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Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)

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* Fixes #4535

First pass, not sure what the best fields are here

* update output format
This commit is contained in:
Greg Landrum
2021-09-28 19:40:43 +02:00
committed by GitHub
parent 22da97b836
commit 092552349c
4 changed files with 50 additions and 4 deletions
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2
Code/GraphMol/CMakeLists.txt
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@@ -7,7 +7,7 @@ rdkit_library(GraphMol
MolDiscriminators.cpp ConjugHybrid.cpp AddHs.cpp
Matrices.cpp Chirality.cpp RingInfo.cpp Conformer.cpp
Renumber.cpp AdjustQuery.cpp Resonance.cpp StereoGroup.cpp
new_canon.cpp SubstanceGroup.cpp FindStereo.cpp
new_canon.cpp SubstanceGroup.cpp FindStereo.cpp MonomerInfo.cpp
SHARED
LINK_LIBRARIES RDGeometryLib RDGeneral )
target_compile_definitions(GraphMol PRIVATE RDKIT_GRAPHMOL_BUILD)

21
Code/GraphMol/MonomerInfo.cpp Normal file
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@@ -0,0 +1,21 @@
//
// Copyright (C) 2021 Greg Landrum and other RDKit contributors
//
// @@ 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 "MonomerInfo.h"
using namespace RDKit;
//! allows AtomPDBResidueInfo objects to be dumped to streams
std::ostream &operator<<(std::ostream &target, const AtomPDBResidueInfo &apri) {
target << apri.getSerialNumber() << " " << apri.getName() << " "
<< apri.getResidueName() << " " << apri.getChainId() << " "
<< apri.getResidueNumber();
return target;
}

6
Code/GraphMol/MonomerInfo.h
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@@ -1,5 +1,5 @@
//
// Copyright (C) 2013 Greg Landrum
// Copyright (C) 2013-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -13,8 +13,8 @@
*/
#include <RDGeneral/export.h>
#ifndef _RD_MONOMERINFO_H
#define _RD_MONOMERINFO_H
#ifndef RD_MONOMERINFO_H
#define RD_MONOMERINFO_H
#include <string>
#include <utility>

25
Code/GraphMol/catch_graphmol.cpp
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@@ -14,7 +14,9 @@
#include <GraphMol/new_canon.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/MonomerInfo.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/SequenceParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
@@ -2434,4 +2436,27 @@ TEST_CASE("KekulizeIfPossible") {
}
}
}
}
TEST_CASE("Github #4535: operator<< for AtomPDBResidue", "[PDB]") {
SECTION("basics") {
bool sanitize = true;
int flavor = 0;
std::unique_ptr<RWMol> mol(SequenceToMol("KY", sanitize, flavor));
REQUIRE(mol);
REQUIRE(mol->getAtomWithIdx(0)->getMonomerInfo());
auto res = static_cast<AtomPDBResidueInfo *>(
mol->getAtomWithIdx(0)->getMonomerInfo());
REQUIRE(res);
std::stringstream oss;
oss << *res << std::endl;
res = static_cast<AtomPDBResidueInfo *>(
mol->getAtomWithIdx(mol->getNumAtoms() - 1)->getMonomerInfo());
REQUIRE(res);
oss << *res << std::endl;
auto tgt = R"FOO(1 N LYS A 1
22 OXT TYR A 2
)FOO";
CHECK(oss.str() == tgt);
}
}