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rdkit/Code/GraphMol/FileParsers/MolFileParser.cpp
thomp-j a8a718923c Update MolFileParser.cpp 
Remove ill-advised ASCII filter when parsing SDF V3000
2024-12-18 09:08:09 -05:00

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//
// Copyright (C) 2002-2021 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 <RDGeneral/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/tokenizer.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/format.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "FileParsers.h"
#include "FileParserUtils.h"
#include "MolSGroupParsing.h"
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/StereoGroup.h>
#include <GraphMol/SubstanceGroup.h>
#include <GraphMol/Atropisomers.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/GenericGroups/GenericGroups.h>
#include <GraphMol/QueryOps.h>
#include <GraphMol/Chirality.h>
#include <fstream>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/LocaleSwitcher.h>
#include <typeinfo>
#include <exception>
#include <charconv>
#include <regex>
#include <sstream>
#include <locale>
#include <cstdlib>
#include <cstdio>
#include <string_view>
using namespace RDKit::SGroupParsing;
using std::regex;
using std::regex_match;
using std::smatch;
namespace RDKit {
namespace FileParserUtils {
int toInt(const std::string_view input, bool acceptSpaces) {
// don't need to worry about locale stuff here because
// we're not going to have delimiters
// sanity check on the input since strtol doesn't do it for us:
const char *txt = input.data();
for (size_t i = 0u; i < input.size() && *txt != '\x00'; ++i) {
if ((*txt >= '0' && *txt <= '9') || (acceptSpaces && *txt == ' ') ||
*txt == '+' || *txt == '-') {
++txt;
} else {
throw boost::bad_lexical_cast();
}
}
// remove leading spaces
txt = input.data();
unsigned int sz = input.size();
if (acceptSpaces) {
while (*txt == ' ') {
++txt;
--sz;
// have we run off the end of the view?
if (sz < 1U) {
return 0;
}
}
}
int res = 0;
std::from_chars(txt, txt + sz, res);
return res;
}
int toInt(const std::string &input, bool acceptSpaces) {
return toInt(std::string_view(input.c_str()), acceptSpaces);
}
unsigned int toUnsigned(const std::string_view input, bool acceptSpaces) {
// don't need to worry about locale stuff here because
// we're not going to have delimiters
// sanity check on the input since strtol doesn't do it for us:
const char *txt = input.data();
for (size_t i = 0u; i < input.size() && *txt != '\x00'; ++i) {
if ((*txt >= '0' && *txt <= '9') || (acceptSpaces && *txt == ' ') ||
*txt == '+') {
++txt;
} else {
throw boost::bad_lexical_cast();
}
}
// remove leading spaces
txt = input.data();
unsigned int sz = input.size();
if (acceptSpaces) {
while (*txt == ' ') {
++txt;
--sz;
// have we run off the end of the view?
if (sz < 1U) {
return 0;
}
}
}
unsigned int res = 0;
std::from_chars(txt, txt + sz, res);
return res;
}
unsigned int toUnsigned(const std::string &input, bool acceptSpaces) {
return toUnsigned(std::string_view(input.c_str()), acceptSpaces);
}
double toDouble(const std::string_view input, bool acceptSpaces) {
// sanity check on the input since strtol doesn't do it for us:
const char *txt = input.data();
for (size_t i = 0u; i < input.size() && *txt != '\x00'; ++i) {
// check for ',' and '.' because locale
if ((*txt >= '0' && *txt <= '9') || (acceptSpaces && *txt == ' ') ||
*txt == '+' || *txt == '-' || *txt == ',' || *txt == '.') {
++txt;
} else {
throw boost::bad_lexical_cast();
}
}
// unfortunately from_chars() with doubles didn't work on g++ until v11.1
// and the status with clang is hard to figure out... we remain old-school
// remove leading spaces
double res = atof(input.data());
return res;
}
double toDouble(const std::string &input, bool acceptSpaces) {
return toDouble(std::string_view(input.c_str()), acceptSpaces);
}
std::string getV3000Line(std::istream *inStream, unsigned int &line) {
// FIX: technically V3K blocks are case-insensitive. We should really be
// up-casing everything here.
PRECONDITION(inStream, "bad stream");
std::string res;
++line;
auto inl = getLine(inStream);
std::string_view tempStr = inl;
if (tempStr.size() < 7 || tempStr.substr(0, 7) != "M V30 ") {
std::ostringstream errout;
errout << "Line " << line << " does not start with 'M V30 '" << std::endl;
throw FileParseException(errout.str());
}
// FIX: do we need to handle trailing whitespace after a -?
