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rdkit/Code/GraphMol/MolPickler.cpp
Brian Kelley e70599a12e Dev/pickle properties (#1277) 
* Adds pickling of properties (optional)

* Ignores RDKit::Dict::Pairs - previously private

* Fixes AllProps definition

* Fixes BondProps seperation

* Fixes reaction pickling - Adds ability to pickle atom + QueryAtom

* Bumps pickle version

* Removes fugly post-increments

* Changes Default to NoProps

* Tests more options for pickling

* Runs clang format

* Adds get/setDefaultPropertyPickleOptions, exposes to python

* turns tests back on.

* Fixes enum (clang was allowing c++11 semantics)

* Adds global settings test

* Code/GraphMol/testPicklerGlobalSettings.cpp
2017-02-09 16:06:01 +01:00

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// $Id$
//
// Copyright (C) 2001-2013 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 <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/MonomerInfo.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/types.h>
#include <Query/QueryObjects.h>
#include <map>
#include <boost/cstdint.hpp>
#ifdef RDK_THREADSAFE_SSS
#include <boost/thread/once.hpp>
#include <boost/thread/mutex.hpp>
#endif
using boost::int32_t;
using boost::uint32_t;
namespace RDKit {
const int32_t MolPickler::versionMajor = 8;
const int32_t MolPickler::versionMinor = 0;
const int32_t MolPickler::versionPatch = 0;
const int32_t MolPickler::endianId = 0xDEADBEEF;
void streamWrite(std::ostream &ss, MolPickler::Tags tag) {
unsigned char tmp = static_cast<unsigned char>(tag);
streamWrite(ss, tmp);
}
template <typename T>
void streamWrite(std::ostream &ss, MolPickler::Tags tag, const T &what) {
streamWrite(ss, tag);
streamWrite(ss, what);
};
void streamRead(std::istream &ss, MolPickler::Tags &tag, int version) {
if (version < 7000) {
int32_t tmp;
streamRead(ss, tmp, version);
tag = static_cast<MolPickler::Tags>(tmp);
} else {
unsigned char tmp;
streamRead(ss, tmp, version);
tag = static_cast<MolPickler::Tags>(tmp);
}
}
namespace {
static unsigned int defaultProperties = PicklerOps::NoProps;
#ifdef RDK_THREADSAFE_SSS
boost::mutex &propmutex_get() {
// create on demand
static boost::mutex _mutex;
return _mutex;
}
void propmutex_create() {
boost::mutex &mutex = propmutex_get();
boost::mutex::scoped_lock test_lock(mutex);
}
boost::mutex& GetPropMutex() {
#ifdef BOOST_THREAD_PROVIDES_ONCE_CXX11
static boost::once_flag flag;
#else
static boost::once_flag flag = BOOST_ONCE_INIT;
#endif
boost::call_once(&propmutex_create, flag);
return propmutex_get();
}
#endif
}
unsigned int MolPickler::getDefaultPickleProperties() {
#ifdef RDK_THREADSAFE_SSS
boost::mutex::scoped_lock lock(GetPropMutex());
#endif
unsigned int props = defaultProperties;
return props;
}
void MolPickler::setDefaultPickleProperties(unsigned int props) {
#ifdef RDK_THREADSAFE_SSS
boost::mutex::scoped_lock lock(GetPropMutex());
#endif
defaultProperties = props;
}
namespace {
using namespace Queries;
template <class T>
void pickleQuery(std::ostream &ss, const Query<int, T const *, true> *query) {
PRECONDITION(query, "no query");
streamWrite(ss, query->getDescription());
if (query->getNegation()) streamWrite(ss, MolPickler::QUERY_ISNEGATED);
int32_t queryVal;
// if (typeid(*query)==typeid(ATOM_BOOL_QUERY)){
// streamWrite(ss,QUERY_BOOL);
if (typeid(*query) == typeid(AndQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_AND);
} else if (typeid(*query) == typeid(OrQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_OR);
} else if (typeid(*query) == typeid(XOrQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_XOR);
} else if (typeid(*query) == typeid(EqualityQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_EQUALS);
queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) == typeid(GreaterQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_GREATER);
queryVal = static_cast<const GreaterQuery<int, T const *, true> *>(query)
->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal = static_cast<const GreaterQuery<int, T const *, true> *>(query)
->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) ==
typeid(GreaterEqualQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_GREATEREQUAL);
queryVal =
static_cast<const GreaterEqualQuery<int, T const *, true> *>(query)
->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal =
static_cast<const GreaterEqualQuery<int, T const *, true> *>(query)
->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) == typeid(LessQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_LESS);
queryVal =
static_cast<const LessQuery<int, T const *, true> *>(query)->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal =
static_cast<const LessQuery<int, T const *, true> *>(query)->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) == typeid(LessEqualQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_LESSEQUAL);
queryVal = static_cast<const LessEqualQuery<int, T const *, true> *>(query)
->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal = static_cast<const LessEqualQuery<int, T const *, true> *>(query)
->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) == typeid(RangeQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_RANGE);
queryVal = static_cast<const RangeQuery<int, T const *, true> *>(query)
->getLower();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal = static_cast<const RangeQuery<int, T const *, true> *>(query)
->getUpper();
streamWrite(ss, queryVal);
queryVal =
static_cast<const RangeQuery<int, T const *, true> *>(query)->getTol();
streamWrite(ss, queryVal);
char ends;
bool lowerOpen, upperOpen;
boost::tie(lowerOpen, upperOpen) =
static_cast<const RangeQuery<int, T const *, true> *>(query)
->getEndsOpen();
ends = 0 | (rdcast<int>(lowerOpen) << 1) | rdcast<int>(upperOpen);
streamWrite(ss, ends);
} else if (typeid(*query) == typeid(SetQuery<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_SET);
queryVal =
static_cast<const SetQuery<int, T const *, true> *>(query)->size();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
typename SetQuery<int, T const *, true>::CONTAINER_TYPE::const_iterator cit;
for (cit = static_cast<const SetQuery<int, T const *, true> *>(query)
->beginSet();
cit !=
static_cast<const SetQuery<int, T const *, true> *>(query)->endSet();
++cit) {
queryVal = *cit;
streamWrite(ss, queryVal);
}
} else if (typeid(*query) == typeid(AtomRingQuery)) {
streamWrite(ss, MolPickler::QUERY_ATOMRING);
queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
->getVal();
streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
