| 1 | /** \file MoleculeListClass.cpp
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| 2 | *
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| 3 | * Function implementations for the class MoleculeListClass.
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| 4 | *
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| 5 | */
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| 6 |
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| 7 | #include "molecules.hpp"
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| 8 |
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| 9 | /*********************************** Functions for class MoleculeListClass *************************/
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| 10 |
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| 11 | /** Constructor for MoleculeListClass.
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| 12 | */
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| 13 | MoleculeListClass::MoleculeListClass()
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| 14 | {
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| 15 | };
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| 16 |
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| 17 | /** constructor for MoleculeListClass.
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| 18 | * \param NumMolecules number of molecules to allocate for
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| 19 | * \param NumAtoms number of atoms to allocate for
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| 20 | */
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| 21 | MoleculeListClass::MoleculeListClass(int NumMolecules, int NumAtoms)
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| 22 | {
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| 23 | ListOfMolecules = (molecule **) Malloc(sizeof(molecule *)*NumMolecules, "MoleculeListClass:MoleculeListClass: **ListOfMolecules");
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| 24 | for (int i=NumMolecules;i--;)
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| 25 | ListOfMolecules[i] = NULL;
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| 26 | NumberOfMolecules = NumMolecules;
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| 27 | NumberOfTopAtoms = NumAtoms;
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| 28 | };
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| 29 |
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| 30 |
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| 31 | /** Destructor for MoleculeListClass.
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| 32 | */
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| 33 | MoleculeListClass::~MoleculeListClass()
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| 34 | {
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| 35 | cout << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
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| 36 | for (int i=NumberOfMolecules;i--;) {
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| 37 | if (ListOfMolecules[i] != NULL) { // if NULL don't free
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| 38 | cout << Verbose(4) << "ListOfMolecules: Freeing " << ListOfMolecules[i] << "." << endl;
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| 39 | delete(ListOfMolecules[i]);
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| 40 | ListOfMolecules[i] = NULL;
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| 41 | }
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| 42 | }
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| 43 | cout << Verbose(4) << "Freeing ListOfMolecules." << endl;
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| 44 | Free((void **)&ListOfMolecules, "MoleculeListClass:MoleculeListClass: **ListOfMolecules");
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| 45 | };
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| 46 |
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| 47 | /** Compare whether two molecules are equal.
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| 48 | * \param *a molecule one
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| 49 | * \param *n molecule two
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| 50 | * \return lexical value (-1, 0, +1)
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| 51 | */
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| 52 | int MolCompare(const void *a, const void *b)
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| 53 | {
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| 54 | int *aList = NULL, *bList = NULL;
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| 55 | int Count, Counter, aCounter, bCounter;
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| 56 | int flag;
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| 57 | atom *aWalker = NULL;
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| 58 | atom *bWalker = NULL;
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| 59 |
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| 60 | // sort each atom list and put the numbers into a list, then go through
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| 61 | //cout << "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << "." << endl;
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| 62 | if ( (**(molecule **)a).AtomCount < (**(molecule **)b).AtomCount ) {
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| 63 | return -1;
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| 64 | } else { if ((**(molecule **)a).AtomCount > (**(molecule **)b).AtomCount)
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| 65 | return +1;
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| 66 | else {
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| 67 | Count = (**(molecule **)a).AtomCount;
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| 68 | aList = new int[Count];
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| 69 | bList = new int[Count];
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| 70 |
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| 71 | // fill the lists
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| 72 | aWalker = (**(molecule **)a).start;
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| 73 | bWalker = (**(molecule **)b).start;
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| 74 | Counter = 0;
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| 75 | aCounter = 0;
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| 76 | bCounter = 0;
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| 77 | while ((aWalker->next != (**(molecule **)a).end) && (bWalker->next != (**(molecule **)b).end)) {
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| 78 | aWalker = aWalker->next;
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| 79 | bWalker = bWalker->next;
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| 80 | if (aWalker->GetTrueFather() == NULL)
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| 81 | aList[Counter] = Count + (aCounter++);
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| 82 | else
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| 83 | aList[Counter] = aWalker->GetTrueFather()->nr;
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| 84 | if (bWalker->GetTrueFather() == NULL)
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| 85 | bList[Counter] = Count + (bCounter++);
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| 86 | else
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| 87 | bList[Counter] = bWalker->GetTrueFather()->nr;
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| 88 | Counter++;
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| 89 | }
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| 90 | // check if AtomCount was for real
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| 91 | flag = 0;
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| 92 | if ((aWalker->next == (**(molecule **)a).end) && (bWalker->next != (**(molecule **)b).end)) {
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| 93 | flag = -1;
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| 94 | } else {