while (tempStr.back() == '-') {
// continuation character, append what we read:
res += tempStr.substr(7, tempStr.length() - 8);
// and then read another line:
++line;
inl = getLine(inStream);
tempStr = inl;
if (tempStr.size() < 7 || tempStr.substr(0, 7) != "M V30 ") {
std::ostringstream errout;
errout << "Line " << line << " does not start with 'M V30 '"
<< std::endl;
throw FileParseException(errout.str());
}
}
res += tempStr.substr(7, tempStr.length() - 7);
return res;
}
Atom *replaceAtomWithQueryAtom(RWMol *mol, Atom *atom) {
return QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
} // namespace FileParserUtils
using RDKit::FileParserUtils::getV3000Line;
namespace {
bool startsWith(const std::string &haystack, const char *needle, size_t size) {
return haystack.compare(0u, size, needle, size) == 0;
}
//! parse a collection block to find enhanced stereo groups
std::string parseEnhancedStereo(std::istream *inStream, unsigned int &line,
RWMol *mol) {
// Lines like (absolute, relative, racemic):
// M V30 MDLV30/STEABS ATOMS=(2 2 3)
// M V30 MDLV30/STEREL1 ATOMS=(1 12)
// M V30 MDLV30/STERAC1 ATOMS=(1 12)
const regex stereo_label(
R"regex(MDLV30/STE(...)([0-9]*) +ATOMS=\(([0-9]+) +(.*)\) *)regex");
smatch match;
std::vector<StereoGroup> groups;
// Read the collection until the end
auto tempStr = getV3000Line(inStream, line);
boost::to_upper(tempStr);
while (!startsWith(tempStr, "END", 3)) {
// If this line in the collection is part of a stereo group
if (regex_match(tempStr, match, stereo_label)) {
StereoGroupType grouptype = RDKit::StereoGroupType::STEREO_ABSOLUTE;
unsigned groupid = 0;
if (match[1] == "ABS") {
grouptype = RDKit::StereoGroupType::STEREO_ABSOLUTE;
} else if (match[1] == "REL") {
grouptype = RDKit::StereoGroupType::STEREO_OR;
groupid = FileParserUtils::toUnsigned(match[2], true);
} else if (match[1] == "RAC") {
grouptype = RDKit::StereoGroupType::STEREO_AND;
groupid = FileParserUtils::toUnsigned(match[2], true);
} else {
std::ostringstream errout;
errout << "Unrecognized stereogroup type : '" << tempStr << "' on line"
<< line;
throw FileParseException(errout.str());
}
const unsigned int count = FileParserUtils::toUnsigned(match[3], true);
std::vector<Atom *> atoms;
std::stringstream ss(match[4]);
unsigned int index;
for (size_t i = 0; i < count; ++i) {
ss >> index;
// atoms are 1 indexed in molfiles
atoms.push_back(mol->getAtomWithIdx(index - 1));
}
std::vector<Bond *> newBonds;
groups.emplace_back(grouptype, std::move(atoms), std::move(newBonds),
groupid);
} else {
// skip collection types we don't know how to read. Only one documented
// is MDLV30/HILITE
BOOST_LOG(rdWarningLog) << "Skipping unrecognized collection type at "
"line "
<< line << ": " << tempStr << std::endl;
}
tempStr = getV3000Line(inStream, line);
}
if (!groups.empty()) {
mol->setStereoGroups(std::move(groups));
}
tempStr = getV3000Line(inStream, line);
return tempStr;
}
//*************************************
//
// Every effort has been made to adhere to MDL's standard
// for mol files
//
//*************************************
void ParseOldAtomList(RWMol *mol, const std::string_view &text,
unsigned int line) {
PRECONDITION(mol, "bad mol");
unsigned int idx;
try {
idx = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(0, 3)) -
1;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(0, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
URANGE_CHECK(idx, mol->getNumAtoms());
QueryAtom a(*(mol->getAtomWithIdx(idx)));
auto *q = new ATOM_OR_QUERY;
q->setDescription("AtomOr");
switch (text[4]) {
case 'T':
q->setNegation(true);
break;
case 'F':
q->setNegation(false);
break;
default:
delete q;
std::ostringstream errout;
errout << "Unrecognized atom-list query modifier: '" << text[4]
<< "' on line " << line;
throw FileParseException(errout.str());
}
int nQueries;
try {
nQueries = FileParserUtils::toInt(text.substr(9, 1));
} catch (const std::out_of_range &) {
delete q;
std::ostringstream errout;
errout << "Cannot convert position 9 of '" << text << "' to int on line "
<< line;
throw FileParseException(errout.str());
} catch (boost::bad_lexical_cast &) {
delete q;
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(9, 1) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
RANGE_CHECK(0, nQueries, 5);
for (int i = 0; i < nQueries; i++) {
int pos = 11 + i * 4;
int atNum;
try {
atNum = FileParserUtils::toInt(text.substr(pos, 3));
} catch (const std::out_of_range &) {
delete q;
std::ostringstream errout;
errout << "Cannot convert position " << pos << " of '" << text
<< "' to int on line " << line;
throw FileParseException(errout.str());
} catch (boost::bad_lexical_cast &) {
delete q;
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(pos, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
RANGE_CHECK(0, atNum, 200); // goofy!
