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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_FORMAT_PDBFILE_H
# include <BALL/FORMAT/PDBFile.h>
#endif
#ifndef BALL_STRUCTURE_FRAGMENTDB_H
# include <BALL/STRUCTURE/fragmentDB.h>
#endif
#include <BALL/STRUCTURE/buildBondsProcessor.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
#include <iostream>
using namespace std;
using namespace BALL;
void usage (const char *progname);
int main (int argc, char **argv)
{
CommandlineParser parpars("PDBCutter", "separate ligand and receptor ", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("i", "input pdb-file");
parpars.registerMandatoryOutputFile("rec", "receptor output pdb-file");
parpars.registerMandatoryOutputFile("lig", "ligand output pdb-file");
parpars.registerMandatoryStringParameter("lig_chain", "chain-name of ligand");
parpars.registerMandatoryStringParameter("lig_name", "ligand name");
parpars.registerOptionalStringListParameter("rm_ch", "protein chains that are to be deleted");
parpars.registerOptionalStringListParameter("rm_res", "pdb-residues that are to be deleted (e.g. water or ions)");
String man = "This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.\n\nThe name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.\nOptionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.\n\nOutput of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.";
parpars.setToolManual(man);
parpars.setSupportedFormats("i","pdb");
parpars.setSupportedFormats("rec","pdb");
parpars.setSupportedFormats("lig","pdb");
parpars.parse(argc, argv);
PDBFile f0;
f0.open(parpars.get("i"));
System sys0;
f0 >> sys0;
Protein protein;
protein.insert(sys0);
Protein ligand;
String lig_chain_name = parpars.get("lig_chain");
String lig_name = parpars.get("lig_name");
set<String> delete_chains;
set<String> delete_residues;
list<String> plist = parpars.getList("rm_ch");
for (list < String > ::iterator it = plist.begin(); it != plist.end(); it++)
{
delete_chains.insert(*it);
}
plist = parpars.getList("rm_res");
for (list < String > ::iterator it = plist.begin(); it != plist.end(); it++)
{
delete_residues.insert(*it);
}
bool del_res = (delete_residues.size()>0);
for (ChainIterator it_ch = protein.beginChain(); it_ch != protein.endChain(); ++it_ch)
{
if (it_ch->getName() == lig_chain_name)
{
for (ResidueIterator it_res = it_ch->beginResidue(); it_res != it_ch->endResidue(); ++ it_res)
{
if (it_res->getName() == lig_name)
{
Residue* new_res = new Residue(*it_res);
ligand.append(*new_res);
it_res->select();
}
else if (delete_residues.find(it_res->getName()) != delete_residues.end())
{
it_res->select();
}
}
}
else if (del_res)
{
for (ResidueIterator it_res = it_ch->beginResidue(); it_res != it_ch->endResidue(); ++ it_res)
{
if (delete_residues.find(it_res->getName()) != delete_residues.end())
{
it_res->select();
}
}
}
if (delete_chains.find(it_ch->getName()) != delete_chains.end())
{
it_ch->select();
}
}
protein.removeSelected();
PDBFile f2(parpars.get("lig"), std::ios::out);
f2 << ligand;
f2.close();
PDBFile f3(parpars.get("rec"), std::ios::out);
f3 << protein;
f3.close();
return 0;
}
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