Changeset bb6193 for src


Ignore:
Timestamp:
Aug 28, 2010, 12:57:56 AM (15 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
21585f
Parents:
5c6946
git-author:
Frederik Heber <heber@…> (08/27/10 10:37:13)
git-committer:
Frederik Heber <heber@…> (08/28/10 00:57:56)
Message:

Added PdbParser with save capability.

  • load does not yet work.
  • added test part to Simple_configuration/2 (new file test.pdb)
Location:
src/Parser
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • src/Parser/FormatParserStorage.cpp

    r5c6946 rbb6193  
    2828#include "Parser/MpqcParser.hpp"
    2929#include "Parser/PcpParser.hpp"
     30#include "Parser/PdbParser.hpp"
    3031#include "Parser/TremoloParser.hpp"
    3132#include "Parser/XyzParser.hpp"
    … …  
    5859  ParserNames[mpqc] = "mpqc";
    5960  ParserNames[pcp] = "pcp";
     61  ParserNames[pdb] = "pdb";
    6062  ParserNames[tremolo] = "tremolo";
    6163  ParserNames[xyz] = "xyz";
    … …  
    6668  ParserSuffix[mpqc] = "in";
    6769  ParserSuffix[pcp] = "conf";
     70  ParserSuffix[pdb] = "pdb";
    6871  ParserSuffix[tremolo] = "data";
    6972  ParserSuffix[xyz] = "xyz";
    … …  
    7174  ParserAddFunction[mpqc] = &FormatParserStorage::addMpqc;
    7275  ParserAddFunction[pcp] = &FormatParserStorage::addPcp;
     76  ParserAddFunction[pdb] = &FormatParserStorage::addPdb;
    7377  ParserAddFunction[tremolo] = &FormatParserStorage::addTremolo;
    7478  ParserAddFunction[xyz] = &FormatParserStorage::addXyz;
    … …  
    135139  } else
    136140    DoeLog(1) && (eLog() << Verbose(1) << "Parser pcp is already present." << endl);
     141}
     142
     143
     144/** Adds an PdbParser to the storage.
     145 */
     146void FormatParserStorage::addPdb()
     147{
     148  if (!ParserPresent[pdb]) {
     149    ParserList[pdb] = new PdbParser();
     150    ParserPresent[pdb] = true;
     151  } else
     152    DoeLog(1) && (eLog() << Verbose(1) << "Parser pdb is already present." << endl);
    137153}
    138154
    … …  
    203219  } else if (suffix == ParserSuffix[pcp]) {
    204220    getPcp().load(&input);
     221  } else if (suffix == ParserSuffix[pdb]) {
     222    getPdb().load(&input);
    205223  } else if (suffix == ParserSuffix[tremolo]) {
    206224    getTremolo().load(&input);
    … …  
    234252}
    235253
     254/** Returns reference to the output PdbParser, adds if not present.
     255 * \return reference to the output PdbParser
     256 */
     257PdbParser &FormatParserStorage::getPdb()
     258{
     259  if (!ParserPresent[pdb])
     260    addPdb();
     261  return dynamic_cast<PdbParser &>(*ParserList[pdb]);
     262}
     263
    236264/** Returns reference to the output TremoloParser, adds if not present.
