mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
10fbd483bb
* Add parameter to skip proximity bonding during PDB reading * Test proximityBonding flag * Remove multivalent Hs and bonds to metals in PDB * Add tests for multivalent Hs and metal unbinding * Remove covalent bonds to waters * Test unbinding of HOHs * Refactor funxtions * Rename flag for cosistency * Include flavor in double bond perception * Add metalorganic test (APW ligand) * Validate input foe IsBlacklistedPair and minor changes.
59 lines
1.8 KiB
C++
59 lines
1.8 KiB
C++
//
|
|
// 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;
|
|
}
|
|
}
|