q->addChild(
QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(makeAtomNumQuery(atNum)));
if (!i) {
a.setAtomicNum(atNum);
}
}
a.setQuery(q);
a.setProp(common_properties::_MolFileAtomQuery, 1);
mol->replaceAtom(idx, &a);
}
void ParseChargeLine(RWMol *mol, const std::string &text, bool firstCall,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M CHG"), "bad charge line");
// if this line is specified all the atom other than those specified
// here should carry a charge of 0; but we should only do this once:
if (firstCall) {
for (ROMol::AtomIterator ai = mol->beginAtoms(); ai != mol->endAtoms();
++ai) {
(*ai)->setFormalCharge(0);
}
}
int ie, nent;
try {
nent = FileParserUtils::toInt(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
int spos = 9;
for (ie = 0; ie < nent; ie++) {
int aid, chg;
try {
aid = FileParserUtils::toInt(text.substr(spos, 4));
spos += 4;
chg = FileParserUtils::toInt(text.substr(spos, 4));
spos += 4;
mol->getAtomWithIdx(aid - 1)->setFormalCharge(chg);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseRadicalLine(RWMol *mol, const std::string &text, bool firstCall,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M RAD"), "bad charge line");
// if this line is specified all the atom other than those specified
// here should carry a charge of 0; but we should only do this once:
if (firstCall) {
for (ROMol::AtomIterator ai = mol->beginAtoms(); ai != mol->endAtoms();
++ai) {
(*ai)->setFormalCharge(0);
}
}
int ie, nent;
try {
nent = FileParserUtils::toInt(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
int spos = 9;
for (ie = 0; ie < nent; ie++) {
int aid, rad;
std::ostringstream errout;
try {
aid = FileParserUtils::toInt(text.substr(spos, 4));
spos += 4;
rad = FileParserUtils::toInt(text.substr(spos, 4));
spos += 4;
switch (rad) {
case 0:
// This shouldn't be required, but let's make sure.
mol->getAtomWithIdx(aid - 1)->setNumRadicalElectrons(0);
break;
case 1:
mol->getAtomWithIdx(aid - 1)->setNumRadicalElectrons(2);
break;
case 2:
mol->getAtomWithIdx(aid - 1)->setNumRadicalElectrons(1);
break;
case 3:
mol->getAtomWithIdx(aid - 1)->setNumRadicalElectrons(2);
break;
default:
errout << "Unrecognized radical value " << rad << " for atom "
<< aid - 1 << " on line " << line << std::endl;
throw FileParseException(errout.str());
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParsePXALine(RWMol *mol, const std::string &text, unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == "M PXA", "bad PXA line");
unsigned int pos = 7;
try {
auto atIdx =
FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(pos, 3));
pos += 3;
mol->getAtomWithIdx(atIdx - 1)->setProp(
"_MolFile_PXA", text.substr(pos, text.length() - pos));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(pos, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
}
void ParseIsotopeLine(RWMol *mol, const std::string &text, unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M ISO"), "bad isotope line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
Atom *atom = mol->getAtomWithIdx(aid - 1);
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
int isotope = FileParserUtils::toInt(text.substr(spos, 4));
if (isotope < 0) {
BOOST_LOG(rdErrorLog)
<< " atom " << aid
<< " has a negative isotope value. line: " << line << std::endl;
} else {
atom->setIsotope(isotope);
}
}
spos += 4;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseSubstitutionCountLine(RWMol *mol, const std::string &text,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M SUB"), "bad SUB line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid;
int count = 0;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
Atom *atom = mol->getAtomWithIdx(aid - 1);
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
count = FileParserUtils::toInt(text.substr(spos, 4));
}
spos += 4;
if (count == 0) {
continue;
}
ATOM_EQUALS_QUERY *q = makeAtomExplicitDegreeQuery(0);
switch (count) {
case -1:
q->setVal(0);
break;
case -2:
q->setVal(atom->getDegree());
break;
case 1:
case 2:
case 3:
case 4:
case 5:
q->setVal(count);
break;
case 6:
BOOST_LOG(rdWarningLog) << " atom degree query with value 6 found. "
"This will not match degree >6. The MDL "
"spec says it should. line: "
<< line;
q->setVal(6);
break;
default:
std::ostringstream errout;
errout << "Value " << count
<< " is not supported as a degree query. line: " << line;
throw FileParseException(errout.str());
}
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
atom->expandQuery(q, Queries::COMPOSITE_AND);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseUnsaturationLine(RWMol *mol, const std::string &text,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M UNS"), "bad UNS line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid;
int count = 0;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
Atom *atom = mol->getAtomWithIdx(aid - 1);
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
count = FileParserUtils::toInt(text.substr(spos, 4));
}
spos += 4;
if (count == 0) {
continue;
} else if (count == 1) {
ATOM_EQUALS_QUERY *q = makeAtomUnsaturatedQuery();
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
atom->expandQuery(q, Queries::COMPOSITE_AND);
} else {
std::ostringstream errout;