    237265 * \return reference to the output TremoloParser

  • src/Parser/FormatParserStorage.hpp

    r5c6946 rbb6193  
    2222class FormatParser;
    2323class MpqcParser;
     24class PdbParser;
    2425class PcpParser;
    2526class TremoloParser;
    … …  
    2728
    2829// enum has to be outside of class for operator++ to be possible
    29 enum ParserTypes { mpqc, pcp, tremolo, xyz, ParserTypes_end, ParserTypes_begin = mpqc };
     30enum ParserTypes { mpqc, pcp, pdb, tremolo, xyz, ParserTypes_end, ParserTypes_begin = mpqc };
    3031typedef enum ParserTypes ParserTypes;
    3132
    … …  
    3839  void addMpqc();
    3940  void addPcp();
     41  void addPdb();
    4042  void addTremolo();
    4143  void addXyz();
    … …  
    4648  MpqcParser &getMpqc();
    4749  PcpParser &getPcp();
     50  PdbParser &getPdb();
    4851  TremoloParser &getTremolo();
    4952  XyzParser &getXyz();

  • src/Parser/PdbParser.cpp

    r5c6946 rbb6193  
    2626#include "World.hpp"
    2727#include "atom.hpp"
     28#include "bond.hpp"
    2829#include "element.hpp"
    29 #include "bond.hpp"
     30#include "molecule.hpp"
    3031#include "periodentafel.hpp"
    3132#include "Descriptors/AtomIdDescriptor.hpp"
     33
    3234#include <map>
    3335#include <vector>
    3436
     37#include <iostream>
     38#include <iomanip>
    3539
    3640using namespace std;
    … …  
    4044 */
    4145PdbParser::PdbParser() {
    42   knownKeys[" "] = TremoloKey::noKey; // with this we can detect invalid keys
    43   knownKeys["x"] = TremoloKey::x;
    44   knownKeys["u"] = TremoloKey::u;
    45   knownKeys["F"] = TremoloKey::F;
    46   knownKeys["stress"] = TremoloKey::stress;
    47   knownKeys["Id"] = TremoloKey::Id;
    48   knownKeys["neighbors"] = TremoloKey::neighbors;
    49   knownKeys["imprData"] = TremoloKey::imprData;
    50   knownKeys["GroupMeasureTypeNo"] = TremoloKey::GroupMeasureTypeNo;
    51   knownKeys["Type"] = TremoloKey::Type;
    52   knownKeys["extType"] = TremoloKey::extType;
    53   knownKeys["name"] = TremoloKey::name;
    54   knownKeys["resName"] = TremoloKey::resName;
    55   knownKeys["chainID"] = TremoloKey::chainID;
    56   knownKeys["resSeq"] = TremoloKey::resSeq;
    57   knownKeys["occupancy"] = TremoloKey::occupancy;
    58   knownKeys["tempFactor"] = TremoloKey::tempFactor;
    59   knownKeys["segID"] = TremoloKey::segID;
    60   knownKeys["Charge"] = TremoloKey::Charge;
    61   knownKeys["charge"] = TremoloKey::charge;
    62   knownKeys["GrpTypeNo"] = TremoloKey::GrpTypeNo;
    63   knownKeys["torsion"] = TremoloKey::torsion;
    64 
    65   // default behavior: use all possible keys on output
    66   for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
    67     usedFields.push_back(iter->first);
     46  knownKeys[" "] = PdbKey::noKey; // with this we can detect invalid keys
     47  knownKeys["x"] = PdbKey::x;
     48  knownKeys["Id"] = PdbKey::Id;
     49  knownKeys["Type"] = PdbKey::Type;
     50  knownKeys["extType"] = PdbKey::extType;
     51  knownKeys["name"] = PdbKey::name;
     52  knownKeys["resName"] = PdbKey::resName;
     53  knownKeys["chainID"] = PdbKey::chainID;
     54  knownKeys["resSeq"] = PdbKey::resSeq;
     55  knownKeys["occupancy"] = PdbKey::occupancy;
     56  knownKeys["tempFactor"] = PdbKey::tempFactor;
     57  knownKeys["segID"] = PdbKey::segID;
     58  knownKeys["charge"] = PdbKey::charge;
    6859}
    6960
    … …  
    7263 */
    7364PdbParser::~PdbParser() {
    74   usedFields.clear();
    7565  additionalAtomData.clear();
    7666  atomIdMap.clear();
    … …  
    8474 */
    8575void PdbParser::load(istream* file) {
    86   string line;
    87   string::size_type location;
    88 
    89   usedFields.clear();
    90   while (file->good()) {
    91     std::getline(*file, line, '\n');
    92     if (usedFields.empty()) {
    93       location = line.find("ATOMDATA", 0);
    94       if (location != string::npos) {
    95        parseAtomDataKeysLine(line, location + 8);
     76//  string line;
     77//  string::size_type location;
     78//
     79//  usedFields.clear();
     80//  while (file->good()) {
     81//    std::getline(*file, line, '\n');
     82//    if (usedFields.empty()) {
     83//      location = line.find("ATOMDATA", 0);
     84//      if (location != string::npos) {
     85//       parseAtomDataKeysLine(line, location + 8);
     86//      }
     87//    }
     88//    if (line.length() > 0 && line.at(0) != '#') {
     89//      readAtomDataLine(line);
     90//    }
     91//  }
     92//
     93//  processNeighborInformation();
     94//  adaptImprData();
     95//  adaptTorsion();
     96}
     97
     98/**
     99 * Saves the World's current state into as a tremolo file.
