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//
// Copyright (C) 2013 Greg Landrum and NextMove Software
//
// @@ 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 <iostream>
#include <fstream>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
namespace RDKit {
PDBMolSupplier::PDBMolSupplier(std::istream *inStream, bool takeOwnership,
bool sanitize, bool removeHs,
unsigned int flavor, bool proximityBonding) {
dp_inStream = inStream;
df_owner = takeOwnership;
df_sanitize = sanitize;
df_removeHs = removeHs;
d_flavor = flavor;
df_proximityBonding = proximityBonding;
}
PDBMolSupplier::PDBMolSupplier(const std::string &fileName, bool sanitize,
bool removeHs, unsigned int flavor, bool proximityBonding) {
auto *ifs = new std::ifstream(fileName.c_str(), std::ios_base::binary);
if (!ifs || !(*ifs) || ifs->bad()) {
std::ostringstream errout;
errout << "Bad input file " << fileName;
throw BadFileException(errout.str());
}
dp_inStream = (std::istream *)ifs;
df_owner = true;
df_sanitize = sanitize;
df_removeHs = removeHs;
d_flavor = flavor;
df_proximityBonding = proximityBonding;
}
void PDBMolSupplier::init() {}
void PDBMolSupplier::reset() {}
ROMol *PDBMolSupplier::next() {
return (ROMol *)PDBDataStreamToMol(dp_inStream, df_sanitize, df_removeHs,
d_flavor, df_proximityBonding);
}
bool PDBMolSupplier::atEnd() {
if (dp_inStream->eof()) return true;
int ch = dp_inStream->peek();
return ch == -1;
}
}
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