->getTol();
streamWrite(ss, queryVal);
} else if (typeid(*query) == typeid(RecursiveStructureQuery)) {
streamWrite(ss, MolPickler::QUERY_RECURSIVE);
streamWrite(ss, MolPickler::QUERY_VALUE);
MolPickler::pickleMol(
((const RecursiveStructureQuery *)query)->getQueryMol(), ss);
} else if (typeid(*query) == typeid(Query<int, T const *, true>)) {
streamWrite(ss, MolPickler::QUERY_NULL);
} else {
throw MolPicklerException("do not know how to pickle part of the query.");
}
// now the children:
streamWrite(ss, MolPickler::QUERY_NUMCHILDREN,
static_cast<unsigned char>(query->endChildren() -
query->beginChildren()));
typename Query<int, T const *, true>::CHILD_VECT_CI cit;
for (cit = query->beginChildren(); cit != query->endChildren(); ++cit) {
pickleQuery(ss, cit->get());
}
}
void finalizeQueryFromDescription(Query<int, Atom const *, true> *query,
Atom const *owner) {
RDUNUSED_PARAM(owner);
std::string descr = query->getDescription();
Query<int, Atom const *, true> *tmpQuery;
if (descr == "AtomRingBondCount") {
query->setDataFunc(queryAtomRingBondCount);
} else if (descr == "AtomHasRingBond") {
query->setDataFunc(queryAtomHasRingBond);
} else if (descr == "AtomRingSize") {
tmpQuery = makeAtomInRingOfSizeQuery(
static_cast<ATOM_EQUALS_QUERY *>(query)->getVal());
query->setDataFunc(tmpQuery->getDataFunc());
delete tmpQuery;
} else if (descr == "AtomMinRingSize") {
query->setDataFunc(queryAtomMinRingSize);
} else if (descr == "AtomRingBondCount") {
query->setDataFunc(queryAtomRingBondCount);
} else if (descr == "AtomImplicitValence") {
query->setDataFunc(queryAtomImplicitValence);
} else if (descr == "AtomTotalValence") {
query->setDataFunc(queryAtomTotalValence);
} else if (descr == "AtomAtomicNum") {
query->setDataFunc(queryAtomNum);
} else if (descr == "AtomExplicitDegree") {
query->setDataFunc(queryAtomExplicitDegree);
} else if (descr == "AtomTotalDegree") {
query->setDataFunc(queryAtomTotalDegree);
} else if (descr == "AtomHCount") {
query->setDataFunc(queryAtomHCount);
} else if (descr == "AtomImplicitHCount") {
query->setDataFunc(queryAtomImplicitHCount);
} else if (descr == "AtomHasImplicitH") {
query->setDataFunc(queryAtomHasImplicitH);
} else if (descr == "AtomIsAromatic") {
query->setDataFunc(queryAtomAromatic);
} else if (descr == "AtomIsAliphatic") {
query->setDataFunc(queryAtomAliphatic);
} else if (descr == "AtomUnsaturated") {
query->setDataFunc(queryAtomUnsaturated);
} else if (descr == "AtomMass") {
query->setDataFunc(queryAtomMass);
} else if (descr == "AtomIsotope") {
query->setDataFunc(queryAtomIsotope);
} else if (descr == "AtomFormalCharge") {
query->setDataFunc(queryAtomFormalCharge);
} else if (descr == "AtomHybridization") {
query->setDataFunc(queryAtomHybridization);
} else if (descr == "AtomInRing") {
query->setDataFunc(queryIsAtomInRing);
} else if (descr == "AtomInNRings") {
query->setDataFunc(queryIsAtomInNRings);
} else if (descr == "AtomNull") {
query->setDataFunc(nullDataFun);
query->setMatchFunc(nullQueryFun);
} else if (descr == "AtomInNRings" || descr == "RecursiveStructure") {
// don't need to do anything here because the classes
// automatically have everything set
} else if (descr == "AtomAnd" || descr == "AtomOr" || descr == "AtomXor") {
// don't need to do anything here because the classes
// automatically have everything set
} else {
throw MolPicklerException("Do not know how to finalize query: '" + descr +
"'");
}
}
void finalizeQueryFromDescription(Query<int, Bond const *, true> *query,
Bond const *owner) {
RDUNUSED_PARAM(owner);
std::string descr = query->getDescription();
Query<int, Bond const *, true> *tmpQuery;
if (descr == "BondRingSize") {
tmpQuery = makeBondInRingOfSizeQuery(
static_cast<BOND_EQUALS_QUERY *>(query)->getVal());
query->setDataFunc(tmpQuery->getDataFunc());
delete tmpQuery;
} else if (descr == "BondMinRingSize") {
query->setDataFunc(queryBondMinRingSize);
} else if (descr == "BondOrder") {
query->setDataFunc(queryBondOrder);
} else if (descr == "BondDir") {
query->setDataFunc(queryBondDir);
} else if (descr == "BondInRing") {
query->setDataFunc(queryIsBondInRing);
} else if (descr == "BondInNRings") {
query->setDataFunc(queryIsBondInNRings);
} else if (descr == "BondNull") {
query->setDataFunc(nullDataFun);
query->setMatchFunc(nullQueryFun);
} else if (descr == "BondAnd" || descr == "BondOr" || descr == "BondXor") {
// don't need to do anything here because the classes
// automatically have everything set
} else {
throw MolPicklerException("Do not know how to finalize query: '" + descr +
"'");
}
}
template <class T>
Query<int, T const *, true> *buildBaseQuery(std::istream &ss, T const *owner,
MolPickler::Tags tag, int version) {
PRECONDITION(owner, "no query");
std::string descr;
Query<int, T const *, true> *res = 0;
int32_t val;
int32_t nMembers;
switch (tag) {
case MolPickler::QUERY_AND:
res = new AndQuery<int, T const *, true>();
break;
case MolPickler::QUERY_OR:
res = new OrQuery<int, T const *, true>();
break;
case MolPickler::QUERY_XOR:
res = new XOrQuery<int, T const *, true>();
break;
case MolPickler::QUERY_EQUALS:
res = new EqualityQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<EqualityQuery<int, T const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<EqualityQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_GREATER:
res = new GreaterQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<GreaterQuery<int, T const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<GreaterQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_GREATEREQUAL:
res = new GreaterEqualQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<GreaterEqualQuery<int, T const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<GreaterEqualQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_LESS:
res = new LessQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<LessQuery<int, T const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<LessQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_LESSEQUAL:
res = new LessEqualQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<LessEqualQuery<int, T const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<LessEqualQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_RANGE:
res = new RangeQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<RangeQuery<int, T const *, true> *>(res)->setLower(val);
streamRead(ss, val, version);
static_cast<RangeQuery<int, T const *, true> *>(res)->setUpper(val);
streamRead(ss, val, version);