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| 95 | if ((aWalker->next != (**(molecule **)a).end) && (bWalker->next == (**(molecule **)b).end))
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| 96 | flag = 1;
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| 97 | }
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| 98 | if (flag == 0) {
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| 99 | // sort the lists
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| 100 | gsl_heapsort(aList,Count, sizeof(int), CompareDoubles);
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| 101 | gsl_heapsort(bList,Count, sizeof(int), CompareDoubles);
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| 102 | // compare the lists
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| 103 |
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| 104 | flag = 0;
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| 105 | for(int i=0;i<Count;i++) {
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| 106 | if (aList[i] < bList[i]) {
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| 107 | flag = -1;
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| 108 | } else {
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| 109 | if (aList[i] > bList[i])
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| 110 | flag = 1;
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| 111 | }
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| 112 | if (flag != 0)
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| 113 | break;
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| 114 | }
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| 115 | }
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| 116 | delete[](aList);
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| 117 | delete[](bList);
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| 118 | return flag;
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| 119 | }
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| 120 | }
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| 121 | return -1;
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| 122 | };
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| 123 |
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| 124 | /** Simple output of the pointers in ListOfMolecules.
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| 125 | * \param *out output stream
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| 126 | */
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| 127 | void MoleculeListClass::Output(ofstream *out)
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| 128 | {
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| 129 | *out<< Verbose(1) << "MoleculeList: ";
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| 130 | for (int i=0;i<NumberOfMolecules;i++)
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| 131 | *out << ListOfMolecules[i] << "\t";
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| 132 | *out << endl;
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| 133 | };
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| 134 |
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| 135 |
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| 136 | /** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
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| 137 | * \param *out output stream for debugging
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| 138 | * \param *path path to file
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| 139 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
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| 140 | * \return true - file written successfully, false - writing failed
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| 141 | */
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| 142 | bool MoleculeListClass::StoreForcesFile(ofstream *out, char *path, int *SortIndex)
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| 143 | {
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| 144 | bool status = true;
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| 145 | ofstream ForcesFile;
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| 146 | stringstream line;
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| 147 | atom *Walker = NULL;
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| 148 | element *runner = NULL;
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| 149 |
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| 150 | // open file for the force factors
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| 151 | *out << Verbose(1) << "Saving force factors ... ";
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| 152 | line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
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| 153 | ForcesFile.open(line.str().c_str(), ios::out);
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| 154 | if (ForcesFile != NULL) {
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| 155 | //cout << Verbose(1) << "Final AtomicForcesList: ";
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| 156 | //output << prefix << "Forces" << endl;
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| 157 | for(int j=0;j<NumberOfMolecules;j++) {
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| 158 | //if (TEList[j] != 0) {
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| 159 | runner = ListOfMolecules[j]->elemente->start;
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| 160 | while (runner->next != ListOfMolecules[j]->elemente->end) { // go through every element
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| 161 | runner = runner->next;
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| 162 | if (ListOfMolecules[j]->ElementsInMolecule[runner->Z]) { // if this element got atoms
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| 163 | Walker = ListOfMolecules[j]->start;
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| 164 | while (Walker->next != ListOfMolecules[j]->end) { // go through every atom of this element
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| 165 | Walker = Walker->next;
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| 166 | if (Walker->type->Z == runner->Z) {
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| 167 | if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
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| 168 | //cout << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
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| 169 | ForcesFile << SortIndex[Walker->GetTrueFather()->nr] << "\t";
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| 170 | } else // otherwise a -1 to indicate an added saturation hydrogen
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| 171 | ForcesFile << "-1\t";
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| 172 | }
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| 173 | }
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| 174 | }
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| 175 | }
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| 176 | ForcesFile << endl;
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| 177 | }
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| 178 | ForcesFile.close();
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| 179 | *out << Verbose(1) << "done." << endl;
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| 180 | } else {
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| 181 | status = false;
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| 182 | *out << Verbose(1) << "failed to open file " << line.str() << "." << endl;
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| 183 | }
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| 184 | ForcesFile.close();
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| 185 |
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| 186 | return status;
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| 187 | };
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| 188 |
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| 189 | /** Writes a config file for each molecule in the given \a **FragmentList.