errout << "Value " << count
<< " is not supported as an unsaturation "
"query (only 0 and 1 are allowed). "
"line: "
<< line;
throw FileParseException(errout.str());
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseRingBondCountLine(RWMol *mol, const std::string &text,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M RBC"), "bad RBC line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid;
int count = 0;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
Atom *atom = mol->getAtomWithIdx(aid - 1);
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
count = FileParserUtils::toInt(text.substr(spos, 4));
}
spos += 4;
if (count == 0) {
continue;
}
ATOM_EQUALS_QUERY *q = makeAtomRingBondCountQuery(0);
switch (count) {
case -1:
q->setVal(0);
break;
case -2:
q->setVal(0xDEADBEEF);
mol->setProp(common_properties::_NeedsQueryScan, 1);
break;
case 1:
case 2:
case 3:
q->setVal(count);
break;
case 4:
delete q;
q = static_cast<ATOM_EQUALS_QUERY *>(new ATOM_LESSEQUAL_QUERY);
q->setVal(4);
q->setDescription("AtomRingBondCount");
q->setDataFunc(queryAtomRingBondCount);
break;
default:
std::ostringstream errout;
errout << "Value " << count
<< " is not supported as a ring-bond count query. line: "
<< line;
throw FileParseException(errout.str());
}
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
atom->expandQuery(q, Queries::COMPOSITE_AND);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseZCHLine(RWMol *mol, const std::string &text, unsigned int line) {
// part of Alex Clark's ZBO proposal
// from JCIM 51:3149-57 (2011)
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M ZCH"), "bad ZCH line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid = 0;
int val = 0;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
val = FileParserUtils::stripSpacesAndCast<int>(text.substr(spos, 4));
}
if (!aid || aid > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "Bad ZCH specification on line " << line;
throw FileParseException(errout.str());
}
spos += 4;
--aid;
Atom *atom = mol->getAtomWithIdx(aid);
if (!atom) {
std::ostringstream errout;
errout << "Atom " << aid << " from ZCH specification on line " << line
<< " not found";
throw FileParseException(errout.str());
} else {
atom->setFormalCharge(val);
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseHYDLine(RWMol *mol, const std::string &text, unsigned int line) {
// part of Alex Clark's ZBO proposal
// from JCIM 51:3149-57 (2011)
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M HYD"), "bad HYD line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid = 0;
int val = -1;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
val = FileParserUtils::stripSpacesAndCast<int>(text.substr(spos, 4));
}
if (!aid || aid > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "Bad HYD specification on line " << line;
throw FileParseException(errout.str());
}
spos += 4;
--aid;
Atom *atom = mol->getAtomWithIdx(aid);
if (!atom) {
std::ostringstream errout;
errout << "Atom " << aid << " from HYD specification on line " << line
<< " not found";
throw FileParseException(errout.str());
} else {
if (val >= 0) {
atom->setProp("_ZBO_H", true);
atom->setNumExplicitHs(val);
}
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseZBOLine(RWMol *mol, const std::string &text, unsigned int line) {
// part of Alex Clark's ZBO proposal
// from JCIM 51:3149-57 (2011)
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M ZBO"), "bad ZBO line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int bid = 0;
unsigned int order = 0;
try {
bid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
order = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
}
if (!bid || bid > mol->getNumBonds()) {
std::ostringstream errout;
errout << "Bad ZBO specification on line " << line;
throw FileParseException(errout.str());
}
spos += 4;
--bid;
Bond *bnd = mol->getBondWithIdx(bid);
if (!bnd) {
std::ostringstream errout;
errout << "Bond " << bid << " from ZBO specification on line " << line
<< " not found";
throw FileParseException(errout.str());
} else {
if (order == 0) {
bnd->setBondType(Bond::ZERO);
} else {
bnd->setBondType(static_cast<Bond::BondType>(order));
}
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
void ParseMarvinSmartsLine(RWMol *mol, const std::string &text,
unsigned int line) {
const unsigned int atomNumStart = 10;
const unsigned int smartsStart = 15;
// M MRV SMA 1 [*;A]
// 01234567890123456789
// 1111111111
if (text.substr(0, 10) != "M MRV SMA") {
return;
}
unsigned int idx;
std::string idxTxt = text.substr(atomNumStart, smartsStart - atomNumStart);
try {
idx = FileParserUtils::stripSpacesAndCast<unsigned int>(idxTxt) - 1;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << idxTxt << "' to an atom index on line "
<< line;
throw FileParseException(errout.str());
}
URANGE_CHECK(idx, mol->getNumAtoms());
// Should we check the validity of the marvin line here? Should we
// automatically
// Add these as recursive smarts? I tend to think so...
std::string sma = text.substr(smartsStart);
Atom *at = mol->getAtomWithIdx(idx);
at->setProp(common_properties::MRV_SMA, sma);
RWMol *m = nullptr;
try {
m = SmartsToMol(sma);
} catch (...) {
// Is this ever used?