static_cast<RangeQuery<int, T const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_SET:
res = new SetQuery<int, T const *, true>();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, nMembers);
while (nMembers > 0) {
streamRead(ss, val, version);
static_cast<SetQuery<int, T const *, true> *>(res)->insert(val);
--nMembers;
}
break;
case MolPickler::QUERY_NULL:
res = new Query<int, T const *, true>();
break;
default:
throw MolPicklerException("unknown query-type tag encountered");
}
POSTCONDITION(res, "no match found");
return res;
}
Query<int, Atom const *, true> *unpickleQuery(std::istream &ss,
Atom const *owner, int version) {
PRECONDITION(owner, "no query");
std::string descr;
bool isNegated = false;
Query<int, Atom const *, true> *res;
streamRead(ss, descr, version);
MolPickler::Tags tag;
streamRead(ss, tag, version);
if (tag == MolPickler::QUERY_ISNEGATED) {
isNegated = true;
streamRead(ss, tag, version);
}
int32_t val;
ROMol *tmpMol;
switch (tag) {
case MolPickler::QUERY_ATOMRING:
res = new AtomRingQuery();
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
streamRead(ss, val, version);
static_cast<EqualityQuery<int, Atom const *, true> *>(res)->setVal(val);
streamRead(ss, val, version);
static_cast<EqualityQuery<int, Atom const *, true> *>(res)->setTol(val);
break;
case MolPickler::QUERY_RECURSIVE:
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_VALUE) {
throw MolPicklerException(
"Bad pickle format: QUERY_VALUE tag not found.");
}
tmpMol = new ROMol();
MolPickler::molFromPickle(ss, tmpMol);
res = new RecursiveStructureQuery(tmpMol);
break;
default:
res = buildBaseQuery(ss, owner, tag, version);
break;
}
CHECK_INVARIANT(res, "no query!");
res->setNegation(isNegated);
res->setDescription(descr);
finalizeQueryFromDescription(res, owner);
// read in the children:
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_NUMCHILDREN) {
throw MolPicklerException(
"Bad pickle format: QUERY_NUMCHILDREN tag not found.");
}
unsigned char numChildren;
streamRead(ss, numChildren, version);
while (numChildren > 0) {
Query<int, Atom const *, true> *child = unpickleQuery(ss, owner, version);
res->addChild(Query<int, Atom const *, true>::CHILD_TYPE(child));
--numChildren;
}
return res;
}
Query<int, Bond const *, true> *unpickleQuery(std::istream &ss,
Bond const *owner, int version) {
PRECONDITION(owner, "no query");
std::string descr;
bool isNegated = false;
Query<int, Bond const *, true> *res;
streamRead(ss, descr, version);
MolPickler::Tags tag;
streamRead(ss, tag, version);
if (tag == MolPickler::QUERY_ISNEGATED) {
isNegated = true;
streamRead(ss, tag, version);
}
res = buildBaseQuery(ss, owner, tag, version);
CHECK_INVARIANT(res, "no query!");
res->setNegation(isNegated);
res->setDescription(descr);
finalizeQueryFromDescription(res, owner);
// read in the children:
streamRead(ss, tag, version);
if (tag != MolPickler::QUERY_NUMCHILDREN) {
throw MolPicklerException(
"Bad pickle format: QUERY_NUMCHILDREN tag not found.");
}
unsigned char numChildren;
streamRead(ss, numChildren, version);
while (numChildren > 0) {
Query<int, Bond const *, true> *child = unpickleQuery(ss, owner, version);
res->addChild(Query<int, Bond const *, true>::CHILD_TYPE(child));
--numChildren;
}
return res;
}
void pickleAtomPDBResidueInfo(std::ostream &ss,
const AtomPDBResidueInfo *info) {
PRECONDITION(info, "no info");
if (info->getSerialNumber())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SERIALNUMBER,
info->getSerialNumber());
if (info->getAltLoc() != "")
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_ALTLOC, info->getAltLoc());
if (info->getResidueName() != "")
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_RESIDUENAME,
info->getResidueName());
if (info->getResidueNumber())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_RESIDUENUMBER,
info->getResidueNumber());
if (info->getChainId() != "")
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_CHAINID, info->getChainId());
if (info->getInsertionCode() != "")
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_INSERTIONCODE,
info->getInsertionCode());
if (info->getOccupancy())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_OCCUPANCY,
info->getOccupancy());
if (info->getTempFactor())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_TEMPFACTOR,
info->getTempFactor());
if (info->getIsHeteroAtom())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_ISHETEROATOM,
static_cast<char>(info->getIsHeteroAtom()));
if (info->getSecondaryStructure())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE,
info->getSecondaryStructure());
if (info->getSegmentNumber())
streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SEGMENTNUMBER,
info->getSegmentNumber());
}
void unpickleAtomPDBResidueInfo(std::istream &ss, AtomPDBResidueInfo *info,
int version) {
PRECONDITION(info, "no info");
std::string sval;
double dval;
char cval;
unsigned int uival;
int ival;
MolPickler::Tags tag = MolPickler::BEGIN_ATOM_MONOMER;
while (tag != MolPickler::END_ATOM_MONOMER) {
streamRead(ss, tag, version);
switch (tag) {
case MolPickler::ATOM_PDB_RESIDUE_SERIALNUMBER:
streamRead(ss, ival, version);
info->setSerialNumber(ival);
break;
case MolPickler::ATOM_PDB_RESIDUE_ALTLOC:
streamRead(ss, sval, version);
info->setAltLoc(sval);
break;
case MolPickler::ATOM_PDB_RESIDUE_RESIDUENAME:
streamRead(ss, sval, version);
info->setResidueName(sval);
break;
case MolPickler::ATOM_PDB_RESIDUE_RESIDUENUMBER:
streamRead(ss, ival, version);
info->setResidueNumber(ival);
break;
case MolPickler::ATOM_PDB_RESIDUE_CHAINID:
streamRead(ss, sval, version);
info->setChainId(sval);
break;
case MolPickler::ATOM_PDB_RESIDUE_INSERTIONCODE:
streamRead(ss, sval, version);
info->setInsertionCode(sval);
break;
case MolPickler::ATOM_PDB_RESIDUE_OCCUPANCY:
streamRead(ss, dval, version);
info->setOccupancy(dval);
break;
case MolPickler::ATOM_PDB_RESIDUE_TEMPFACTOR:
streamRead(ss, dval, version);
info->setTempFactor(dval);
break;
case MolPickler::ATOM_PDB_RESIDUE_ISHETEROATOM:
streamRead(ss, cval, version);
info->setIsHeteroAtom(cval);
break;
case MolPickler::ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE:
streamRead(ss, uival, version);
info->setSecondaryStructure(uival);
break;
case MolPickler::ATOM_PDB_RESIDUE_SEGMENTNUMBER:
streamRead(ss, uival, version);
info->setSegmentNumber(uival);
break;
case MolPickler::END_ATOM_MONOMER:
break;
default:
throw MolPicklerException(
"unrecognized tag while parsing atom peptide residue info");
}
}
}
void pickleAtomMonomerInfo(std::ostream &ss, const AtomMonomerInfo *info) {
PRECONDITION(info, "no info");