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| 190 | * \param *out output stream for debugging
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| 191 | * \param *configuration standard configuration to attach atoms in fragment molecule to.
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| 192 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
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| 193 | * \return true - success (each file was written), false - something went wrong.
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| 194 | */
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| 195 | bool MoleculeListClass::OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex)
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| 196 | {
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| 197 | ofstream outputFragment;
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| 198 | char FragmentName[MAXSTRINGSIZE];
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| 199 | char PathBackup[MAXSTRINGSIZE];
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| 200 | bool result = true;
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| 201 | bool intermediateResult = true;
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| 202 | atom *Walker = NULL;
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| 203 | vector BoxDimension;
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| 204 | char *FragmentNumber;
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| 205 | int FragmentCounter = 0;
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| 206 | ofstream output;
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| 207 |
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| 208 | // store the fragments as config and as xyz
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| 209 | for(int i=0;i<NumberOfMolecules;i++) {
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| 210 | // save default path as it is changed for each fragment
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| 211 | strcpy(PathBackup, configuration->GetDefaultPath());
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| 212 |
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| 213 | // correct periodic
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| 214 | ListOfMolecules[i]->ScanForPeriodicCorrection(out);
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| 215 |
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| 216 | // output xyz file
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| 217 | FragmentNumber = FixedDigitNumber(NumberOfMolecules, FragmentCounter++);
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| 218 | sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
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| 219 | outputFragment.open(FragmentName, ios::out);
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| 220 | *out << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << " as XYZ ...";
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| 221 | if (intermediateResult = ListOfMolecules[i]->OutputXYZ(&outputFragment))
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| 222 | *out << " done." << endl;
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| 223 | else
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| 224 | *out << " failed." << endl;
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| 225 | result = result && intermediateResult;
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| 226 | outputFragment.close();
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| 227 | outputFragment.clear();
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| 228 |
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| 229 | *out << Verbose(2) << "Contained atoms: ";
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| 230 | Walker = ListOfMolecules[i]->start;
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| 231 | while (Walker->next != ListOfMolecules[i]->end) {
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| 232 | Walker = Walker->next;
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| 233 | *out << Walker->Name << " ";
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| 234 | }
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| 235 | *out << endl;
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| 236 | // prepare output of config file
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| 237 | sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
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| 238 | outputFragment.open(FragmentName, ios::out);
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| 239 | strcpy(PathBackup, configuration->configpath);
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| 240 | sprintf(FragmentName, "%s/%s%s/", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
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| 241 |
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| 242 | // center on edge
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| 243 | ListOfMolecules[i]->CenterEdge(out, &BoxDimension);
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| 244 | ListOfMolecules[i]->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
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| 245 | int j = -1;
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| 246 | for (int k=0;k<NDIM;k++) {
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| 247 | j += k+1;
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| 248 | BoxDimension.x[k] = 5.;
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| 249 | ListOfMolecules[i]->cell_size[j] += BoxDimension.x[k]*2.;
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| 250 | }
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| 251 | ListOfMolecules[i]->Translate(&BoxDimension);
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| 252 |
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| 253 | // also calculate necessary orbitals
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| 254 | ListOfMolecules[i]->CountElements(); // this is a bugfix, atoms should should actually be added correctly to this fragment
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| 255 | ListOfMolecules[i]->CalculateOrbitals(*configuration);
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| 256 |
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| 257 | // change path in config
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| 258 | configuration->SetDefaultPath(FragmentName);
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| 259 | *out << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << " as config ...";
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| 260 | if (intermediateResult = configuration->Save(&outputFragment, ListOfMolecules[i]->elemente, ListOfMolecules[i]))
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| 261 | *out << " done." << endl;
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| 262 | else
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| 263 | *out << " failed." << endl;
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| 264 | // restore old config
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| 265 | configuration->SetDefaultPath(PathBackup);
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| 266 |
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| 267 | result = result && intermediateResult;
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| 268 | outputFragment.close();
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| 269 | outputFragment.clear();
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| 270 | delete(FragmentNumber);
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| 271 | //Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
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| 272 | }
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| 273 | cout << " done." << endl;
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| 274 |
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| 275 | // printing final number
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| 276 | *out << "Final number of fragments: " << FragmentCounter << "." << endl;
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| 277 |
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| 278 | return result;
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| 279 | };
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| 280 |
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| 281 | /******************************************* Class MoleculeLeafClass ************************************************/
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| 282 |
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| 283 | /** Constructor for MoleculeLeafClass root leaf.
