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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A small program for assigning chemical shifts to a molecule
// given an NMRStar file.
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/FORMAT/NMRStarFile.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/peptides.h>
#include <BALL/NMR/shiftModule.h>
#include <BALL/SYSTEM/path.h>
using namespace std;
using namespace BALL;
int main(int argc, char** argv)
{
Log << "Loading pdb file ...";
PDBFile pdb_file("../../TEST/data/NMRStarFile_test_1z0r.pdb");
if (!pdb_file.good())
{
// if file does not exist: complain and abort
Log.error() << "error opening pdb file" << endl;
return 2;
}
System system;
pdb_file >> system;
Log << " done." << endl;
Log << "Initializing FragmentDB...";
FragmentDB db("");
Log << " done." << endl;
Log << "Normalizing names...";
system.apply(db.normalize_names);
Log << " done." << endl;
Chain& chain = *(system.beginChain());
Log << "Loading NMRStar file...";
NMRStarFile nmr_file;
try{
nmr_file.open("../../TEST/data/NMRStarFile_test_1z0r.bmr", std::ios::in);
nmr_file.read();
}
catch(...){
Log.error() << "error opening the NMRStar file" << endl;
return 2;
}
Log << " done." << endl;
Log << "File contains " << nmr_file.getNumberOfAtoms() << " chemical shifts" << endl;
Log << "Number of samples: " << nmr_file.getNumberOfSamples() << endl;
NMRStarFile::MolecularSystem nmr_mol_sys = nmr_file.getMolecularInformation();
Log << "Molecular systems name: " << nmr_mol_sys.system_name << endl;
Log << "Number of possible chemical units: " << nmr_mol_sys.getNumberOfChemicalUnits() << endl;
// the chemical units of this file
for (Size k=0; k < nmr_mol_sys.getNumberOfChemicalUnits(); k++)
{
NMRStarFile::MolecularSystem::ChemicalUnit cu = nmr_mol_sys.getChemicalUnit(k);
Log << " " << k << " : " << cu.component_name
<< " " << cu.label << endl;
}
// get the shift data
std::vector<NMRStarFile::NMRAtomDataSet> const& nmr_data = nmr_file.getNMRData();
Log << "Number of shift sets: " << nmr_data.size() << endl;
for (Size k=0; k < nmr_data.size(); k++)
{
Log << " " << k << " shift set name: " << nmr_data[k].name << " -- condition name: " << nmr_data[k].condition << endl;
}
// decide for a chemical unit
NMRStarFile::MolecularSystem::ChemicalUnit cu = nmr_mol_sys.getChemicalUnit(0);
String chemical_unit_label = cu.label;
Log << "Consider chemical unit named " << cu.component_name << endl;
// get the ChemicalUnit by label
NMRStarFile::MolecularSystem::ChemicalUnit chemical_unit = nmr_file.getChemicalUnitByLabel(chemical_unit_label);
// find the corresponding SampleCondition
String pH, temperature, pressure;
if (chemical_unit.shifts && nmr_file.hasSampleCondition(chemical_unit.shifts->condition))
{
NMRStarFile::SampleCondition& condition = nmr_file.getSampleConditionByName(chemical_unit.shifts->condition);
if (condition.hasType("pH"))
pH = condition.values["pH"];
if (condition.hasType("pH*"))
pH = condition.values["pH*"];
if (condition.hasType("temperature"))
temperature = condition.values["temperature"];
if (condition.hasType("pressure"))
pressure = condition.values["pressure"];
Log << "NMR conditions: pH=" << pH << ", temp=" << temperature << ", press=" << pressure << endl;
}
// get the sequences to compute an alignment
Log << "Sequences to align: " << endl;
Log << " " << Peptides::GetSequence(chain) << endl;
Log << " " << nmr_file.getResidueSequence(0) << endl;
// decide for a chemical unit
Log << "Label of selected chemical unit: " << chemical_unit_label << endl;
// create a mapping based on an alignment
Log << "Create a mapping... " ;
NMRStarFile::BALLToBMRBMapper mapper(chain, nmr_file, chemical_unit_label);
mapper.createMapping("MKSTGIVRKVDELGR-VVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT", "MKSTGIVRKVDELGRVV-IPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT");
Log << " done." << endl;
Log << "Number of mismatches: " << mapper.getNumberOfMismatches() << endl;
Log << "Number of gaps: " << mapper.getNumberOfGaps() << endl;
// assign the shifts
Log << "Assign the chemical shifts..." ;
nmr_file.assignShifts(mapper);
Log << "done." << endl;
Log << "Assigned " << nmr_file.getNumberOfShiftsAssigned()
<< " shifts given " << nmr_file.getNumberOfAtoms() << " chemical shifts." << endl << endl;
// print
for (AtomIterator at_it = chain.beginAtom(); at_it != chain.endAtom(); at_it++)
{
if (at_it->hasProperty(ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT))
{
cout << " " << at_it->getFullName() << " has shift "
<< at_it->getProperty(ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT).getFloat() << endl;
}
}
return 0;
}
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