streamWrite(ss, info->getName());
streamWrite(ss, static_cast<unsigned int>(info->getMonomerType()));
switch (info->getMonomerType()) {
case AtomMonomerInfo::UNKNOWN:
case AtomMonomerInfo::OTHER:
break;
case AtomMonomerInfo::PDBRESIDUE:
pickleAtomPDBResidueInfo(ss,
static_cast<const AtomPDBResidueInfo *>(info));
break;
default:
throw MolPicklerException("unrecognized MonomerType");
}
}
AtomMonomerInfo *unpickleAtomMonomerInfo(std::istream &ss, int version) {
MolPickler::Tags tag;
std::string nm;
streamRead(ss, nm, version);
unsigned int typ;
streamRead(ss, typ, version);
AtomMonomerInfo *res;
switch (typ) {
case AtomMonomerInfo::UNKNOWN:
case AtomMonomerInfo::OTHER:
res =
new AtomMonomerInfo(RDKit::AtomMonomerInfo::AtomMonomerType(typ), nm);
streamRead(ss, tag, version);
if (tag != MolPickler::END_ATOM_MONOMER)
throw MolPicklerException(
"did not find expected end of atom monomer info");
break;
case AtomMonomerInfo::PDBRESIDUE:
res = static_cast<AtomMonomerInfo *>(new AtomPDBResidueInfo(nm));
unpickleAtomPDBResidueInfo(ss, static_cast<AtomPDBResidueInfo *>(res),
version);
break;
default:
throw MolPicklerException("unrecognized MonomerType");
}
return res;
}
} // end of anonymous namespace
void MolPickler::pickleMol(const ROMol *mol, std::ostream &ss) {
pickleMol(mol, ss, MolPickler::getDefaultPickleProperties());
}
void MolPickler::pickleMol(const ROMol *mol, std::ostream &ss,
unsigned int propertyFlags) {
PRECONDITION(mol, "empty molecule");
streamWrite(ss, endianId);
streamWrite(ss, static_cast<int>(VERSION));
streamWrite(ss, versionMajor);
streamWrite(ss, versionMinor);
streamWrite(ss, versionPatch);
#ifndef OLD_PICKLE
if (mol->getNumAtoms() > 255) {
_pickle<int32_t>(mol, ss, propertyFlags);
} else {
_pickle<unsigned char>(mol, ss, propertyFlags);
}
#else
_pickleV1(mol, ss);
#endif
}
void MolPickler::pickleMol(const ROMol &mol, std::ostream &ss) {
pickleMol(&mol, ss, MolPickler::getDefaultPickleProperties());
}
void MolPickler::pickleMol(const ROMol *mol, std::string &res) {
pickleMol(mol, res, MolPickler::getDefaultPickleProperties());
}
void MolPickler::pickleMol(const ROMol *mol, std::string &res,
unsigned int pickleFlags) {
PRECONDITION(mol, "empty molecule");
std::stringstream ss(std::ios_base::binary | std::ios_base::out |
std::ios_base::in);
MolPickler::pickleMol(mol, ss, pickleFlags);
res = ss.str();
}
void MolPickler::pickleMol(const ROMol &mol, std::string &ss) {
pickleMol(&mol, ss, MolPickler::getDefaultPickleProperties());
}
// NOTE: if the mol passed in here already has atoms and bonds, they will
// be left intact. The side effect is that ALL atom and bond bookmarks
// will be blown out by the end of this process.
void MolPickler::molFromPickle(std::istream &ss, ROMol *mol) {
PRECONDITION(mol, "empty molecule");
int32_t tmpInt;
mol->clearAllAtomBookmarks();
mol->clearAllBondBookmarks();
streamRead(ss, tmpInt);
if (tmpInt != endianId) {
throw MolPicklerException(
"Bad pickle format: bad endian ID or invalid file format");
}
streamRead(ss, tmpInt);
if (static_cast<Tags>(tmpInt) != VERSION) {
throw MolPicklerException("Bad pickle format: no version tag");
}
int32_t majorVersion, minorVersion, patchVersion;
streamRead(ss, majorVersion);
streamRead(ss, minorVersion);
streamRead(ss, patchVersion);
if (majorVersion > versionMajor ||
(majorVersion == versionMajor && minorVersion > versionMinor)) {
BOOST_LOG(rdWarningLog) << "Depickling from a version number ("
<< majorVersion << "." << minorVersion << ")"
<< "that is higher than our version ("
<< versionMajor << "." << versionMinor
<< ").\nThis probably won't work." << std::endl;
}
majorVersion = 1000 * majorVersion + minorVersion * 10 + patchVersion;
if (majorVersion == 1) {
_depickleV1(ss, mol);
} else {
int32_t numAtoms;
streamRead(ss, numAtoms, majorVersion);
if (numAtoms > 255) {
_depickle<int32_t>(ss, mol, majorVersion, numAtoms);
} else {
_depickle<unsigned char>(ss, mol, majorVersion, numAtoms);
}
}
mol->clearAllAtomBookmarks();
mol->clearAllBondBookmarks();
if (majorVersion < 4000) {
// FIX for issue 220 - probably better to change the pickle format later
MolOps::assignStereochemistry(*mol, true);
}
}
void MolPickler::molFromPickle(const std::string &pickle, ROMol *mol) {
PRECONDITION(mol, "empty molecule");
std::stringstream ss(std::ios_base::binary | std::ios_base::out |
std::ios_base::in);
ss.write(pickle.c_str(), pickle.length());
MolPickler::molFromPickle(ss, mol);
}
//--------------------------------------
//
// Molecules
//
//--------------------------------------
template <typename T>
void MolPickler::_pickle(const ROMol *mol, std::ostream &ss,
unsigned int propertyFlags) {
PRECONDITION(mol, "empty molecule");
int32_t tmpInt;
bool includeAtomCoords = true;
std::map<int, int> atomIdxMap;
tmpInt = static_cast<int32_t>(mol->getNumAtoms());
streamWrite(ss, tmpInt);
tmpInt = static_cast<int32_t>(mol->getNumBonds());
streamWrite(ss, tmpInt);
char flag = 0;
if (includeAtomCoords) flag |= 0x1 << 7;
streamWrite(ss, flag);
// -------------------
//
// Write Atoms
//
// -------------------
streamWrite(ss, BEGINATOM);
ROMol::ConstAtomIterator atIt;
int nWritten = 0;
for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); ++atIt) {
_pickleAtom<T>(ss, *atIt);
atomIdxMap[(*atIt)->getIdx()] = nWritten;
nWritten++;
}
// -------------------
//
// Write Bonds
//
// -------------------
streamWrite(ss, BEGINBOND);
for (unsigned int i = 0; i < mol->getNumBonds(); i++) {
_pickleBond<T>(ss, mol->getBondWithIdx(i), atomIdxMap);
}
// -------------------
//
// Write Rings (if present)
//
// -------------------
const RingInfo *ringInfo = mol->getRingInfo();
if (ringInfo && ringInfo->isInitialized()) {
streamWrite(ss, BEGINSSSR);
_pickleSSSR<T>(ss, ringInfo, atomIdxMap);
}
// pickle the conformations if necessary
if (includeAtomCoords) {
streamWrite(ss, BEGINCONFS);
tmpInt = static_cast<int32_t>(mol->getNumConformers());
streamWrite(ss, tmpInt);
ROMol::ConstConformerIterator ci;
for (ci = mol->beginConformers(); ci != mol->endConformers(); ++ci) {
const Conformer *conf = ci->get();
_pickleConformer<T>(ss, conf);
}
}
if (propertyFlags & PicklerOps::MolProps) {
streamWrite(ss, BEGINPROPS);
_pickleProperties(ss, *mol, propertyFlags);
streamWrite(ss, ENDPROPS);
}
if (propertyFlags & PicklerOps::AtomProps) {
streamWrite(ss, BEGINATOMPROPS);
for (ROMol::ConstAtomIterator atIt = mol->beginAtoms();
atIt != mol->endAtoms(); ++atIt) {
_pickleProperties(ss, **atIt, propertyFlags);
}
streamWrite(ss, ENDPROPS);
}
if (propertyFlags & PicklerOps::BondProps) {