     100 *
     101 * \param file where to save the state
     102 */
     103void PdbParser::save(ostream* file) {
     104  DoLog(0) && (Log() << Verbose(0) << "Saving changes to pdb." << std::endl);
     105
     106  {
     107    // add initial remark
     108    *file << "REMARK created by molecuilder on ";
     109    time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     110    // ctime ends in \n\0, we have to cut away the newline
     111    std::string time(ctime(&now));
     112    size_t pos = time.find('\n');
     113    if (pos != 0)
     114      *file << time.substr(0,pos);
     115    else
     116      *file << time;
     117    *file << endl;
     118  }
     119
     120  {
     121    vector<atom *> AtomList = World::getInstance().getAllAtoms();
     122
     123    std::vector<int> elementNo(MAX_ELEMENTS,1);
     124    char name[MAXSTRINGSIZE];
     125
     126    // write ATOMs
     127    int AtomNo = 1; // serial number starts at 1 in pdb
     128    int MolNo = 1;  // residue number starts at 1 in pdb
     129    for (vector<atom *>::iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
     130      const size_t  Z = (*atomIt)->getType()->getAtomicNumber();
     131      sprintf(name, "%2s%02d",(*atomIt)->getType()->getSymbol().c_str(), elementNo[Z]);
     132      elementNo[Z] = (elementNo[Z]+1) % 100;   // confine to two digits
     133      const molecule *mol = (*atomIt)->getMolecule();
     134      if (mol == NULL) {  // for homeless atoms, MolNo = 0 is reserved
     135        MolNo = 0;
     136      } else {
     137        MolNo = mol->getId();
    96138      }
     139      saveLine(file, *atomIt, name, AtomNo, MolNo);
     140      atomIdMap.insert( pair<int, int>((*atomIt)->getId(), AtomNo) );
     141      AtomNo++;
    97142    }
    98     if (line.length() > 0 && line.at(0) != '#') {
    99       readAtomDataLine(line);
     143
     144    // write CONECTs
     145    for (vector<atom *>::iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
     146      writeNeighbors(file, 4, *atomIt);
    100147    }
    101148  }
    102149
    103   processNeighborInformation();
    104   adaptImprData();
    105   adaptTorsion();
    106 }
    107 
    108 /**
    109  * Saves the World's current state into as a tremolo file.
    110  *
    111  * \param file where to save the state
    112  */
    113 void PdbParser::save(ostream* file) {
    114   DoLog(0) && (Log() << Verbose(0) << "Saving changes to tremolo." << std::endl);
    115 
    116   vector<atom*>::iterator atomIt;
    117   vector<string>::iterator it;
    118 
    119   *file << "# ATOMDATA";
    120   for (it=usedFields.begin(); it < usedFields.end(); it++) {
    121     *file << "\t" << *it;
    122   }
     150  // END
     151  *file << "END" << endl;
     152}
     153
     154/**
     155 * Writes one line of tremolo-formatted data to the provided stream.
     156 *
     157 * \param stream where to write the line to
     158 * \param *currentAtom the atom of which information should be written
     159 * \param *name name of atom, i.e. H01
     160 * \param AtomNo serial number of atom
     161 * \param ResidueNo number of residue
     162 */
     163void PdbParser::saveLine(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResidueNo) {
     164  *file << "ATOM ";
     165  *file << setw(6) << AtomNo; /* atom serial number */
     166  *file << setw(1) << " ";
     167  *file << setfill(' ') << left << setw(4) << name << right;  /* atom name */
     168  *file << setw(1) << " ";
     169  *file << setfill(' ') << setw(3) << ((currentAtom->getMolecule() != NULL) ? currentAtom->getMolecule()->getName().substr(0,3) : "-");  /* residue name */
     170  *file << setw(1) << " ";
     171  *file << setfill(' ') << setw(1) << (char)('a'+(unsigned char)(AtomNo % 26)); /* letter for chain */
     172  *file << setw(4) << ResidueNo; /* residue sequence number */
     173  *file << setw(4) << "    ";
     174  for (int i=0;i<NDIM;i++) {
     175    *file << setw(8) << setprecision(3) << showpoint << currentAtom->at(i); /* positional coordinate in Angstroem */
     176  }
     177  *file << setw(6) << setprecision(2) << showpoint << (double)currentAtom->getType()->getValence(); /* occupancy */
     178  *file << setw(6) << setprecision(2) << showpoint << (double)currentAtom->getType()->getNoValenceOrbitals(); /* temperature factor */
     179  *file << noshowpoint;
     180  *file << setw(6) << "      ";
     181  *file << setw(4) << "0";
     182  *file << setfill(' ') << setw(2) << currentAtom->getType()->getSymbol();
     183  *file << setw(2) << "0";
     184
    123185  *file << endl;
    124   vector<atom *> AtomList = World::getInstance().getAllAtoms();
    125   for (atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
    126     saveLine(file, *atomIt);
    127   }
    128 }
    129 
    130 /**
    131  * Sets the keys for which data should be written to the stream when save is
    132  * called.
