| 1 | /*
|
|---|
| 2 | * Project: MoleCuilder
|
|---|
| 3 | * Description: creates and alters molecular systems
|
|---|
| 4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
|
|---|
| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
|
|---|
| 6 | */
|
|---|
| 7 |
|
|---|
| 8 | /*
|
|---|
| 9 | * XyzParser.cpp
|
|---|
| 10 | *
|
|---|
| 11 | * Created on: Mar 2, 2010
|
|---|
| 12 | * Author: metzler
|
|---|
| 13 | */
|
|---|
| 14 |
|
|---|
| 15 | // include config.h
|
|---|
| 16 | #ifdef HAVE_CONFIG_H
|
|---|
| 17 | #include <config.h>
|
|---|
| 18 | #endif
|
|---|
| 19 |
|
|---|
| 20 | #include "Helpers/MemDebug.hpp"
|
|---|
| 21 |
|
|---|
| 22 | #include "Helpers/Log.hpp"
|
|---|
| 23 | #include "Helpers/Verbose.hpp"
|
|---|
| 24 | #include "XyzParser.hpp"
|
|---|
| 25 | #include "World.hpp"
|
|---|
| 26 | #include "atom.hpp"
|
|---|
| 27 | #include "molecule.hpp"
|
|---|
| 28 | #include "element.hpp"
|
|---|
| 29 | #include "periodentafel.hpp"
|
|---|
| 30 |
|
|---|
| 31 | using namespace std;
|
|---|
| 32 |
|
|---|
| 33 | /**
|
|---|
| 34 | * Constructor.
|
|---|
| 35 | */
|
|---|
| 36 | XyzParser::XyzParser() :
|
|---|
| 37 | comment("")
|
|---|
| 38 | {}
|
|---|
| 39 |
|
|---|
| 40 | /**
|
|---|
| 41 | * Destructor.
|
|---|
| 42 | */
|
|---|
| 43 | XyzParser::~XyzParser() {
|
|---|
| 44 | }
|
|---|
| 45 |
|
|---|
| 46 | /**
|
|---|
| 47 | * Loads an XYZ file into the World.
|
|---|
| 48 | *
|
|---|
| 49 | * \param XYZ file
|
|---|
| 50 | */
|
|---|
| 51 | void XyzParser::load(istream* file) {
|
|---|
| 52 | atom* newAtom = NULL;
|
|---|
| 53 | molecule* newmol = NULL;
|
|---|
| 54 | int numberOfAtoms;
|
|---|
| 55 | char commentBuffer[512], type[3];
|
|---|
| 56 | double tmp;
|
|---|
| 57 |
|
|---|
| 58 | // the first line tells number of atoms, the second line is always a comment
|
|---|
| 59 | *file >> numberOfAtoms >> ws;
|
|---|
| 60 | file->getline(commentBuffer, 512);
|
|---|
| 61 | comment = commentBuffer;
|
|---|
| 62 |
|
|---|
| 63 | newmol = World::getInstance().createMolecule();
|
|---|
| 64 | newmol->ActiveFlag = true;
|
|---|
| 65 | // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
|
|---|
| 66 | World::getInstance().getMolecules()->insert(newmol);
|
|---|
| 67 | for (int i = 0; i < numberOfAtoms; i++) {
|
|---|
| 68 | newAtom = World::getInstance().createAtom();
|
|---|
| 69 | *file >> type;
|
|---|
| 70 | for (int j=0;j<NDIM;j++) {
|
|---|
| 71 | *file >> tmp;
|
|---|
| 72 | newAtom->set(j, tmp);
|
|---|
| 73 | }
|
|---|
| 74 | newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
|
|---|
| 75 | newmol->AddAtom(newAtom);
|
|---|
| 76 | }
|
|---|
| 77 | }
|
|---|
| 78 |
|
|---|
| 79 | /**
|
|---|
| 80 | * Saves the current state of the World into the given XYZ file.
|
|---|
| 81 | *
|
|---|
| 82 | * \param XYZ file
|
|---|
| 83 | */
|
|---|
| 84 | void XyzParser::save(ostream* file) {
|
|---|
| 85 | DoLog(0) && (Log() << Verbose(0) << "Saving changes to xyz." << std::endl);
|
|---|
| 86 | if (comment == "") {
|
|---|
| 87 | time_t now = time((time_t *)NULL); // Get the system time and put it into 'now' as 'calender time'
|
|---|
| 88 | comment = "Created by molecuilder on ";
|
|---|
| 89 | // ctime ends in \n\0, we have to cut away the newline
|
|---|
| 90 | std::string time(ctime(&now));
|
|---|
| 91 | size_t pos = time.find('\n');
|
|---|
| 92 | if (pos != 0)
|
|---|
| 93 | comment += time.substr(0,pos);
|
|---|
| 94 | else
|
|---|
| 95 | comment += time;
|
|---|
| 96 | }
|
|---|
| 97 | *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
|
|---|
| 98 |
|
|---|
| 99 | vector<atom*> atoms = World::getInstance().getAllAtoms();
|
|---|
| 100 | for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
|
|---|
| 101 | *file << noshowpoint << (*it)->getType()->getSymbol() << "\t" << (*it)->at(0) << "\t" << (*it)->at(1) << "\t" << (*it)->at(2) << endl;
|
|---|
| 102 | }
|
|---|
| 103 | }
|
|---|