streamWrite(ss, BEGINBONDPROPS);
for (ROMol::ConstBondIterator bondIt = mol->beginBonds();
bondIt != mol->endBonds(); ++bondIt) {
_pickleProperties(ss, **bondIt, propertyFlags);
}
streamWrite(ss, ENDPROPS);
}
if (propertyFlags & PicklerOps::QueryAtomData) {
streamWrite(ss, BEGINQUERYATOMDATA);
for (ROMol::ConstAtomIterator atIt = mol->beginAtoms();
atIt != mol->endAtoms(); ++atIt) {
_pickleQueryAtomData(ss, *atIt);
}
streamWrite(ss, ENDPROPS);
}
streamWrite(ss, ENDMOL);
}
template <typename T>
void MolPickler::_depickle(std::istream &ss, ROMol *mol, int version,
int numAtoms) {
PRECONDITION(mol, "empty molecule");
bool directMap = mol->getNumAtoms() == 0;
Tags tag;
int32_t tmpInt;
// int numAtoms,numBonds;
int numBonds;
bool haveQuery = false;
streamRead(ss, tmpInt, version);
numBonds = tmpInt;
// did we include coordinates
bool includeCoords = false;
if (version >= 3000) {
char flag;
streamRead(ss, flag, version);
if (flag & 0x1 << 7) includeCoords = true;
}
// -------------------
//
// Read Atoms
//
// -------------------
streamRead(ss, tag, version);
if (tag != BEGINATOM) {
throw MolPicklerException("Bad pickle format: BEGINATOM tag not found.");
}
Conformer *conf = 0;
if ((version >= 2000 && version < 3000) && includeCoords) {
// there can only one conformation - since the poositions were stored on
// the atoms themselves in this version
conf = new Conformer(numAtoms);
mol->addConformer(conf, true);
}
for (int i = 0; i < numAtoms; i++) {
RDGeom::Point3D pos;
Atom *atom = _addAtomFromPickle<T>(ss, mol, pos, version, directMap);
if ((version >= 2000 && version < 3000) && includeCoords) {
// this is a older pickle so we go the pos
conf->setAtomPos(i, pos);
}
if (!directMap) {
mol->setAtomBookmark(atom, i);
}
if (atom->hasQuery()) {
haveQuery = true;
}
}
// -------------------
//
// Read Bonds
//
// -------------------
streamRead(ss, tag, version);
if (tag != BEGINBOND) {
throw MolPicklerException("Bad pickle format: BEGINBOND tag not found.");
}
for (int i = 0; i < numBonds; i++) {
Bond *bond = _addBondFromPickle<T>(ss, mol, version, directMap);
if (!directMap) {
mol->setBondBookmark(bond, i);
}
}
// -------------------
//
// Read Rings (if needed)
//
// -------------------
streamRead(ss, tag, version);
if (tag == BEGINSSSR) {
_addRingInfoFromPickle<T>(ss, mol, version, directMap);
streamRead(ss, tag, version);
}
if (tag == BEGINCONFS) {
// read in the conformation
streamRead(ss, tmpInt, version);
int i;
for (i = 0; i < tmpInt; i++) {
Conformer *conf = _conformerFromPickle<T>(ss, version);
mol->addConformer(conf);
}
streamRead(ss, tag, version);
}
while (tag != ENDMOL) {
if (tag == BEGINPROPS) {
_unpickleProperties(ss, *mol);
streamRead(ss, tag, version);
} else if (tag == BEGINATOMPROPS) {
for (ROMol::AtomIterator atIt = mol->beginAtoms();
atIt != mol->endAtoms(); ++atIt) {
_unpickleProperties(ss, **atIt);
}
streamRead(ss, tag, version);
} else if (tag == BEGINBONDPROPS) {
for (ROMol::BondIterator bdIt = mol->beginBonds();
bdIt != mol->endBonds(); ++bdIt) {
_unpickleProperties(ss, **bdIt);
}
streamRead(ss, tag, version);
} else if (tag == BEGINQUERYATOMDATA) {
for (ROMol::AtomIterator atIt = mol->beginAtoms();
atIt != mol->endAtoms(); ++atIt) {
_unpickleAtomData(ss, *atIt, version);
}
streamRead(ss, tag, version);
} else {
break; // break to tag != ENDMOL
}
if (tag != ENDPROPS) {
throw MolPicklerException("Bad pickle format: ENDPROPS tag not found.");
}
streamRead(ss, tag, version);
}
if (tag != ENDMOL) {
throw MolPicklerException("Bad pickle format: ENDMOL tag not found.");
}
if (haveQuery) {
// we didn't read any property info for atoms with associated
// queries. update their property caches
// (was sf.net Issue 3316407)
for (ROMol::AtomIterator atIt = mol->beginAtoms(); atIt != mol->endAtoms();
++atIt) {
Atom *atom = *atIt;
if (atom->hasQuery()) {
atom->updatePropertyCache(false);
}
}
}
}
//--------------------------------------
//
// Atoms
//
//--------------------------------------
namespace {
bool getAtomMapNumber(const Atom *atom, int &mapNum) {
PRECONDITION(atom, "bad atom");
if (!atom->hasProp(common_properties::molAtomMapNumber)) return false;
bool res = true;
int tmpInt;
try {
atom->getProp(common_properties::molAtomMapNumber, tmpInt);
} catch (boost::bad_any_cast &) {
const std::string &tmpSVal =
atom->getProp<std::string>(common_properties::molAtomMapNumber);
try {
tmpInt = boost::lexical_cast<int>(tmpSVal);
} catch (boost::bad_lexical_cast &) {
res = false;
}
}
if (res) mapNum = tmpInt;
return res;
}
}
int32_t MolPickler::_pickleAtomData(std::ostream &tss, const Atom *atom) {
int32_t propFlags = 0;
char tmpChar;
signed char tmpSchar;
// tmpFloat=atom->getMass()-PeriodicTable::getTable()->getAtomicWeight(atom->getAtomicNum());
// if(fabs(tmpFloat)>.0001){
// propFlags |= 1;
// streamWrite(tss,tmpFloat);
// }
tmpSchar = static_cast<signed char>(atom->getFormalCharge());
if (tmpSchar != 0) {
propFlags |= 1 << 1;
streamWrite(tss, tmpSchar);
}
tmpChar = static_cast<char>(atom->getChiralTag());
if (tmpChar != 0) {
propFlags |= 1 << 2;
streamWrite(tss, tmpChar);
}
tmpChar = static_cast<char>(atom->getHybridization());
if (tmpChar != static_cast<char>(Atom::SP3)) {
propFlags |= 1 << 3;
streamWrite(tss, tmpChar);
}
tmpChar = static_cast<char>(atom->getNumExplicitHs());
if (tmpChar != 0) {
propFlags |= 1 << 4;
streamWrite(tss, tmpChar);
}
if (atom->d_explicitValence > 0) {
tmpChar = static_cast<char>(atom->d_explicitValence);
propFlags |= 1 << 5;
streamWrite(tss, tmpChar);
}
if (atom->d_implicitValence > 0) {
tmpChar = static_cast<char>(atom->d_implicitValence);
propFlags |= 1 << 6;
streamWrite(tss, tmpChar);
}
tmpChar = static_cast<char>(atom->getNumRadicalElectrons());
if (tmpChar != 0) {
propFlags |= 1 << 7;
streamWrite(tss, tmpChar);
}
unsigned int tmpuint = atom->getIsotope();
if (tmpuint > 0) {
propFlags |= 1 << 8;
streamWrite(tss, tmpuint);
}
return propFlags;
}
void MolPickler::_unpickleAtomData(std::istream &ss, Atom *atom, int version) {
int propFlags;
char tmpChar;
signed char tmpSchar;
streamRead(ss, propFlags, version);
if (propFlags & 1) {
float tmpFloat;
streamRead(ss, tmpFloat, version);
int iso = static_cast<int>(floor(tmpFloat + atom->getMass() + .0001));
atom->setIsotope(iso);
}
if (propFlags & (1 << 1)) {
streamRead(ss, tmpSchar, version);
} else {
tmpSchar = 0;
}
atom->setFormalCharge(static_cast<int>(tmpSchar));
if (propFlags & (1 << 2)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = 0;
}
atom->setChiralTag(static_cast<Atom::ChiralType>(tmpChar));