    133  *
    134  * \param string of field names with the same syntax as for an ATOMDATA line
    135  *        but without the prexix "ATOMDATA"
    136  */
    137 void PdbParser::setFieldsForSave(std::string atomDataLine) {
    138   parseAtomDataKeysLine(atomDataLine, 0);
    139 }
    140 
    141 
    142 /**
    143  * Writes one line of tremolo-formatted data to the provided stream.
    144  *
    145  * \param stream where to write the line to
    146  * \param reference to the atom of which information should be written
    147  */
    148 void PdbParser::saveLine(ostream* file, atom* currentAtom) {
    149   vector<string>::iterator it;
    150   TremoloKey::atomDataKey currentField;
    151 
    152   for (it = usedFields.begin(); it != usedFields.end(); it++) {
    153     currentField = knownKeys[it->substr(0, it->find("="))];
    154     switch (currentField) {
    155       case TremoloKey::x :
    156         // for the moment, assume there are always three dimensions
    157         *file << currentAtom->at(0) << "\t";
    158         *file << currentAtom->at(1) << "\t";
    159         *file << currentAtom->at(2) << "\t";
    160         break;
    161       case TremoloKey::u :
    162         // for the moment, assume there are always three dimensions
    163         *file << currentAtom->AtomicVelocity[0] << "\t";
    164         *file << currentAtom->AtomicVelocity[1] << "\t";
    165         *file << currentAtom->AtomicVelocity[2] << "\t";
    166         break;
    167       case TremoloKey::Type :
    168         *file << currentAtom->getType()->getSymbol() << "\t";
    169         break;
    170       case TremoloKey::Id :
    171         *file << currentAtom->getId() << "\t";
    172         break;
    173       case TremoloKey::neighbors :
    174         writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
    175         break;
    176       default :
    177         *file << (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()
    178           ? additionalAtomData[currentAtom->getId()].get(currentField)
    179           : defaultAdditionalData.get(currentField));
    180         *file << "\t";
    181         break;
     186}
     187
     188/**
     189 * Writes the neighbor information of one atom to the provided stream.
     190 *
     191 * \param *file  where to write neighbor information to
     192 * \param MaxnumberOfNeighbors of neighbors
     193 * \param *currentAtom to the atom of which to take the neighbor information
     194 */
     195void PdbParser::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
     196  if (!currentAtom->ListOfBonds.empty()) {
     197    *file << "CONECT";
     198    int MaxNo = 0;
     199    for(BondList::iterator currentBond = currentAtom->ListOfBonds.begin(); currentBond != currentAtom->ListOfBonds.end(); ++currentBond) {
     200      if (MaxNo < MaxnumberOfNeighbors) {
     201        ASSERT(atomIdMap.find((*currentBond)->GetOtherAtom(currentAtom)->getId()) != atomIdMap.end(), "Id of atom not stored in PdbParser::atomIdMap.");
     202        *file << setw(5) << atomIdMap[(*currentBond)->GetOtherAtom(currentAtom)->getId()];
     203      }
     204      MaxNo++;
    182205    }
    183   }
    184 
    185   *file << endl;
    186 }
    187 
    188 /**
    189  * Writes the neighbor information of one atom to the provided stream.