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| 284 | * \param *Up Leaf on upper level
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| 285 | * \param *PreviousLeaf NULL - We are the first leaf on this level, otherwise points to previous in list
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| 286 | */
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| 287 | //MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *Up = NULL, MoleculeLeafClass *Previous = NULL)
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| 288 | MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf = NULL)
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| 289 | {
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| 290 | // if (Up != NULL)
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| 291 | // if (Up->DownLeaf == NULL) // are we the first down leaf for the upper leaf?
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| 292 | // Up->DownLeaf = this;
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| 293 | // UpLeaf = Up;
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| 294 | // DownLeaf = NULL;
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| 295 | Leaf = NULL;
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| 296 | previous = PreviousLeaf;
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| 297 | if (previous != NULL) {
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| 298 | MoleculeLeafClass *Walker = previous->next;
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| 299 | previous->next = this;
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| 300 | next = Walker;
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| 301 | } else {
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| 302 | next = NULL;
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| 303 | }
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| 304 | };
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| 305 |
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| 306 | /** Destructor for MoleculeLeafClass.
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| 307 | */
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| 308 | MoleculeLeafClass::~MoleculeLeafClass()
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| 309 | {
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| 310 | // if (DownLeaf != NULL) {// drop leaves further down
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| 311 | // MoleculeLeafClass *Walker = DownLeaf;
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| 312 | // MoleculeLeafClass *Next;
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| 313 | // do {
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| 314 | // Next = Walker->NextLeaf;
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| 315 | // delete(Walker);
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| 316 | // Walker = Next;
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| 317 | // } while (Walker != NULL);
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| 318 | // // Last Walker sets DownLeaf automatically to NULL
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| 319 | // }
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| 320 | // remove the leaf itself
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| 321 | if (Leaf != NULL) {
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| 322 | delete(Leaf);
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| 323 | Leaf = NULL;
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| 324 | }
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| 325 | // remove this Leaf from level list
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| 326 | if (previous != NULL)
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| 327 | previous->next = next;
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| 328 | // } else { // we are first in list (connects to UpLeaf->DownLeaf)
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| 329 | // if ((NextLeaf != NULL) && (NextLeaf->UpLeaf == NULL))
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| 330 | // NextLeaf->UpLeaf = UpLeaf; // either null as we are top level or the upleaf of the first node
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| 331 | // if (UpLeaf != NULL)
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| 332 | // UpLeaf->DownLeaf = NextLeaf; // either null as we are only leaf or NextLeaf if we are just the first
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| 333 | // }
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| 334 | // UpLeaf = NULL;
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| 335 | if (next != NULL) // are we last in list
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| 336 | next->previous = previous;
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| 337 | next = NULL;
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| 338 | previous = NULL;
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| 339 | };
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| 340 |
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| 341 | /** Adds \a molecule leaf to the tree.