if (propFlags & (1 << 3)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = Atom::SP3;
}
atom->setHybridization(static_cast<Atom::HybridizationType>(tmpChar));
if (propFlags & (1 << 4)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = 0;
}
atom->setNumExplicitHs(tmpChar);
if (propFlags & (1 << 5)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = 0;
}
atom->d_explicitValence = tmpChar;
if (propFlags & (1 << 6)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = 0;
}
atom->d_implicitValence = tmpChar;
if (propFlags & (1 << 7)) {
streamRead(ss, tmpChar, version);
} else {
tmpChar = 0;
}
atom->d_numRadicalElectrons = static_cast<unsigned int>(tmpChar);
atom->d_isotope = 0;
if (propFlags & (1 << 8)) {
unsigned int tmpuint;
streamRead(ss, tmpuint, version);
atom->setIsotope(tmpuint);
}
}
void MolPickler::_pickleQueryAtomData(std::ostream &ss, const Atom *atom) {
if (atom->hasQuery()) {
std::stringstream tss(std::ios_base::binary | std::ios_base::out |
std::ios_base::in);
int32_t propFlags = _pickleAtomData(tss, atom);
streamWrite(ss, propFlags);
ss.write(tss.str().c_str(), tss.str().size());
} else {
// not a query so do nothing
int32_t propFlags = 0;
streamWrite(ss, propFlags);
}
}
// T refers to the type of the atom indices written
template <typename T>
void MolPickler::_pickleAtom(std::ostream &ss, const Atom *atom) {
PRECONDITION(atom, "empty atom");
char tmpChar;
unsigned char tmpUchar;
int tmpInt;
char flags;
tmpUchar = atom->getAtomicNum() % 256;
streamWrite(ss, tmpUchar);
flags = 0;
if (atom->getIsAromatic()) flags |= 0x1 << 6;
if (atom->getNoImplicit()) flags |= 0x1 << 5;
if (atom->hasQuery()) flags |= 0x1 << 4;
if (getAtomMapNumber(atom, tmpInt)) flags |= 0x1 << 3;
if (atom->hasProp(common_properties::dummyLabel)) flags |= 0x1 << 2;
if (atom->getMonomerInfo()) flags |= 0x1 << 1;
streamWrite(ss, flags);
if (!atom->hasQuery()) {
std::stringstream tss(std::ios_base::binary | std::ios_base::out |
std::ios_base::in);
int32_t propFlags = _pickleAtomData(tss, atom);
streamWrite(ss, propFlags);
ss.write(tss.str().c_str(), tss.str().size());
} else {
streamWrite(ss, BEGINQUERY);
pickleQuery(ss, static_cast<const QueryAtom *>(atom)->getQuery());
streamWrite(ss, ENDQUERY);
}
if (getAtomMapNumber(atom, tmpInt)) {
tmpChar = static_cast<char>(tmpInt % 256);
streamWrite(ss, ATOM_MAPNUMBER, tmpChar);
}
if (atom->hasProp(common_properties::dummyLabel)) {
streamWrite(ss, ATOM_DUMMYLABEL,
atom->getProp<std::string>(common_properties::dummyLabel));
}
if (atom->getMonomerInfo()) {
streamWrite(ss, BEGIN_ATOM_MONOMER);
pickleAtomMonomerInfo(ss, atom->getMonomerInfo());
streamWrite(ss, END_ATOM_MONOMER);
}
}
template <typename T>
void MolPickler::_pickleConformer(std::ostream &ss, const Conformer *conf) {
PRECONDITION(conf, "empty conformer");
char tmpChr = static_cast<int>(conf->is3D());
streamWrite(ss, tmpChr);
int32_t tmpInt = static_cast<int32_t>(conf->getId());
streamWrite(ss, tmpInt);
T tmpT = static_cast<T>(conf->getNumAtoms());
streamWrite(ss, tmpT);
const RDGeom::POINT3D_VECT &pts = conf->getPositions();
for (RDGeom::POINT3D_VECT_CI pti = pts.begin(); pti != pts.end(); pti++) {
float tmpFloat;
tmpFloat = static_cast<float>(pti->x);
streamWrite(ss, tmpFloat);
tmpFloat = static_cast<float>(pti->y);
streamWrite(ss, tmpFloat);
tmpFloat = static_cast<float>(pti->z);
streamWrite(ss, tmpFloat);
}
}
template <typename T>
Conformer *MolPickler::_conformerFromPickle(std::istream &ss, int version) {
float tmpFloat;
bool is3D = true;
if (version > 4000) {
char tmpChr;
streamRead(ss, tmpChr, version);
is3D = static_cast<bool>(tmpChr);
}
int tmpInt;
streamRead(ss, tmpInt, version);
unsigned int cid = static_cast<unsigned int>(tmpInt);
T tmpT;
streamRead(ss, tmpT, version);
unsigned int numAtoms = static_cast<unsigned int>(tmpT);
Conformer *conf = new Conformer(numAtoms);
conf->setId(cid);
conf->set3D(is3D);
for (unsigned int i = 0; i < numAtoms; i++) {
streamRead(ss, tmpFloat, version);
conf->getAtomPos(i).x = static_cast<double>(tmpFloat);
streamRead(ss, tmpFloat, version);
conf->getAtomPos(i).y = static_cast<double>(tmpFloat);
streamRead(ss, tmpFloat, version);
conf->getAtomPos(i).z = static_cast<double>(tmpFloat);
}
return conf;
}
template <typename T>
Atom *MolPickler::_addAtomFromPickle(std::istream &ss, ROMol *mol,
RDGeom::Point3D &pos, int version,
bool directMap) {
RDUNUSED_PARAM(directMap);
PRECONDITION(mol, "empty molecule");
float x, y, z;
char tmpChar;
unsigned char tmpUchar;
signed char tmpSchar;
char flags;
Tags tag;
Atom *atom = 0;
int atomicNum = 0;
streamRead(ss, tmpUchar, version);
atomicNum = tmpUchar;
bool hasQuery = false;
streamRead(ss, flags, version);
if (version > 5000) {
hasQuery = flags & 0x1 << 4;
}
if (!hasQuery) {
atom = new Atom(atomicNum);
} else {
atom = new QueryAtom();
if (atomicNum) {
// can't set this in the constructor because that builds a
// query and we're going to take care of that later:
atom->setAtomicNum(atomicNum);
}
}
atom->setIsAromatic(flags & 0x1 << 6);
atom->setNoImplicit(flags & 0x1 << 5);
bool hasAtomMap = 0, hasDummyLabel = 0;
if (version >= 6020) {
hasAtomMap = flags & 0x1 << 3;
hasDummyLabel = flags & 0x1 << 2;
}
bool hasMonomerInfo = 0;
if (version >= 7020) {
hasMonomerInfo = flags & 0x1 << 1;
}
// are coordinates present?
if (flags & 0x1 << 7) {
streamRead(ss, x, version);
pos.x = static_cast<double>(x);
streamRead(ss, y, version);
pos.y = static_cast<double>(y);
streamRead(ss, z, version);
pos.z = static_cast<double>(z);
}
if (version <= 5000 || !hasQuery) {
if (version < 7000) {
if (version < 6030) {
streamRead(ss, tmpSchar, version);
// FIX: technically should be handling this in order to maintain true
// backwards compatibility
// atom->setMass(PeriodicTable::getTable()->getAtomicWeight(atom->getAtomicNum())+
// static_cast<int>(tmpSchar));
} else {
float tmpFloat;
streamRead(ss, tmpFloat, version);
// FIX: technically should be handling this in order to maintain true
// backwards compatibility
// atom->setMass(tmpFloat);
}
streamRead(ss, tmpSchar, version);
atom->setFormalCharge(static_cast<int>(tmpSchar));
streamRead(ss, tmpChar, version);
atom->setChiralTag(static_cast<Atom::ChiralType>(tmpChar));
streamRead(ss, tmpChar, version);
atom->setHybridization(static_cast<Atom::HybridizationType>(tmpChar));
streamRead(ss, tmpChar, version);
atom->setNumExplicitHs(static_cast<int>(tmpChar));
streamRead(ss, tmpChar, version);
atom->d_explicitValence = tmpChar;
streamRead(ss, tmpChar, version);
atom->d_implicitValence = tmpChar;
if (version > 6000) {
streamRead(ss, tmpChar, version);