    190  *
    191  * \param stream where to write neighbor information to
    192  * \param number of neighbors
    193  * \param reference to the atom of which to take the neighbor information
    194  */
    195 void PdbParser::writeNeighbors(ostream* file, int numberOfNeighbors, atom* currentAtom) {
    196   BondList::iterator currentBond = currentAtom->ListOfBonds.begin();
    197   for (int i = 0; i < numberOfNeighbors; i++) {
    198     *file << (currentBond != currentAtom->ListOfBonds.end()
    199         ? (*currentBond)->GetOtherAtom(currentAtom)->getId() : 0) << "\t";
    200   }
    201 }
    202 
    203 /**
    204  * Stores keys from the ATOMDATA line.
    205  *
    206  * \param line to parse the keys from
    207  * \param with which offset the keys begin within the line
    208  */
    209 void PdbParser::parseAtomDataKeysLine(string line, int offset) {
    210   string keyword;
    211   stringstream lineStream;
    212 
    213   lineStream << line.substr(offset);
    214   usedFields.clear();
    215   while (lineStream.good()) {
    216     lineStream >> keyword;
    217     if (knownKeys[keyword.substr(0, keyword.find("="))] == TremoloKey::noKey) {
    218       // TODO: throw exception about unknown key
    219       cout << "Unknown key: " << keyword << " is not part of the tremolo format specification." << endl;
    220       break;
    221     }
    222     usedFields.push_back(keyword);
     206    *file << endl;
    223207  }
    224208}
    … …  
    231215 */
    232216void PdbParser::readAtomDataLine(string line) {
    233   vector<string>::iterator it;
    234   stringstream lineStream;
    235   atom* newAtom = World::getInstance().createAtom();
    236   TremoloAtomInfoContainer *atomInfo = NULL;
    237   additionalAtomData[newAtom->getId()] = *(new TremoloAtomInfoContainer);
    238   atomInfo = &additionalAtomData[newAtom->getId()];
    239   TremoloKey::atomDataKey currentField;
    240   string word;
    241   int oldId;
    242   double tmp;
    243 
    244   lineStream << line;
    245   for (it = usedFields.begin(); it < usedFields.end(); it++) {
    246     currentField = knownKeys[it->substr(0, it->find("="))];
    247     switch (currentField) {
    248       case TremoloKey::x :
    249         // for the moment, assume there are always three dimensions
    250         for (int i=0;i<NDIM;i++) {
    251           lineStream >> tmp;
    252           newAtom->set(i, tmp);
    253         }
    254         break;
    255       case TremoloKey::u :
    256         // for the moment, assume there are always three dimensions
    257         lineStream >> newAtom->AtomicVelocity[0];
    258         lineStream >> newAtom->AtomicVelocity[1];
    259         lineStream >> newAtom->AtomicVelocity[2];
    260         break;
    261       case TremoloKey::Type :
    262         char type[3];
    263         lineStream >> type;
    264         newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
    265         ASSERT(newAtom->getType(), "Type was not set for this atom");
    266         break;
    267       case TremoloKey::Id :
    268         lineStream >> oldId;
    269         atomIdMap[oldId] = newAtom->getId();
    270         break;
    271       case TremoloKey::neighbors :
    272         readNeighbors(&lineStream,
    273             atoi(it->substr(it->find("=") + 1, 1).c_str()), newAtom->getId());
    274         break;
    275       default :
    276         lineStream >> word;
    277         atomInfo->set(currentField, word);
    278         break;
    279     }
    280   }
     217//  vector<string>::iterator it;
     218//  stringstream lineStream;
     219//  atom* newAtom = World::getInstance().createAtom();
     220//  PdbAtomInfoContainer *atomInfo = NULL;
     221//  additionalAtomData[newAtom->getId()] = *(new PdbAtomInfoContainer);
     222//  atomInfo = &additionalAtomData[newAtom->getId()];
     223//  PdbKey::atomDataKey currentField;
     224//  string word;
     225//  int oldId;
     226//  double tmp;
     227//
     228//  lineStream << line;
     229//  for (it = usedFields.begin(); it < usedFields.end(); it++) {
     230//    currentField = knownKeys[it->substr(0, it->find("="))];
     231//    switch (currentField) {
     232//      case PdbKey::x :
     233//        // for the moment, assume there are always three dimensions
     234//        for (int i=0;i<NDIM;i++) {
     235//          lineStream >> tmp;
     236//          newAtom->set(i, tmp);
     237//        }
     238//        break;