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| 342 | * \param *ptr ptr to molecule to be added
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| 343 | * \param *Previous previous MoleculeLeafClass referencing level and which on the level
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| 344 | * \return true - success, false - something went wrong
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| 345 | */
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| 346 | bool MoleculeLeafClass::AddLeaf(molecule *ptr, MoleculeLeafClass *Previous)
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| 347 | {
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| 348 | return false;
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| 349 | };
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| 350 |
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| 351 | /** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
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| 352 | * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
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| 353 | * \param *out output stream for debugging
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| 354 | * \param *reference reference molecule with the bond structure to be copied
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| 355 | * \param &FragmentCounter Counter needed to address \a **ListOfLocalAtoms
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| 356 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
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| 357 | * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
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| 358 | * \return true - success, false - faoilure
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| 359 | */
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| 360 | bool MoleculeLeafClass::FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList)
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| 361 | {
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| 362 | atom *Walker = NULL, *OtherWalker = NULL;
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| 363 | bond *Binder = NULL;
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| 364 | bool status = true;
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| 365 | int AtomNo;
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| 366 |
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| 367 | // fill ListOfLocalAtoms if NULL was given
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| 368 | if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
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| 369 | *out << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
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| 370 | return false;
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| 371 | }
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| 372 |
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| 373 | if (status) {
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| 374 | *out << Verbose(1) << "Creating adjacency list for subgraph " << this << "." << endl;
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| 375 | Walker = Leaf->start;
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| 376 | while (Walker->next != Leaf->end) {
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| 377 | Walker = Walker->next;
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| 378 | AtomNo = Walker->father->nr; // global id of the current walker
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| 379 | for(int i=0;i<reference->NumberOfBondsPerAtom[AtomNo];i++) { // go through father's bonds and copy them all
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| 380 | Binder = reference->ListOfBondsPerAtom[AtomNo][i];
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| 381 | OtherWalker = ListOfLocalAtoms[FragmentCounter][Binder->GetOtherAtom(Walker->father)->nr]; // local copy of current bond partner of walker
|
|---|
| 382 | if (OtherWalker != NULL) {
|
|---|
| 383 | if (OtherWalker->nr > Walker->nr)
|
|---|
| 384 | Leaf->AddBond(Walker, OtherWalker, Binder->BondDegree);
|
|---|
| 385 | } else {
|
|---|
| 386 | *out << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << Binder->GetOtherAtom(Walker->father)->nr << "] is NULL!" << endl;
|
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| 387 | status = false;
|
|---|
| 388 | }
|
|---|
| 389 | }
|
|---|
| 390 | }
|
|---|
| 391 | Leaf->CreateListOfBondsPerAtom(out);
|
|---|
| 392 | FragmentCounter++;
|
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| 393 | if (next != NULL)
|
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| 394 | status = next->FillBondStructureFromReference(out, reference, FragmentCounter, ListOfLocalAtoms);
|
|---|
| 395 | }
|
|---|
| 396 |
|
|---|
| 397 | if (FreeList) {
|
|---|
| 398 | // free the index lookup list
|
|---|
| 399 | Free((void **)&ListOfLocalAtoms[FragmentCounter], "MoleculeLeafClass::FillBondStructureFromReference - **ListOfLocalAtoms[]");
|
|---|
| 400 | if (ListOfLocalAtoms[FragmentCounter] == NULL)
|
|---|
| 401 | Free((void **)&ListOfLocalAtoms, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
|
|---|
| 402 | }
|
|---|
| 403 | FragmentCounter--;
|
|---|
| 404 | return status;
|
|---|
| 405 | };
|
|---|
| 406 |
|
|---|
| 407 | /** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