atom->d_numRadicalElectrons = static_cast<unsigned int>(tmpChar);
}
} else {
_unpickleAtomData(ss, atom, version);
}
} else if (version > 5000) {
// we have a query:
streamRead(ss, tag, version);
if (tag != BEGINQUERY) {
throw MolPicklerException("Bad pickle format: BEGINQUERY tag not found.");
}
static_cast<QueryAtom *>(atom)->setQuery(unpickleQuery(ss, atom, version));
streamRead(ss, tag, version);
if (tag != ENDQUERY) {
throw MolPicklerException("Bad pickle format: ENDQUERY tag not found.");
}
atom->setNumExplicitHs(0);
}
if (version > 5000) {
if (version < 6020) {
unsigned int sPos = rdcast<unsigned int>(ss.tellg());
Tags tag;
streamRead(ss, tag, version);
if (tag == ATOM_MAPNUMBER) {
int tmpInt;
streamRead(ss, tmpChar, version);
tmpInt = tmpChar;
atom->setProp(common_properties::molAtomMapNumber, tmpInt);
} else {
ss.seekg(sPos);
}
} else {
if (hasAtomMap) {
Tags tag;
streamRead(ss, tag, version);
if (tag != ATOM_MAPNUMBER) {
throw MolPicklerException(
"Bad pickle format: ATOM_MAPNUMBER tag not found.");
}
int tmpInt;
streamRead(ss, tmpChar, version);
tmpInt = tmpChar;
atom->setProp(common_properties::molAtomMapNumber, tmpInt);
}
if (hasDummyLabel) {
streamRead(ss, tag, version);
if (tag != ATOM_DUMMYLABEL) {
throw MolPicklerException(
"Bad pickle format: ATOM_DUMMYLABEL tag not found.");
}
std::string tmpStr;
streamRead(ss, tmpStr, version);
atom->setProp(common_properties::dummyLabel, tmpStr);
}
}
}
if (version >= 7020) {
if (hasMonomerInfo) {
streamRead(ss, tag, version);
if (tag != BEGIN_ATOM_MONOMER) {
throw MolPicklerException(
"Bad pickle format: BEGIN_ATOM_MONOMER tag not found.");
}
atom->setMonomerInfo(unpickleAtomMonomerInfo(ss, version));
}
}
mol->addAtom(atom, false, true);
return atom;
}
//--------------------------------------
//
// Bonds
//
//--------------------------------------
template <typename T>
void MolPickler::_pickleBond(std::ostream &ss, const Bond *bond,
std::map<int, int> &atomIdxMap) {
PRECONDITION(bond, "empty bond");
T tmpT;
char tmpChar;
char flags;
tmpT = static_cast<T>(atomIdxMap[bond->getBeginAtomIdx()]);
streamWrite(ss, tmpT);
tmpT = static_cast<T>(atomIdxMap[bond->getEndAtomIdx()]);
streamWrite(ss, tmpT);
flags = 0;
if (bond->getIsAromatic()) flags |= 0x1 << 6;
if (bond->getIsConjugated()) flags |= 0x1 << 5;
if (bond->hasQuery()) flags |= 0x1 << 4;
if (bond->getBondType() != Bond::SINGLE) flags |= 0x1 << 3;
if (bond->getBondDir() != Bond::NONE) flags |= 0x1 << 2;
if (bond->getStereo() != Bond::STEREONONE) flags |= 0x1 << 1;
streamWrite(ss, flags);
if (bond->getBondType() != Bond::SINGLE) {
tmpChar = static_cast<char>(bond->getBondType());
streamWrite(ss, tmpChar);
}
if (bond->getBondDir() != Bond::NONE) {
tmpChar = static_cast<char>(bond->getBondDir());
streamWrite(ss, tmpChar);
}
// write info about the stereochemistry:
if (bond->getStereo() != Bond::STEREONONE) {
tmpChar = static_cast<char>(bond->getStereo());
streamWrite(ss, tmpChar);
const INT_VECT &stereoAts = bond->getStereoAtoms();
tmpChar = rdcast<unsigned int>(stereoAts.size());
streamWrite(ss, tmpChar);
for (INT_VECT_CI idxIt = stereoAts.begin(); idxIt != stereoAts.end();
++idxIt) {
tmpT = static_cast<T>(*idxIt);
streamWrite(ss, tmpT);
}
}
if (bond->hasQuery()) {
streamWrite(ss, BEGINQUERY);
pickleQuery(ss, static_cast<const QueryBond *>(bond)->getQuery());
streamWrite(ss, ENDQUERY);
}
}
template <typename T>
Bond *MolPickler::_addBondFromPickle(std::istream &ss, ROMol *mol, int version,
bool directMap) {
PRECONDITION(mol, "empty molecule");
char tmpChar;
char flags;
int begIdx, endIdx;
T tmpT;
Bond *bond = NULL;
streamRead(ss, tmpT, version);
if (directMap) {
begIdx = tmpT;
} else {
begIdx = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
}
streamRead(ss, tmpT, version);
if (directMap) {
endIdx = tmpT;
} else {
endIdx = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
}
streamRead(ss, flags, version);
bool hasQuery = flags & 0x1 << 4;
if (version <= 5000 || (version <= 7000 && !hasQuery) || version > 7000) {
bond = new Bond();
bond->setIsAromatic(flags & 0x1 << 6);
bond->setIsConjugated(flags & 0x1 << 5);
if (version < 7000) {
streamRead(ss, tmpChar, version);
bond->setBondType(static_cast<Bond::BondType>(tmpChar));
streamRead(ss, tmpChar, version);
bond->setBondDir(static_cast<Bond::BondDir>(tmpChar));
if (version > 3000) {
streamRead(ss, tmpChar, version);
Bond::BondStereo stereo = static_cast<Bond::BondStereo>(tmpChar);
bond->setStereo(stereo);
if (stereo != Bond::STEREONONE) {
streamRead(ss, tmpChar, version);
for (char i = 0; i < tmpChar; ++i) {
streamRead(ss, tmpT, version);
bond->getStereoAtoms().push_back(static_cast<int>(tmpT));
}
}
}
} else {
if (flags & (0x1 << 3)) {
streamRead(ss, tmpChar, version);
bond->setBondType(static_cast<Bond::BondType>(tmpChar));
} else {
bond->setBondType(Bond::SINGLE);
}
if (flags & (0x1 << 2)) {
streamRead(ss, tmpChar, version);
bond->setBondDir(static_cast<Bond::BondDir>(tmpChar));
} else {
bond->setBondDir(Bond::NONE);
}
if (flags & (0x1 << 1)) {
streamRead(ss, tmpChar, version);
Bond::BondStereo stereo = static_cast<Bond::BondStereo>(tmpChar);
bond->setStereo(stereo);
streamRead(ss, tmpChar, version);
for (char i = 0; i < tmpChar; ++i) {
streamRead(ss, tmpT, version);
bond->getStereoAtoms().push_back(static_cast<int>(tmpT));
}
} else {
bond->setStereo(Bond::STEREONONE);
}
}
}
if (version > 5000 && hasQuery) {
Tags tag;
if (bond) {
Bond *tbond = bond;
bond = new QueryBond(*bond);
delete tbond;
} else {
bond = new QueryBond();
}
// we have a query:
streamRead(ss, tag, version);
if (tag != BEGINQUERY) {
throw MolPicklerException("Bad pickle format: BEGINQUERY tag not found.");
}
static_cast<QueryBond *>(bond)->setQuery(unpickleQuery(ss, bond, version));
streamRead(ss, tag, version);
if (tag != ENDQUERY) {
throw MolPicklerException("Bad pickle format: ENDQUERY tag not found.");
}
}
if (bond) {
bond->setBeginAtomIdx(begIdx);
bond->setEndAtomIdx(endIdx);
mol->addBond(bond, true);
}
return bond;
}
//--------------------------------------
//
// Rings
//
//--------------------------------------
template <typename T>
void MolPickler::_pickleSSSR(std::ostream &ss, const RingInfo *ringInfo,
std::map<int, int> &atomIdxMap) {
PRECONDITION(ringInfo, "missing ring info");
T tmpT;
tmpT = ringInfo->numRings();
streamWrite(ss, tmpT);
for (unsigned int i = 0; i < ringInfo->numRings(); i++) {
INT_VECT ring;
ring = ringInfo->atomRings()[i];
tmpT = static_cast<T>(ring.size());
streamWrite(ss, tmpT);
for (unsigned int j = 0; j < ring.size(); j++) {
