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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/SYSTEM/timer.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/DCDFile.h>
#include <BALL/STRUCTURE/structureMapper.h>
#include <BALL/MATHS/matrix44.h>
#include <BALL/DOCKING/COMMON/dockResult.h>
#include <iostream>
#include <map>
using namespace std;
using namespace BALL;
int main(int argc, char** argv)
{
// print usage information
if (argc < 5)
{
Log.error() << "Compute the C_alpha-RMSD values after a rigid docking run." << endl;
Log.error() << "Usage: " << argv[0] << " reference.pdb docked.pdb dockResult.bdr static_chain_name" << endl;
return 1;
}
map<String, Position> type_map;
type_map["ALA"] = 0;
type_map["GLY"] = 1;
type_map["VAL"] = 2;
type_map["LEU"] = 3;
type_map["ILE"] = 4;
type_map["SER"] = 5;
type_map["CYS"] = 6;
type_map["THR"] = 7;
type_map["MET"] = 8;
type_map["PHE"] = 9;
type_map["TYR"] = 10;
type_map["TRP"] = 11;
type_map["PRO"] = 12;
type_map["HIS"] = 13;
type_map["LYS"] = 14;
type_map["ARG"] = 15;
type_map["ASP"] = 16;
type_map["GLU"] = 17;
type_map["ASN"] = 18;
type_map["GLN"] = 19;
// define two systems and two proteins
System reference, docked;
Protein static_reference, static_docked;
// we'll need that one later
System docked_backup;
// and a PDB file to read and write the proteins
PDBFile pdb_file;
// read the proteins
pdb_file.open(argv[1]);
Log.info() << "Reading reference " << argv[1] << "... " << flush;
pdb_file >> reference;
Log.info() << "Read " << reference.countAtoms() << " atoms." << endl;
pdb_file.close();
pdb_file.open(argv[2]);
Log.info() << "Reading docked " << argv[2] << "... " << flush;
pdb_file >> docked;
Log.info() << "Read " << docked.countAtoms() << " atoms." << endl;
pdb_file.close();
docked_backup = docked;
// Find the static chain
// Remark: insert removes the chain in the original system!
// that's why we need docked_backup
ChainIterator pi = reference.beginChain();
for (; +pi; ++pi)
{
if (pi->getName() == argv[4])
static_reference.insert(*pi);
}
for (pi = docked.beginChain(); +pi; ++pi)
{
if (pi->getName() == argv[4])
static_docked.insert(*pi);
}
// map the two static chains
Matrix4x4 T;
StructureMapper mapper;
Size no_ca;
double rmsd;
Log.info() << "Mapping static chain of " << argv[1] << " onto static chain of " << argv[2] << endl;
Log.info() << " (this may take a while)..." << endl;
Timer t;
t.start();
// default values
double upper = 8.0;
double lower = 4.0;
double tolerance = 0.6;
T = mapper.mapProteins(static_reference, static_docked, type_map, no_ca, rmsd, upper, lower, tolerance);
t.stop();
if (no_ca < 1)
{
Log.info() << "Sorry - couldn't map (no CA atoms?)" << endl;
return 1;
}
Log.info() << "Mapped " << no_ca << " CA atoms." << endl;
Log.info() << "RMSD (CA only): " << rmsd << " A" << endl;
Log.info() << endl << "Transformation: " << endl;
Log.info() << T;
Log.info() << "Time to map the proteins: " << t.getClockTime() << "s" << endl;
Log.info() << "Transforming " << argv[1] << endl;
/** The static chain is still stored in static_..., while the remainder is stored
* in docked and reference.
*/
mapper.setTransformation(T);
reference.apply(mapper);
static_reference.apply(mapper);
Log.info() << "Reading the docking results..." << endl;
DockResult dr;
dr.readDockResult(argv[3]);
const ConformationSet* conformation_set = dr.getConformationSet();
vector<ConformationSet::Conformation> conformations = conformation_set->getScoring();
Log.info() << "Done." << endl;
Log.info() << "Computing RMSD values..." << endl;
SnapShot snap;
ofstream out("docking_rmsds.txt");
// Calculate RMSD for each snapshot
for (Size i=0; i<conformations.size(); ++i)
{
// get the whole docked system (static AND mobile chain), to apply the snapshot
docked = docked_backup;
snap = (*conformation_set)[i];
snap.applySnapShot(docked);
// split static chain from docked since we want to calculate the RMSD for static and mobile sperately
for (pi = docked.beginChain(); +pi; ++pi)
{
if (pi->getName() == argv[4])
static_docked.insert(*pi);
}
rmsd = 0.; // RMSD for whole complex
float rmsd_1 = 0.; // RMSD for mobile chains
float rmsd_2 = 0.; // RMSD for static chains
int count = 0;
int count_1 = 0;
int count_2 = 0;
// calculate RMSD of CA atoms for mobile chains
AtomIterator docked_atom=docked.beginAtom(), reference_atom=reference.beginAtom();
while (+docked_atom && +reference_atom)
{
while (+docked_atom && docked_atom->getName() != "CA") docked_atom++;
while (+reference_atom && reference_atom->getName() != "CA") reference_atom++;
if (+docked_atom && +reference_atom)
{
rmsd += (docked_atom->getPosition() - reference_atom->getPosition()).getSquareLength();
count++;
rmsd_1 += (docked_atom->getPosition() - reference_atom->getPosition()).getSquareLength();
count_1++;
docked_atom++;
reference_atom++;
}
}
// calculate RMSD of CA atoms for static chains
docked_atom=static_docked.beginAtom(), reference_atom=static_reference.beginAtom();
while (+docked_atom && +reference_atom)
{
while (+docked_atom && docked_atom->getName() != "CA") docked_atom++;
while (+reference_atom && reference_atom->getName() != "CA") reference_atom++;
if (+docked_atom && +reference_atom)
{
rmsd += (docked_atom->getPosition() - reference_atom->getPosition()).getSquareLength();
count++;
rmsd_2 += (docked_atom->getPosition() - reference_atom->getPosition()).getSquareLength();
count_2++;
docked_atom++;
reference_atom++;
}
}
Log.info() << "***** Snaphot " << i << " *****" << endl;
Log.info() << "RMSD is " << sqrt(rmsd / count) << " for " << count << " atoms." << endl;
Log.info() << "RMSD of static protein " << sqrt(rmsd_2 / count_2) << " for " << count_2 << " atoms." << endl;
Log.info() << "RMSD of mobile protein " << sqrt(rmsd_1 / count_1) << " for " << count_1 << " atoms." << endl;
Log.info() << endl;
// write out score of ith snapshot and calculated RMSD
out << conformations[i].second << " " << sqrt(rmsd/count) << endl;
}
Log.info() << "Done." << endl;
out.close();
return 0;
}
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