     239//      case PdbKey::u :
     240//        // for the moment, assume there are always three dimensions
     241//        lineStream >> newAtom->AtomicVelocity[0];
     242//        lineStream >> newAtom->AtomicVelocity[1];
     243//        lineStream >> newAtom->AtomicVelocity[2];
     244//        break;
     245//      case PdbKey::Type :
     246//        char type[3];
     247//        lineStream >> type;
     248//        newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
     249//        ASSERT(newAtom->getType(), "Type was not set for this atom");
     250//        break;
     251//      case PdbKey::Id :
     252//        lineStream >> oldId;
     253//        atomIdMap[oldId] = newAtom->getId();
     254//        break;
     255//      case PdbKey::neighbors :
     256//        readNeighbors(&lineStream,
     257//            atoi(it->substr(it->find("=") + 1, 1).c_str()), newAtom->getId());
     258//        break;
     259//      default :
     260//        lineStream >> word;
     261//        atomInfo->set(currentField, word);
     262//        break;
     263//    }
     264//  }
    281265}
    282266
    … …  
    289273 */
    290274void PdbParser::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
    291   int neighborId = 0;
    292   for (int i = 0; i < numberOfNeighbors; i++) {
    293     *line >> neighborId;
    294     // 0 is used to fill empty neighbor positions in the tremolo file.
    295     if (neighborId > 0) {
    296       additionalAtomData[atomId].neighbors.push_back(neighborId);
    297     }
    298   }
    299 }
    300 
    301 /**
    302  * Checks whether the provided name is within the list of used fields.
    303  *
    304  * \param field name to check
    305  *
    306  * \return true if the field name is used
    307  */
    308 bool PdbParser::isUsedField(string fieldName) {
    309   bool fieldNameExists = false;
    310   for (vector<string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
    311     if (usedField->substr(0, usedField->find("=")) == fieldName)
    312       fieldNameExists = true;
    313   }
    314 
    315   return fieldNameExists;
    316 }
    317 
     275//  int neighborId = 0;
     276//  for (int i = 0; i < numberOfNeighbors; i++) {
     277//    *line >> neighborId;
     278//    // 0 is used to fill empty neighbor positions in the tremolo file.
     279//    if (neighborId > 0) {
     280//      additionalAtomData[atomId].neighbors.push_back(neighborId);
     281//    }
     282//  }
     283}
    318284
    319285/**
    … …  
    323289 */
    324290void PdbParser::processNeighborInformation() {
    325   if (!isUsedField("neighbors")) {
    326     return;
    327   }
    328 
    329   for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
    330     currentInfo != additionalAtomData.end(); currentInfo++
    331   ) {
    332     for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
    333       neighbor != currentInfo->second.neighbors.end(); neighbor++
    334     ) {
    335       World::getInstance().getAtom(AtomById(currentInfo->first))
    336           ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
    337     }
    338   }
     291//  if (!isUsedField("neighbors")) {
     292//    return;
     293//  }
     294//
     295//  for(map<int, PdbAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
     296//    currentInfo != additionalAtomData.end(); currentInfo++
     297//  ) {
     298//    for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
     299//      neighbor != currentInfo->second.neighbors.end(); neighbor++
     300//    ) {
     301//      World::getInstance().getAtom(AtomById(currentInfo->first))
     302//          ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
     303//    }
     304//  }
    339305}
    340306
    … …  
    349315 */
    350316string PdbParser::adaptIdDependentDataString(string data) {
    351   // there might be no IDs
    352   if (data == "-") {
    353     return "-";
    354   }
    355 
    356   char separator;
    357   int id;
    358   stringstream line, result;
    359   line << data;
    360 
    361   line >> id;
    362   result << atomIdMap[id];
    363   while (line.good()) {
    364     line >> separator >> id;
    365     result << separator << atomIdMap[id];
    366   }
    367 
    368   return result.str();
    369 }
    370 
    371 /**
    372  * Corrects the atom IDs in each imprData entry to the corresponding world IDs
    373  * as they might differ from the originally read IDs.