}
if (m) {
QueryAtom::QUERYATOM_QUERY *query = new RecursiveStructureQuery(m);
if (!at->hasQuery()) {
QueryAtom qAt(*at);
int oidx = at->getIdx();
mol->replaceAtom(oidx, &qAt);
at = mol->getAtomWithIdx(oidx);
}
at->expandQuery(query, Queries::COMPOSITE_AND);
at->setProp(common_properties::_MolFileAtomQuery, 1);
} else {
std::ostringstream errout;
errout << "Cannot parse smarts: '" << sma << "' on line " << line;
throw FileParseException(errout.str());
}
}
void ParseAttachPointLine(RWMol *mol, const std::string &text,
unsigned int line, bool strictParsing) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M APO"), "bad APO line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
unsigned int aid = 0;
int val = 0;
try {
aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
val = FileParserUtils::stripSpacesAndCast<int>(text.substr(spos, 4));
}
if (!aid || aid > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "Bad APO specification on line " << line;
throw FileParseException(errout.str());
}
spos += 4;
--aid;
Atom *atom = mol->getAtomWithIdx(aid);
if (!atom) {
std::ostringstream errout;
errout << "Atom " << aid << " from APO specification on line " << line
<< " not found";
throw FileParseException(errout.str());
} else {
if (val < 0 || val > 3) {
std::ostringstream errout;
errout << "Value " << val << " from APO specification on line "
<< line << " is invalid";
throw FileParseException(errout.str());
} else if (val) {
if (val == 3) {
// this is -1 in v3k mol blocks, so use that:
val = -1;
}
if (atom->hasProp(common_properties::molAttachPoint)) {
std::ostringstream errout;
errout << "Multiple ATTCHPT values for atom " << atom->getIdx() + 1
<< " on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
} else {
atom->setProp(common_properties::molAttachPoint, val);
}
}
}
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
}
}
// the format differs between V2000 and V3000, so we have to do a bit of
// translation here
void ParseLinkNodeLine(RWMol *mol, const std::string &text, unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M LIN"), "bad LIN line");
unsigned int nent;
try {
nent = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
std::string propVal = "";
unsigned int spos = 9;
for (unsigned int ie = 0; ie < nent; ie++) {
try {
auto aid = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
if (!aid || aid > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "LIN specification has bad atom idx on line " << line;
throw FileParseException(errout.str());
}
spos += 4;
if (text.size() < spos + 4 || text.substr(spos, 4) == " ") {
std::ostringstream errout;
errout << "LIN specification missing repeat count on line " << line;
throw FileParseException(errout.str());
}
auto repeatCount = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
spos += 4;
if (repeatCount < 2) {
std::ostringstream errout;
errout << "LIN specification: repeat count must be >=2 on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int substB = 0;
unsigned int substC = 0;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
substB = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
}
spos += 4;
if (text.size() >= spos + 4 && text.substr(spos, 4) != " ") {
substC = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(spos, 4));
}
spos += 4;
if (!substB || substB > mol->getNumAtoms() ||
substC > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "LIN specification has bad substituent idx on line " << line;
throw FileParseException(errout.str());
}
boost::format formatter;
if (substC) {
formatter = boost::format("1 %1% 2 %2% %3% %2% %4%") % repeatCount %
aid % substB % substC;
} else {
formatter = boost::format("1 %1% 1 %2% %3%") % repeatCount % aid %
substB % substC;
}
if (!propVal.empty()) {
propVal += "|";
}
propVal += formatter.str();
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 4)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
mol->setProp(common_properties::molFileLinkNodes, propVal);
}
}
// Recursively populates queryVect with COMPOSITE_AND queries
// present in the input query. If the logic of the input query
// is more complex, it returns nullptr and empty set.
// The returned ptr should only be checked for not being null
// and not used for any other purposes, as the actual result is
// the queryVect
const QueryAtom::QUERYATOM_QUERY *getAndQueries(
const QueryAtom::QUERYATOM_QUERY *q,
std::vector<const QueryAtom::QUERYATOM_QUERY *> &queryVect) {
if (q) {
auto qOrig = q;
for (auto cq = qOrig->beginChildren(); cq != qOrig->endChildren(); ++cq) {
if (q == qOrig && q->getDescription() != "AtomAnd") {
q = nullptr;
break;
}
q = getAndQueries(cq->get(), queryVect);
}
if (q == qOrig) {
queryVect.push_back(q);
}
}
if (!q) {
queryVect.clear();
}
return q;
}
void ParseNewAtomList(RWMol *mol, const std::string &text, unsigned int line) {
if (text.size() < 15) {
std::ostringstream errout;
errout << "Atom list line too short: '" << text << "'";
throw FileParseException(errout.str());
}
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M ALS"),
"bad atom list line");
unsigned int idx;
try {
idx = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(7, 3)) -
