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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/genericMolFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/KERNEL/molecule.h>
#include "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char* argv[])
{
CommandlineParser parpars("PropertyModifier", "modify molecule property tags", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("i", "input file");
parpars.registerMandatoryOutputFile("o", "output file");
parpars.registerMandatoryStringParameter("mode", "'delete', 'add' or 'rename' properties");
parpars.registerMandatoryStringParameter("name", "property name ('all' will erase all properties if in delete-mode)");
parpars.registerOptionalStringParameter("value", "property value (in case of prop. adding only)");
parpars.registerOptionalStringParameter("new_name", "new property name (in case of renaming only)");
parpars.registerFlag("rm", "remove input file when finished");
String man = "With this tools you can add, rename or delete molecule property tags.\nThese tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.\nThe output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).";
parpars.setToolManual(man);
list<String> slist;
slist.push_back("add");
slist.push_back("rename");
slist.push_back("delete");
parpars.setParameterRestrictions("mode",slist);
parpars.setSupportedFormats("i","mol2,sdf,drf");
parpars.setSupportedFormats("o","mol2,sdf,drf");
parpars.parse(argc, argv);
const String& nf = CommandlineParser::NOT_FOUND;
String mode = parpars.get("mode");
bool delete_mode = (mode == "delete");
bool add_mode = (mode == "add");
bool rename_mode = (mode == "rename");
int n = delete_mode+add_mode+rename_mode;
if (n != 1)
{
cerr<<"[Error:] Please set parameter 'mode' to either 'add' or 'delete' or 'rename'!"<<endl;
return 1;
}
String prop_name = parpars.get("name");
String new_prop_name = parpars.get("new_name");
if (new_prop_name == nf && rename_mode)
{
Log.error()<<"[Error:] 'new_prop_name' needs to be specified in rename-mode!"<<endl;
return 1;
}
String value = parpars.get("value");
GenericMolFile* input = MolFileFactory::open(parpars.get("i"), ios::in);
GenericMolFile* output = MolFileFactory::open(parpars.get("o"), ios::out, input);
list<String> l = parpars.getList("name");
list<String> v;
if (add_mode) v = parpars.getList("value");
else if (rename_mode) v = parpars.getList("new_name");
map<String, String> names;
list<String>::iterator it2 = v.begin();
for (list < String > ::iterator it = l.begin(); it != l.end(); it++)
{
if (it2 != v.end())
{
names.insert(make_pair(*it, *it2));
it2++;
}
else names.insert(make_pair(*it, ""));
}
for (Molecule* mol = input->read(); mol; delete mol, mol = input->read())
{
if (delete_mode)
{
if (prop_name != "all")
{
for (map < String, String > ::iterator it = names.begin(); it != names.end(); it++)
{
mol->clearProperty(it->first);
}
}
else mol->PropertyManager::clear();
}
else if (rename_mode)
{
for (NamedPropertyIterator it = mol->beginNamedProperty(); it != mol->endNamedProperty(); it++)
{
map<String, String>::iterator map_it = names.find(it->getName());
if (map_it != names.end())
{
*it = NamedProperty(map_it->second, it->toString());
}
}
}
else if (add_mode)
{
for (map < String, String > ::iterator it = names.begin(); it != names.end(); it++)
{
mol->setProperty(it->first, it->second);
}
}
*output << *mol;
}
input->close();
output->close();
delete input;
delete output;
if (parpars.has("rm"))
{
File::remove(parpars.get("i"));
}
}
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