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// $Id: FragCatParams.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "FragCatParams.h"
#include "FragCatalogUtils.h"
#include <GraphMol/RDKitBase.h>
#include <sstream>
#include <boost/cstdint.hpp>
namespace RDKit{
using boost::int32_t;
using boost::uint32_t;
FragCatParams::FragCatParams(unsigned int lLen, unsigned int uLen,
std::string fgroupFile, double tol) {
d_funcGroups.clear();
d_typeStr = "Fragment Catalog Parameters";
CHECK_INVARIANT(lLen<=uLen,"The upper length for fragments must be >= lower length");
d_lowerFragLen = lLen;
d_upperFragLen = uLen;
d_tolerance = tol;
d_funcGroups = readFuncGroups(fgroupFile);
}
FragCatParams::FragCatParams(const FragCatParams &other) {
d_funcGroups.clear();
// copy consttructor
d_typeStr = other.getTypeStr();
d_lowerFragLen = other.getLowerFragLength();
d_upperFragLen = other.getUpperFragLength();
d_tolerance = other.getTolerance();
// std::cout << "In param copier\n";
const MOL_SPTR_VECT &ofgrps = other.getFuncGroups();
//const MOL_PTR_VECT &ofgrps = other.getFuncGroups();
MOL_SPTR_VECT::const_iterator fgi;
//MOL_PTR_VECT_CI fgi;
for (fgi = ofgrps.begin(); fgi != ofgrps.end(); fgi++) {
ROMol *nmol = new ROMol(*(fgi->get()));
//ROMol *nmol = new ROMol(*(*fgi));
d_funcGroups.push_back(ROMOL_SPTR(nmol));
//d_funcGroups.push_back(nmol);
}
}
FragCatParams::FragCatParams(const std::string &pickle) {
d_typeStr = "Fragment Catalog Parameters";
this->initFromString(pickle);
}
FragCatParams::~FragCatParams() {
}
const MOL_SPTR_VECT &FragCatParams::getFuncGroups() const {
return d_funcGroups;
}
const ROMol *FragCatParams::getFuncGroup(unsigned int fid) const {
RANGE_CHECK(0, fid, d_funcGroups.size());
//return d_funcGroups[fid];
return d_funcGroups[fid].get();
}
void FragCatParams::toStream(std::ostream &ss) const {
ss << d_lowerFragLen << " " << d_upperFragLen << " " << d_tolerance << "\n";
ss << d_funcGroups.size() << "\n";
for(MOL_SPTR_VECT::const_iterator funcGroup=d_funcGroups.begin();
funcGroup != d_funcGroups.end();
funcGroup++){
std::string text;
(*funcGroup)->getProp("_Name",text);
ss << text;
ss << "\t";
(*funcGroup)->getProp("_fragSMARTS",text);
ss << text;
ss << "\n";
}
}
std::string FragCatParams::Serialize() const {
std::stringstream ss;
toStream(ss);
return ss.str();
}
void FragCatParams::initFromString(const std::string &text){
std::stringstream ss(text);
initFromStream(ss);
}
void FragCatParams::initFromStream(std::istream &ss){
ss >> d_lowerFragLen;
ss >> d_upperFragLen;
ss >> d_tolerance;
int nGroups;
ss >> nGroups;
//std::cout << "Reading " << nGroups << " Groups" << std::endl;
d_funcGroups = readFuncGroups(ss,nGroups);
}
}
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