|
|---|
| 408 | * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
|
|---|
| 409 | * \param *out output stream for debugging
|
|---|
| 410 | * \param *&RootStack stack to be filled
|
|---|
| 411 | * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site
|
|---|
| 412 | * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
|
|---|
| 413 | * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
|
|---|
| 414 | */
|
|---|
| 415 | bool MoleculeLeafClass::FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter)
|
|---|
| 416 | {
|
|---|
| 417 | atom *Walker = NULL, *Father = NULL;
|
|---|
| 418 |
|
|---|
| 419 | if (RootStack != NULL) {
|
|---|
| 420 | // find first root candidates
|
|---|
| 421 | if (&(RootStack[FragmentCounter]) != NULL) {
|
|---|
| 422 | RootStack[FragmentCounter].clear();
|
|---|
| 423 | Walker = Leaf->start;
|
|---|
| 424 | while (Walker->next != Leaf->end) { // go through all (non-hydrogen) atoms
|
|---|
| 425 | Walker = Walker->next;
|
|---|
| 426 | Father = Walker->GetTrueFather();
|
|---|
| 427 | if (AtomMask[Father->nr]) // apply mask
|
|---|
| 428 | #ifdef ADDHYDROGEN
|
|---|
| 429 | if (Walker->type->Z != 1) // skip hydrogen
|
|---|
| 430 | #endif
|
|---|
| 431 | RootStack[FragmentCounter].push_front(Walker->nr);
|
|---|
| 432 | }
|
|---|
| 433 | if (next != NULL)
|
|---|
| 434 | next->FillRootStackForSubgraphs(out, RootStack, AtomMask, ++FragmentCounter);
|
|---|
| 435 | } else {
|
|---|
| 436 | *out << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl;
|
|---|
| 437 | return false;
|
|---|
| 438 | }
|
|---|
| 439 | FragmentCounter--;
|
|---|
| 440 | return true;
|
|---|
| 441 | } else {
|
|---|
| 442 | *out << Verbose(1) << "Rootstack is NULL." << endl;
|
|---|
| 443 | return false;
|
|---|
| 444 | }
|
|---|
| 445 | };
|
|---|
| 446 |
|
|---|
| 447 | /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
|
|---|
| 448 | * \param *out output stream fro debugging
|
|---|
| 449 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
|
|---|
| 450 | * \param &FragmentCounter counts the fragments as we move along the list
|
|---|
| 451 | * \param GlobalAtomCount number of atoms in the complete molecule
|
|---|
| 452 | * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
|---|
| 453 | * \return true - succes, false - failure
|
|---|
| 454 | */
|
|---|
| 455 | bool MoleculeLeafClass::FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList)
|
|---|
| 456 | {
|
|---|
| 457 | bool status = true;
|
|---|
| 458 |
|
|---|
| 459 | int Counter = Count();
|
|---|
| 460 | if (ListOfLocalAtoms == NULL) { // allocated initial pointer
|
|---|
| 461 | // allocate and set each field to NULL
|
|---|
| 462 | ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **)*Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
|
|---|
| 463 | if (ListOfLocalAtoms != NULL) {
|
|---|
| 464 | for (int i=Counter;i--;)
|
|---|
| 465 | ListOfLocalAtoms[i] = NULL;
|
|---|
| 466 | FreeList = FreeList && true;
|
|---|
| 467 | } else
|
|---|
| 468 | status = false;
|
|---|
| 469 | }
|
|---|
| 470 |
|
|---|
| 471 | if ((ListOfLocalAtoms != NULL) && (ListOfLocalAtoms[FragmentCounter] == NULL)) { // allocate and fill list of this fragment/subgraph
|
|---|
| 472 | status = status && CreateFatherLookupTable(out, Leaf->start, Leaf->end, ListOfLocalAtoms[FragmentCounter], GlobalAtomCount);
|
|---|
| 473 | FreeList = FreeList && true;
|
|---|
| 474 | }
|
|---|
| 475 |
|
|---|
| 476 | return status;
|
|---|
| 477 | };
|
|---|
| 478 |
|
|---|
| 479 | /** The indices per keyset are compared to the respective father's Atom::nr in each subgraph and thus put into \a **&FragmentList.
|
|---|
| 480 | * \param *out output stream fro debugging
|
|---|
| 481 | * \param *reference reference molecule with the bond structure to be copied
|
|---|
| 482 | * \param *KeySetList list with all keysets
|
|---|
| 483 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
|
|---|
| 484 | * \param **&FragmentList list to be allocated and returned
|
|---|
| 485 | * \param &FragmentCounter counts the fragments as we move along the list
|
|---|
| 486 | * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
|---|
| 487 | * \retuen true - success, false - failure
|
|---|
| 488 | */
|
|---|
| 489 | bool MoleculeLeafClass::AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
|
|---|
| 490 | {
|
|---|
| 491 | bool status = true;
|
|---|
| 492 | int KeySetCounter = 0;
|
|---|
| 493 |
|
|---|
| 494 | // fill ListOfLocalAtoms if NULL was given
|
|---|
| 495 | if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
|
|---|
| 496 | *out << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
|
|---|
| 497 | return false;
|
|---|
| 498 | }
|
|---|
| 499 |
|
|---|
| 500 | // allocate fragment list
|
|---|
| 501 | if (FragmentList == NULL) {
|
|---|
| 502 | KeySetCounter = Count();
|
|---|
| 503 | FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
|
|---|
| 504 | for(int i=KeySetCounter;i--;)
|
|---|
| 505 | FragmentList[i] = NULL;
|
|---|
| 506 | KeySetCounter = 0;
|
|---|
| 507 | }
|
|---|
| 508 |
|
|---|
| 509 | if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
|
|---|
| 510 | // assign scanned keysets
|
|---|
| 511 | if (FragmentList[FragmentCounter] == NULL)
|
|---|
| 512 | FragmentList[FragmentCounter] = new Graph;
|
|---|
| 513 | KeySet *TempSet = new KeySet;
|
|---|
| 514 | for(Graph::iterator runner = KeySetList->begin();runner != KeySetList->end(); runner++) { // key sets contain global numbers!