1;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(7, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
URANGE_CHECK(idx, mol->getNumAtoms());
int nQueries;
try {
nQueries = FileParserUtils::toInt(text.substr(10, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(10, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
if (!nQueries) {
BOOST_LOG(rdWarningLog) << "Empty atom list: '" << text << "' on line "
<< line << "." << std::endl;
return;
}
if (nQueries < 0) {
std::ostringstream errout;
errout << "negative length atom list: '" << text << "' on line " << line
<< "." << std::endl;
throw FileParseException(errout.str());
}
QueryAtom *a = nullptr;
QueryAtom *qaOrig = nullptr;
QueryAtom::QUERYATOM_QUERY *qOrig = nullptr;
Atom *aOrig = mol->getAtomWithIdx(idx);
for (unsigned int i = 0; i < static_cast<unsigned int>(nQueries); i++) {
unsigned int pos = 16 + i * 4;
if (text.size() < pos + 4) {
std::ostringstream errout;
errout << "Atom list line too short: '" << text << "' on line " << line;
throw FileParseException(errout.str());
}
std::string atSymb = text.substr(pos, 4);
atSymb.erase(atSymb.find(' '), atSymb.size());
int atNum = PeriodicTable::getTable()->getAtomicNumber(atSymb);
if (!i) {
if (aOrig->hasQuery()) {
qaOrig = dynamic_cast<QueryAtom *>(aOrig);
if (qaOrig) {
qOrig = qaOrig->getQuery();
}
}
a = new QueryAtom(*aOrig);
a->setAtomicNum(atNum);
if (!qOrig) {
qOrig = a->getQuery()->copy();
}
a->setQuery(makeAtomNumQuery(atNum));
} else {
a->expandQuery(makeAtomNumQuery(atNum), Queries::COMPOSITE_OR, true);
// For COMPOSITE_OR query atoms, reset atomic num to 0 such that they are
// exported as "*" in SMILES
a->setAtomicNum(0);
}
}
ASSERT_INVARIANT(a, "no atom built");
if (qOrig) {
std::vector<const QueryAtom::QUERYATOM_QUERY *> queryVect;
if (getAndQueries(qOrig, queryVect)) {
for (const auto &q : queryVect) {
if (q->getDescription() != "AtomAtomicNum") {
a->expandQuery(q->copy(), Queries::COMPOSITE_AND, true);
}
}
}
if (!qaOrig) {
delete qOrig;
}
}
a->setProp(common_properties::_MolFileAtomQuery, 1);
switch (text[14]) {
case 'T':
a->getQuery()->setNegation(true);
break;
case 'F':
a->getQuery()->setNegation(false);
break;
default:
std::ostringstream errout;
errout << "Unrecognized atom-list query modifier: '" << text[14]
<< "' on line " << line;
delete a;
throw FileParseException(errout.str());
}
mol->replaceAtom(idx, a);
delete a;
}
void ParseV3000RGroups(RWMol *mol, Atom *&atom, std::string_view text,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(atom, "bad atom");
if (text[0] != '(' || text.back() != ')') {
std::ostringstream errout;
errout << "Bad RGROUPS specification '" << text << "' on line " << line
<< ". Missing parens.";
throw FileParseException(errout.str());
}
std::vector<std::string> splitToken;
std::string resid = std::string(text.substr(1, text.size() - 2));
boost::split(splitToken, resid, boost::is_any_of(std::string(" ")));
if (splitToken.size() < 1) {
std::ostringstream errout;
errout << "Bad RGROUPS specification '" << text << "' on line " << line
<< ". Missing values.";
throw FileParseException(errout.str());
}
unsigned int nRs;
try {
nRs = FileParserUtils::stripSpacesAndCast<unsigned int>(splitToken[0]);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << splitToken[0] << "' to int on line" << line;
throw FileParseException(errout.str());
}
if (splitToken.size() < nRs + 1) {
std::ostringstream errout;
errout << "Bad RGROUPS specification '" << text << "' on line " << line
<< ". Not enough values.";
throw FileParseException(errout.str());
}
for (unsigned int i = 0; i < nRs; ++i) {
unsigned int rLabel;
try {
rLabel =
FileParserUtils::stripSpacesAndCast<unsigned int>(splitToken[i + 1]);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << splitToken[i + 1] << "' to int on line"
<< line;
throw FileParseException(errout.str());
}
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
atom->setProp(common_properties::_MolFileRLabel, rLabel);
std::string dLabel = "R" + std::to_string(rLabel);
atom->setProp(common_properties::dummyLabel, dLabel);
atom->setIsotope(rLabel);
atom->setQuery(makeAtomNullQuery());
}
}
void ParseRGroupLabels(RWMol *mol, const std::string &text, unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 6) == std::string("M RGP"),
"bad R group label line");
int nLabels;
try {
nLabels = FileParserUtils::toInt(text.substr(6, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(6, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
for (int i = 0; i < nLabels; i++) {
int pos = 10 + i * 8;
unsigned int atIdx;
try {
atIdx = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(pos, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(pos, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
unsigned int rLabel;
try {
rLabel = FileParserUtils::stripSpacesAndCast<unsigned int>(
text.substr(pos + 4, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(pos + 4, 3)
<< "' to int on line " << line;
throw FileParseException(errout.str());
}
atIdx -= 1;
if (atIdx > mol->getNumAtoms()) {
std::ostringstream errout;
errout << "Attempt to set R group label on nonexistent atom " << atIdx
<< " on line " << line;
throw FileParseException(errout.str());
}