    374  */
    375 void PdbParser::adaptImprData() {
    376   if (!isUsedField("imprData")) {
    377     return;
    378   }
    379 
    380   for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
    381     currentInfo != additionalAtomData.end(); currentInfo++
    382   ) {
    383     currentInfo->second.imprData = adaptIdDependentDataString(currentInfo->second.imprData);
    384   }
    385 }
    386 
    387 /**
    388  * Corrects the atom IDs in each torsion entry to the corresponding world IDs
    389  * as they might differ from the originally read IDs.
    390  */
    391 void PdbParser::adaptTorsion() {
    392   if (!isUsedField("torsion")) {
    393     return;
    394   }
    395 
    396   for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
    397     currentInfo != additionalAtomData.end(); currentInfo++
    398   ) {
    399     currentInfo->second.torsion = adaptIdDependentDataString(currentInfo->second.torsion);
    400   }
    401 }
    402 
    403 
    404 TremoloAtomInfoContainer::TremoloAtomInfoContainer() :
    405   F("0"),
    406   stress("0"),
    407   imprData("-"),
    408   GroupMeasureTypeNo("0"),
    409   extType("-"),
     317//  // there might be no IDs
     318//  if (data == "-") {
     319//    return "-";
     320//  }
     321//
     322//  char separator;
     323//  int id;
     324//  stringstream line, result;
     325//  line << data;
     326//
     327//  line >> id;
     328//  result << atomIdMap[id];
     329//  while (line.good()) {
     330//    line >> separator >> id;
     331//    result << separator << atomIdMap[id];
     332//  }
     333//
     334//  return result.str();
     335  return "";
     336}
     337
     338
     339PdbAtomInfoContainer::PdbAtomInfoContainer() :
    410340  name("-"),
    411341  resName("-"),
    … …  
    415345  tempFactor("0"),
    416346  segID("0"),
    417   Charge("0"),
    418   charge("0"),
    419   GrpTypeNo("0"),
    420   torsion("-"),
    421   neighbors(vector<int>(0, 5))
     347  charge("0")
    422348{}
    423349
    424 void TremoloAtomInfoContainer::set(TremoloKey::atomDataKey key, string value) {
     350void PdbAtomInfoContainer::set(PdbKey::PdbDataKey key, string value) {
    425351  switch (key) {
    426     case TremoloKey::F :
    427       F = value;
    428       break;
    429     case TremoloKey::stress :
    430       stress = value;
    431      break;
    432     case TremoloKey::imprData :
    433       imprData = value;
    434       break;
    435     case TremoloKey::GroupMeasureTypeNo :
    436       GroupMeasureTypeNo = value;
    437       break;
    438     case TremoloKey::extType :
     352    case PdbKey::extType :
    439353      extType = value;
    440354      break;
    441     case TremoloKey::name :
     355    case PdbKey::name :
    442356      name = value;
    443357      break;
    444     case TremoloKey::resName :
     358    case PdbKey::resName :
    445359      resName = value;
    446360      break;
    447     case TremoloKey::chainID :
     361    case PdbKey::chainID :
    448362      chainID = value;
    449363      break;
    450     case TremoloKey::resSeq :
     364    case PdbKey::resSeq :
    451365      resSeq = value;
    452366      break;
    453     case TremoloKey::occupancy :
     367    case PdbKey::occupancy :
    454368      occupancy = value;
    455369      break;
    456     case TremoloKey::tempFactor :
     370    case PdbKey::tempFactor :
    457371      tempFactor = value;
    458372      break;
    459     case TremoloKey::segID :
     373    case PdbKey::segID :
    460374      segID = value;
    461375      break;
    462     case TremoloKey::Charge :
    463       Charge = value;
    464       break;
    465     case TremoloKey::charge :
     376    case PdbKey::charge :
    466377      charge = value;
    467       break;
    468     case TremoloKey::GrpTypeNo :
    469       GrpTypeNo = value;
    470       break;
    471     case TremoloKey::torsion :
    472       torsion = value;
    473378      break;
    474379    default :
    … …  
    478383}
    479384
    480 string TremoloAtomInfoContainer::get(TremoloKey::atomDataKey key) {
     385string PdbAtomInfoContainer::get(PdbKey::PdbDataKey key) {
    481386  switch (key) {
    482     case TremoloKey::F :
    483       return F;
    484     case TremoloKey::stress :
