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4c1ea25fda
* Fix a hang when trying to read mols from a directory not a file on linux * thrown an exception at construction time * clarify the readme * update release notes * Refactor the stream opening and checking code to a common method Co-authored-by: Brian Kelley <bkelley@relaytx.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
56 lines
1.6 KiB
C++
56 lines
1.6 KiB
C++
//
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// Copyright (C) 2013 Greg Landrum and NextMove Software
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <iostream>
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#include <fstream>
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#include <RDGeneral/BadFileException.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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namespace RDKit {
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PDBMolSupplier::PDBMolSupplier(std::istream *inStream, bool takeOwnership,
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bool sanitize, bool removeHs,
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unsigned int flavor, bool proximityBonding) {
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dp_inStream = inStream;
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df_owner = takeOwnership;
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df_sanitize = sanitize;
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df_removeHs = removeHs;
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d_flavor = flavor;
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df_proximityBonding = proximityBonding;
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}
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PDBMolSupplier::PDBMolSupplier(const std::string &fileName, bool sanitize,
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bool removeHs, unsigned int flavor,
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bool proximityBonding) {
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dp_inStream = openAndCheckStream(fileName);
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df_owner = true;
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df_sanitize = sanitize;
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df_removeHs = removeHs;
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d_flavor = flavor;
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df_proximityBonding = proximityBonding;
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}
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void PDBMolSupplier::init() {}
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void PDBMolSupplier::reset() {}
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ROMol *PDBMolSupplier::next() {
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return (ROMol *)PDBDataStreamToMol(dp_inStream, df_sanitize, df_removeHs,
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d_flavor, df_proximityBonding);
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}
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bool PDBMolSupplier::atEnd() {
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if (dp_inStream->eof()) {
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return true;
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}
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int ch = dp_inStream->peek();
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return ch == -1;
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}
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} // namespace RDKit
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