QueryAtom qatom(*(mol->getAtomWithIdx(atIdx)));
qatom.setProp(common_properties::_MolFileRLabel, rLabel);
// set the dummy label so that this is shown correctly
// in other pieces of the code :
// (this was sf.net issue 3316600)
std::string dLabel = "R" + std::to_string(rLabel);
qatom.setProp(common_properties::dummyLabel, dLabel);
// the CTFile spec (June 2005 version) technically only allows
// R labels up to 32. Since there are three digits, we'll accept
// anything: so long as it's positive and less than 1000:
if (rLabel > 0 && rLabel < 999) {
qatom.setIsotope(rLabel);
}
qatom.setQuery(makeAtomNullQuery());
mol->replaceAtom(atIdx, &qatom);
}
}
void ParseAtomAlias(RWMol *mol, std::string text, const std::string &nextLine,
unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 2) == std::string("A "), "bad atom alias line");
unsigned int idx;
try {
idx = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(3, 3)) -
1;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(3, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
URANGE_CHECK(idx, mol->getNumAtoms());
Atom *at = mol->getAtomWithIdx(idx);
at->setProp(common_properties::molFileAlias, nextLine);
}
void ParseAtomValue(RWMol *mol, std::string text, unsigned int line) {
PRECONDITION(mol, "bad mol");
PRECONDITION(text.substr(0, 2) == std::string("V "), "bad atom value line");
unsigned int idx;
try {
idx = FileParserUtils::stripSpacesAndCast<unsigned int>(text.substr(3, 3)) -
1;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(3, 3) << "' to int on line"
<< line;
throw FileParseException(errout.str());
}
URANGE_CHECK(idx, mol->getNumAtoms());
Atom *at = mol->getAtomWithIdx(idx);
at->setProp(common_properties::molFileValue,
text.substr(7, text.length() - 7));
}
namespace {
void setRGPProps(const std::string_view symb, Atom *res) {
PRECONDITION(res, "bad atom pointer");
// set the dummy label so that this is shown correctly
// in other pieces of the code :
std::string symbc(symb);
res->setProp(common_properties::dummyLabel, symbc);
}
void lookupAtomicNumber(Atom *res, const std::string &symb,
bool strictParsing) {
try {
res->setAtomicNum(PeriodicTable::getTable()->getAtomicNumber(symb));
} catch (const Invar::Invariant &e) {
if (strictParsing || symb.empty()) {
throw FileParseException(e.what());
} else {
res->setAtomicNum(0);
res->setProp(common_properties::dummyLabel, symb);
}
}
}
} // namespace
Atom *ParseMolFileAtomLine(const std::string_view text, RDGeom::Point3D &pos,
unsigned int line, bool strictParsing) {
std::string symb;
int massDiff, chg, hCount;
if ((strictParsing && text.size() < 34) || text.size() < 32) {
std::ostringstream errout;
errout << "Atom line too short: '" << text << "' on line " << line;
throw FileParseException(errout.str());
}
try {
pos.x = FileParserUtils::toDouble(text.substr(0, 10));
pos.y = FileParserUtils::toDouble(text.substr(10, 10));
pos.z = FileParserUtils::toDouble(text.substr(20, 10));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot process coordinates on line " << line;
throw FileParseException(errout.str());
}
symb = text.substr(31, 3);
boost::trim(symb);
// REVIEW: should we handle missing fields at the end of the line?
massDiff = 0;
if (text.size() >= 36 && text.substr(34, 2) != " 0") {
try {
massDiff = FileParserUtils::toInt(text.substr(34, 2), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(34, 2) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
}
chg = 0;
if (text.size() >= 39 && text.substr(36, 3) != " 0") {
try {
chg = FileParserUtils::toInt(text.substr(36, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(36, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
}
hCount = 0;
if (text.size() >= 45 && text.substr(42, 3) != " 0") {
try {
hCount = FileParserUtils::toInt(text.substr(42, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(42, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
}
std::unique_ptr<Atom> res(new Atom);
bool isComplexQueryName =
std::find(complexQueries.begin(), complexQueries.end(), symb) !=
complexQueries.end();
if (isComplexQueryName || symb == "L" || symb == "*" || symb == "LP" ||
symb == "R" || symb == "R#" ||
(symb[0] == 'R' && symb >= "R0" && symb <= "R99")) {
if (isComplexQueryName || symb == "*" || symb == "R") {
auto *query = new QueryAtom(0);
if (symb == "*" || symb == "R") {
// according to the MDL spec, these match anything
query->setQuery(makeAtomNullQuery());
} else if (isComplexQueryName) {
convertComplexNameToQuery(query, symb);
}
res.reset(query);
// queries have no implicit Hs:
res->setNoImplicit(true);
} else {
res->setAtomicNum(0);
}
if (massDiff == 0 && symb[0] == 'R') {
if (symb.length() > 1 && symb >= "R0" && symb <= "R99") {
std::string rlabel = "";
rlabel = symb.substr(1, symb.length() - 1);
int rnumber;
try {
rnumber = boost::lexical_cast<int>(rlabel);
} catch (boost::bad_lexical_cast &) {
rnumber = -1;
}
if (rnumber >= 0) {
res->setIsotope(rnumber);
}
}
}
if (symb[0] == 'R') {
// we used to skip R# here because that really should be handled by an
// RGP spec, but that turned out to not be permissive enough... <sigh>
setRGPProps(symb, res.get());
}
} else if (symb == "D") { // mol blocks support "D" and "T" as shorthand...
