale each to correct BondDistance
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| 431 | // FirstOtherAtom->x.Scale(&BondRescale);
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| 432 | // SecondOtherAtom->x.Scale(&BondRescale);
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| 433 | // ThirdOtherAtom->x.Scale(&BondRescale);
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| 434 |
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| 435 | // and relative to *origin atom
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| 436 | *FirstOtherAtom += Origin->getPosition();
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| 437 | *SecondOtherAtom += Origin->getPosition();
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| 438 | *ThirdOtherAtom += Origin->getPosition();
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| 439 |
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| 440 | // ... and add to molecule
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| 441 | // LOG(4, "INFO: Added " << *FirstOtherAtom << " at: " << FirstOtherAtom->x << ".");
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| 442 | // LOG(4, "INFO: Added " << *SecondOtherAtom << " at: " << SecondOtherAtom->x << ".");
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| 443 | // LOG(4, "INFO: Added " << *ThirdOtherAtom << " at: " << ThirdOtherAtom->x << ".");
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| 444 | break;
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| 445 | default:
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| 446 | ELOG(1, "BondDegree does not state single, double or triple bond!");
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| 447 | AllWentWell = false;
|
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| 448 | break;
|
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| 449 | }
|
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| 450 |
|
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| 451 | return AllWentWell;
|
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| 452 | };
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