    485       return stress;
    486     case TremoloKey::imprData :
    487       return imprData;
    488     case TremoloKey::GroupMeasureTypeNo :
    489       return GroupMeasureTypeNo;
    490     case TremoloKey::extType :
     387    case PdbKey::extType :
    491388      return extType;
    492     case TremoloKey::name :
     389    case PdbKey::name :
    493390      return name;
    494     case TremoloKey::resName :
     391    case PdbKey::resName :
    495392      return resName;
    496     case TremoloKey::chainID :
     393    case PdbKey::chainID :
    497394      return chainID;
    498     case TremoloKey::resSeq :
     395    case PdbKey::resSeq :
    499396      return resSeq;
    500     case TremoloKey::occupancy :
     397    case PdbKey::occupancy :
    501398      return occupancy;
    502     case TremoloKey::tempFactor :
     399    case PdbKey::tempFactor :
    503400      return tempFactor;
    504     case TremoloKey::segID :
     401    case PdbKey::segID :
    505402      return segID;
    506     case TremoloKey::Charge :
    507       return Charge;
    508     case TremoloKey::charge :
     403    case PdbKey::charge :
    509404      return charge;
    510     case TremoloKey::GrpTypeNo :
    511       return GrpTypeNo;
    512     case TremoloKey::torsion :
    513       return torsion;
    514405    default :
    515406      cout << "Unknown key: " << key << endl;

  • src/Parser/PdbParser.hpp

    r5c6946 rbb6193  
    1313
    1414/**
    15  * Known keys for the ATOMDATA line.
     15 * Known keys for the Pdb line.
    1616 */
    17 class TremoloKey {
     17class PdbKey {
    1818public:
    19   enum atomDataKey {
     19  enum PdbDataKey {
    2020    noKey,
    2121    x,
    22     u,
    23     F,
    24     stress,
    2522    Id,
    26     neighbors,
    27     imprData,
    28     GroupMeasureTypeNo,
    2923    Type,
    3024    extType,
    … …  
    3630    tempFactor,
    3731    segID,
    38     Charge,
    39     charge,
    40     GrpTypeNo,
    41     torsion
     32    charge
    4233  };
    4334};
    … …  
    4637 * Holds tremolo-specific information which is not store in the atom class.
    4738 */
    48 class TremoloAtomInfoContainer {
     39class PdbAtomInfoContainer {
    4940public:
    50   TremoloAtomInfoContainer();
    51   void set(TremoloKey::atomDataKey key, std::string value);
    52   std::string get(TremoloKey::atomDataKey key);
    53   std::string F;
    54   std::string stress;
    55   std::string imprData;
    56   std::string GroupMeasureTypeNo;
     41  PdbAtomInfoContainer();
     42  void set(PdbKey::PdbDataKey key, std::string value);
     43  std::string get(PdbKey::PdbDataKey key);
     44  std::string name;
    5745  std::string extType;
    58   std::string name;
    5946  std::string resName;
    6047  std::string chainID;
    … …  
    6350  std::string tempFactor;
    6451  std::string segID;
    65   std::string Charge;
    6652  std::string charge;
    67   std::string GrpTypeNo;
    68   std::string torsion;
    69   std::vector<int> neighbors;
    7053};
    7154
    … …  
    8063  void load(std::istream* file);
    8164  void save(std::ostream* file);
    82   void setFieldsForSave(std::string atomDataLine);
    8365
    8466
    … …  
    9375  bool isUsedField(std::string fieldName);
    9476  void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
    95   void saveLine(std::ostream* file, atom* currentAtom);
     77  void saveLine(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResdueNo);
     78;
    9679
    9780  /**
    9881   * Map to associate the known keys with numbers.
    9982   */
    100   std::map<std::string, TremoloKey::atomDataKey> knownKeys;
    101 
    102   /**
    103    * Fields used in the tremolo file.
    104    */
    105   std::vector<std::string> usedFields;
     83  std::map<std::string, PdbKey::PdbDataKey> knownKeys;
    10684
    10785  /**
    … …  
    10987   * file.
    11088   */
    111   std::map<int, TremoloAtomInfoContainer> additionalAtomData;
     89  std::map<int, PdbAtomInfoContainer> additionalAtomData;
    11290
    11391  /**
    11492   * Default additional atom data.
    11593   */
    116   TremoloAtomInfoContainer defaultAdditionalData;
     94  PdbAtomInfoContainer defaultAdditionalData;
    11795
    11896  /**
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