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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/STRUCTURE/reconstructFragmentProcessor.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
using namespace std;
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object
CommandlineParser parpars("ResidueChecker", "check residues to debug a protein structure wrt to PDB conventions", VERSION, String(__DATE__), "ForceFields");
parpars.registerMandatoryInputFile("pdb", "input pdb file ");
// TODO: offer upload of a distinguished fragDB file?
// shall we normalize names according to force field conventions??
parpars.registerFlag("norm_names", "ensures a consistent naming scheme for all atoms, e.g. PDB conventions", false);
// shall we add bonds
parpars.registerFlag("build_bonds", "add missing bonds", false);
// shall we apply the fragment reconstruction
parpars.registerFlag("frag_reconstruct", "reconstruct incomplete fragments", false);
// an now the tests:
parpars.registerFlag("extra_atoms", "check for extra atoms, i.e. unknown in the reference fragment", false);
parpars.registerFlag("bond_length", "check for invalid bond length", false);
// charges
parpars.registerFlag("int_net_charge", "check if integer charges", false);
parpars.registerFlag("large_charges", "check for too large charges", false);
parpars.registerFlag("large_net_charge", "check for too large net charge", false);
parpars.registerFlag("overlapping_atoms", "check for overlapptin atom positions", false);
parpars.registerFlag("nan_positions", "check for ill-valued atomic positions", false);
parpars.registerFlag("elements", "check if atom names reflect the atomic element", false);
parpars.registerFlag("dublicate_atom_names", "check for dublicated atom names", false);
parpars.registerFlag("unknown_residues", "check for unknown residues", false);
//TODO: offer write Logs to a pdf
// the manual
String man = String("This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances.");
parpars.setToolManual(man);
parpars.setSupportedFormats("pdb", "pdb");
// parse the command line
parpars.parse(argc, argv);
bool norm_names = false;
if (parpars.has("norm_names"))
{
norm_names = parpars.get("norm_names").toBool();
}
bool build_bonds = false;
if (parpars.has("build_bonds"))
{
build_bonds = parpars.get("build_bonds").toBool();
}
bool frag_reconstruct = false;
if (parpars.has("frag_reconstruct"))
{
frag_reconstruct = parpars.get("frag_reconstruct").toBool();
}
PDBFile pdb;
pdb.open(parpars.get("pdb"), std::ios::in);
if (!pdb)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("pdb") << " for input." << std::endl;
exit(2);
}
System sys;
pdb >> sys;
pdb.close();
bool changes = false;
// normalize the names and build all bonds
FragmentDB db("");
if (norm_names)
{
sys.apply(db.normalize_names);
changes = true;
}
if (build_bonds)
{
sys.apply(db.build_bonds);
changes = true;
}
if (frag_reconstruct)
{
ReconstructFragmentProcessor proc(db);
sys.apply(proc);
sys.apply(db.build_bonds);
changes = true;
}
// now specify the ResidueChecker
ResidueChecker check(db);
//MISSING_ATOMS
if (parpars.has("missing_atoms"))
{
check.enable(ResidueChecker::MISSING_ATOMS, parpars.get("missing_atoms").toBool());
}
//EXTRA_ATOMS
if (parpars.has("extra_atoms"))
{
check.enable(ResidueChecker::EXTRA_ATOMS, parpars.get("extra_atoms").toBool());
}
// ELEMENTS,
if (parpars.has("elements"))
{
check.enable(ResidueChecker::ELEMENTS, parpars.get("elements").toBool());
}
// SUSPECT_BOND_LENGTHS,
if (parpars.has("bond_length"))
{
check.enable(ResidueChecker::SUSPECT_BOND_LENGTHS, parpars.get("bond_length").toBool());
}
// NON_INTEGRAL_NET_CHARGE, //TODO: meaning reasonable or integer ??
if (parpars.has("net_charge"))
{
check.enable(ResidueChecker::NON_INTEGRAL_NET_CHARGE, parpars.get("net_charge").toBool());
}
// LARGE_CHARGES,
if (parpars.has("large_charges"))
{
check.enable(ResidueChecker::LARGE_CHARGES, parpars.get("large_charges").toBool());
}
// LARGE_NET_CHARGE,
if (parpars.has("large_net_charge"))
{
check.enable(ResidueChecker::LARGE_NET_CHARGE, parpars.get("large_net_charge").toBool());
}
// NAN_POSITIONS,
if (parpars.has("nan_positions"))
{
check.enable(ResidueChecker::NAN_POSITIONS, parpars.get("nan_positions").toBool());
}
// OVERLAPPING_ATOMS,
if (parpars.has("overlapping_atoms"))
{
check.enable(ResidueChecker::OVERLAPPING_ATOMS, parpars.get("overlapping_atoms").toBool());
check.enable(ResidueChecker::STRONGLY_OVERLAPPING_ATOMS, parpars.get("overlapping_atoms").toBool());
}
// DUPLICATE_ATOM_NAMES,
if (parpars.has("dublicate_atom_names"))
{
check.enable(ResidueChecker::DUPLICATE_ATOM_NAMES, parpars.get("dublicate_atom_names").toBool());
}
// UNKNOWN_RESIDUES,
if (parpars.has("unknown_residues"))
{
check.enable(ResidueChecker::UNKNOWN_RESIDUES, parpars.get("unknown_residues").toBool());
}
// set specified tests
sys.apply(check);
// overwrite
if (changes)
{
pdb.open(parpars.get("pdb"), ios::out);
pdb << sys;
pdb.close();
Log << "changes are written " << std::endl;
}
return 0;
}
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