tmpT = static_cast<T>(atomIdxMap[ring[j]]);
streamWrite(ss, tmpT);
}
#if 0
ring = ringInfo->bondRings()[i];
tmpT = static_cast<T>(ring.size());
streamWrite(ss,tmpT);
for(unsigned int j=0;j<ring.size();j++){
tmpT = static_cast<T>(ring[j]);
streamWrite(ss,tmpT);
}
#endif
}
}
template <typename T>
void MolPickler::_addRingInfoFromPickle(std::istream &ss, ROMol *mol,
int version, bool directMap) {
PRECONDITION(mol, "empty molecule");
RingInfo *ringInfo = mol->getRingInfo();
if (!ringInfo->isInitialized()) ringInfo->initialize();
T numRings;
streamRead(ss, numRings, version);
if (numRings > 0) {
ringInfo->preallocate(mol->getNumAtoms(), mol->getNumBonds());
for (unsigned int i = 0; i < static_cast<unsigned int>(numRings); i++) {
T tmpT;
T ringSize;
streamRead(ss, ringSize, version);
INT_VECT atoms(static_cast<int>(ringSize));
INT_VECT bonds(static_cast<int>(ringSize));
for (unsigned int j = 0; j < static_cast<unsigned int>(ringSize); j++) {
streamRead(ss, tmpT, version);
if (directMap) {
atoms[j] = static_cast<int>(tmpT);
} else {
atoms[j] = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
}
}
if (version < 7000) {
for (unsigned int j = 0; j < static_cast<unsigned int>(ringSize); j++) {
streamRead(ss, tmpT, version);
if (directMap) {
bonds[j] = static_cast<int>(tmpT);
} else {
bonds[j] =
mol->getBondWithBookmark(static_cast<int>(tmpT))->getIdx();
}
}
} else {
for (unsigned int j = 1; j < static_cast<unsigned int>(ringSize); ++j) {
bonds[j - 1] =
mol->getBondBetweenAtoms(atoms[j - 1], atoms[j])->getIdx();
}
bonds[ringSize - 1] =
mol->getBondBetweenAtoms(atoms[0], atoms[ringSize - 1])->getIdx();
}
ringInfo->addRing(atoms, bonds);
}
}
}
void MolPickler::_pickleProperties(std::ostream &ss, const RDProps &props,
unsigned int pickleFlags) {
if (!pickleFlags) return;
streamWriteProps(ss, props, pickleFlags & PicklerOps::PrivateProps,
pickleFlags & PicklerOps::ComputedProps);
}
//! unpickle standard properties
void MolPickler::_unpickleProperties(std::istream &ss, RDProps &props) {
streamReadProps(ss, props);
}
//--------------------------------------
//
// Version 1 Pickler:
//
// NOTE: this is not 64bit clean, but it shouldn't be used anymore anyway
//
//--------------------------------------
void MolPickler::_pickleV1(const ROMol *mol, std::ostream &ss) {
PRECONDITION(mol, "empty molecule");
ROMol::ConstAtomIterator atIt;
const Conformer *conf = 0;
if (mol->getNumConformers() > 0) {
conf = &(mol->getConformer());
}
for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); ++atIt) {
const Atom *atom = *atIt;
streamWrite(ss, BEGINATOM);
streamWrite(ss, ATOM_NUMBER, atom->getAtomicNum());
streamWrite(ss, ATOM_INDEX, atom->getIdx());
streamWrite(ss, ATOM_POS);
RDGeom::Point3D p;
if (conf) {
p = conf->getAtomPos(atom->getIdx());
}
streamWrite(ss, p.x);
streamWrite(ss, p.y);
streamWrite(ss, p.z);
if (atom->getFormalCharge() != 0) {
streamWrite(ss, ATOM_CHARGE, atom->getFormalCharge());
}
if (atom->getNumExplicitHs() != 0) {
streamWrite(ss, ATOM_NEXPLICIT, atom->getNumExplicitHs());
}
if (atom->getChiralTag() != 0) {
streamWrite(ss, ATOM_CHIRALTAG, atom->getChiralTag());
}
if (atom->getIsAromatic()) {
streamWrite(ss, ATOM_ISAROMATIC,
static_cast<char>(atom->getIsAromatic()));
}
streamWrite(ss, ENDATOM);
}
ROMol::ConstBondIterator bondIt;
for (bondIt = mol->beginBonds(); bondIt != mol->endBonds(); ++bondIt) {
const Bond *bond = *bondIt;
streamWrite(ss, BEGINBOND);
streamWrite(ss, BOND_INDEX, bond->getIdx());
streamWrite(ss, BOND_BEGATOMIDX, bond->getBeginAtomIdx());
streamWrite(ss, BOND_ENDATOMIDX, bond->getEndAtomIdx());
streamWrite(ss, BOND_TYPE, bond->getBondType());
if (bond->getBondDir()) {
streamWrite(ss, BOND_DIR, bond->getBondDir());
}
streamWrite(ss, ENDBOND);
}
streamWrite(ss, ENDMOL);
}
void MolPickler::_depickleV1(std::istream &ss, ROMol *mol) {
PRECONDITION(mol, "empty molecule");
Tags tag;
Conformer *conf = new Conformer();
mol->addConformer(conf);
streamRead(ss, tag, 1);
while (tag != ENDMOL) {
switch (tag) {
case BEGINATOM:
_addAtomFromPickleV1(ss, mol);
break;
case BEGINBOND:
_addBondFromPickleV1(ss, mol);
break;
default:
UNDER_CONSTRUCTION("bad tag in pickle");
}
streamRead(ss, tag, 1);
}
mol->clearAllAtomBookmarks();
mol->clearAllBondBookmarks();
}
void MolPickler::_addAtomFromPickleV1(std::istream &ss, ROMol *mol) {
PRECONDITION(mol, "empty molecule");
Tags tag;
int intVar;
double dblVar;
char charVar;
int version = 1;
streamRead(ss, tag, version);
Atom *atom = new Atom();
Conformer &conf = mol->getConformer();
RDGeom::Point3D pos;
while (tag != ENDATOM) {
switch (tag) {
case ATOM_INDEX:
streamRead(ss, intVar, version);
mol->setAtomBookmark(atom, intVar);
break;
case ATOM_NUMBER:
streamRead(ss, intVar, version);
atom->setAtomicNum(intVar);
break;
case ATOM_POS:
streamRead(ss, pos.x, version);
streamRead(ss, pos.y, version);
streamRead(ss, pos.z, version);
break;
case ATOM_CHARGE:
streamRead(ss, intVar, version);
atom->setFormalCharge(intVar);
break;
case ATOM_NEXPLICIT:
streamRead(ss, intVar, version);
atom->setNumExplicitHs(intVar);
break;
case ATOM_CHIRALTAG:
streamRead(ss, intVar, version);
atom->setChiralTag(static_cast<Atom::ChiralType>(intVar));
break;
case ATOM_MASS:
streamRead(ss, dblVar, version);
// we don't need to set this anymore, but we do need to read it in order
// to
// maintain backwards compatibility
break;
case ATOM_ISAROMATIC:
streamRead(ss, charVar, version);
atom->setIsAromatic(charVar);
break;
default:
ASSERT_INVARIANT(0, "bad tag in atom block of pickle");
}
streamRead(ss, tag, version);
}
unsigned int id = mol->addAtom(atom, false, true);
conf.setAtomPos(id, pos);
}
void MolPickler::_addBondFromPickleV1(std::istream &ss, ROMol *mol) {
PRECONDITION(mol, "empty molecule");
Tags tag;
int intVar, idx = -1;
int version = 1;
Bond::BondType bt;
Bond::BondDir bd;
streamRead(ss, tag, version);
Bond *bond = new Bond();
while (tag != ENDBOND) {
switch (tag) {
case BOND_INDEX:
streamRead(ss, idx, version);
break;
case BOND_BEGATOMIDX:
streamRead(ss, intVar, version);
bond->setBeginAtomIdx(mol->getAtomWithBookmark(intVar)->getIdx());
break;
case BOND_ENDATOMIDX:
streamRead(ss, intVar, version);
bond->setEndAtomIdx(mol->getAtomWithBookmark(intVar)->getIdx());
break;
case BOND_TYPE:
streamRead(ss, bt, version);
bond->setBondType(bt);
break;
case BOND_DIR:
streamRead(ss, bd, version);
bond->setBondDir(bd);
break;
default:
ASSERT_INVARIANT(0, "bad tag in bond block of pickle");
}
streamRead(ss, tag, version);
}
mol->addBond(bond, true);
}
};
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