|
|---|
| 515 | if ( ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr]->nr != -1) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
|
|---|
| 516 | // translate keyset to local numbers
|
|---|
| 517 | for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
|---|
| 518 | TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->nr]->nr);
|
|---|
| 519 | // insert into FragmentList
|
|---|
| 520 | FragmentList[FragmentCounter]->insert(GraphPair (*TempSet, pair<int,double>(KeySetCounter++, (*runner).second.second)));
|
|---|
| 521 | }
|
|---|
| 522 | TempSet->clear();
|
|---|
| 523 | }
|
|---|
| 524 | delete(TempSet);
|
|---|
| 525 | if (KeySetCounter == 0) {// if there are no keysets, delete the list
|
|---|
| 526 | *out << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl;
|
|---|
| 527 | delete(FragmentList[FragmentCounter]);
|
|---|
| 528 | } else
|
|---|
| 529 | *out << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl;
|
|---|
| 530 | FragmentCounter++;
|
|---|
| 531 | if (next != NULL)
|
|---|
| 532 | next->AssignKeySetsToFragment(out, reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
|
|---|
| 533 | FragmentCounter--;
|
|---|
| 534 | } else
|
|---|
| 535 | *out << Verbose(1) << "KeySetList is NULL or empty." << endl;
|
|---|
| 536 |
|
|---|
| 537 | return status;
|
|---|
| 538 | };
|
|---|
| 539 |
|
|---|
| 540 | /** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
|
|---|
| 541 | * \param *out output stream for debugging
|
|---|
| 542 | * \param **FragmentList Graph with local numbers per fragment
|
|---|
| 543 | * \param &FragmentCounter counts the fragments as we move along the list
|
|---|
| 544 | * \param &TotalNumberOfKeySets global key set counter
|
|---|
| 545 | * \param &TotalGraph Graph to be filled with global numbers
|
|---|
| 546 | */
|
|---|
| 547 | void MoleculeLeafClass::TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
|
|---|
| 548 | {
|
|---|
| 549 | KeySet *TempSet = new KeySet;
|
|---|
| 550 | if (FragmentList[FragmentCounter] != NULL) {
|
|---|
| 551 | for(Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
|
|---|
| 552 | for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
|---|
| 553 | TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->nr);
|
|---|
| 554 | TotalGraph.insert(GraphPair(*TempSet, pair<int,double>(TotalNumberOfKeySets++, (*runner).second.second)));
|
|---|
| 555 | TempSet->clear();
|
|---|
| 556 | }
|
|---|
| 557 | delete(TempSet);
|
|---|
| 558 | } else {
|
|---|
| 559 | *out << Verbose(1) << "FragmentList is NULL." << endl;
|
|---|
| 560 | }
|
|---|
| 561 | if (next != NULL)
|
|---|
| 562 | next->TranslateIndicesToGlobalIDs(out, FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
|
|---|
| 563 | FragmentCounter--;
|
|---|
| 564 | };
|
|---|
| 565 |
|
|---|
| 566 | /** Simply counts the number of items in the list, from given MoleculeLeafClass.
|
|---|
| 567 | * \return number of items
|
|---|
| 568 | */
|
|---|
| 569 | int MoleculeLeafClass::Count() const
|
|---|
| 570 | {
|
|---|
| 571 | if (next != NULL)
|
|---|
| 572 | return next->Count()+1;
|
|---|
| 573 | else
|
|---|
| 574 | return 1;
|
|---|
| 575 | };
|
|---|