// handle that.
res->setAtomicNum(1);
res->setIsotope(2);
} else if (symb == "T") { // mol blocks support "D" and "T" as shorthand...
// handle that.
res->setAtomicNum(1);
res->setIsotope(3);
} else if (symb == "Pol" || symb == "Mod") {
res->setAtomicNum(0);
res->setProp(common_properties::dummyLabel, symb);
} else if (GenericGroups::genericMatchers.find(symb) !=
GenericGroups::genericMatchers.end()) {
res.reset(new QueryAtom(0));
res->setProp(common_properties::atomLabel, std::string(symb));
} else {
if (symb.size() == 2 && symb[1] >= 'A' && symb[1] <= 'Z') {
symb[1] = static_cast<char>(tolower(symb[1]));
}
lookupAtomicNumber(res.get(), symb, strictParsing);
}
// res->setPos(pX,pY,pZ);
if (chg != 0) {
res->setFormalCharge(4 - chg);
}
if (hCount >= 1) {
if (!res->hasQuery()) {
auto qatom = new QueryAtom(*res);
res.reset(qatom);
}
res->setNoImplicit(true);
if (hCount > 1) {
ATOM_EQUALS_QUERY *oq = makeAtomImplicitHCountQuery(hCount - 1);
auto nq = makeAtomSimpleQuery<ATOM_LESSEQUAL_QUERY>(
hCount - 1, oq->getDataFunc(),
std::string("less_") + oq->getDescription());
res->expandQuery(nq);
delete oq;
} else {
res->expandQuery(makeAtomImplicitHCountQuery(0));
}
}
if (massDiff != 0) {
int defIso =
PeriodicTable::getTable()->getMostCommonIsotope(res->getAtomicNum());
int dIso = defIso + massDiff;
if (dIso < 0) {
BOOST_LOG(rdWarningLog)
<< " atom " << res->getIdx()
<< " has a negative isotope offset. line: " << line << std::endl;
}
res->setIsotope(dIso);
}
if (text.size() >= 42 && text.substr(39, 3) != " 0") {
int parity = 0;
try {
parity = FileParserUtils::toInt(text.substr(39, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(39, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
res->setProp(common_properties::molParity, parity);
}
if (text.size() >= 48 && text.substr(45, 3) != " 0") {
int stereoCare = 0;
try {
stereoCare = FileParserUtils::toInt(text.substr(45, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(45, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
res->setProp(common_properties::molStereoCare, stereoCare);
}
if (text.size() >= 51 && text.substr(48, 3) != " 0") {
int totValence = 0;
try {
totValence = FileParserUtils::toInt(text.substr(48, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(48, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
if (totValence != 0) {
// only set if it's a non-default value
res->setProp(common_properties::molTotValence, totValence);
}
}
if (text.size() >= 57 && text.substr(54, 3) != " 0") {
int rxnRole = 0;
try {
rxnRole = FileParserUtils::toInt(text.substr(54, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(54, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
if (rxnRole != 0) {
// only set if it's a non-default value
res->setProp(common_properties::molRxnRole, rxnRole);
}
}
if (text.size() >= 60 && text.substr(57, 3) != " 0") {
int rxnComponent = 0;
try {
rxnComponent = FileParserUtils::toInt(text.substr(57, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(57, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
if (rxnComponent != 0) {
// only set if it's a non-default value
res->setProp(common_properties::molRxnComponent, rxnComponent);
}
}
if (text.size() >= 63 && text.substr(60, 3) != " 0") {
int atomMapNumber = 0;
try {
atomMapNumber = FileParserUtils::toInt(text.substr(60, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(60, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
res->setProp(common_properties::molAtomMapNumber, atomMapNumber);
}
if (text.size() >= 66 && text.substr(63, 3) != " 0") {
int inversionFlag = 0;
try {
inversionFlag = FileParserUtils::toInt(text.substr(63, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(63, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
res->setProp(common_properties::molInversionFlag, inversionFlag);
}
if (text.size() >= 69 && text.substr(66, 3) != " 0") {
int exactChangeFlag = 0;
try {
exactChangeFlag = FileParserUtils::toInt(text.substr(66, 3), true);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(66, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
res->setProp("molExactChangeFlag", exactChangeFlag);
}
return res.release();
}
Bond *ParseMolFileBondLine(const std::string_view text, unsigned int line) {
unsigned int idx1, idx2, bType, stereo;
int spos = 0;
if (text.size() < 9) {
std::ostringstream errout;
errout << "Bond line too short: '" << text << "' on line " << line;
throw FileParseException(errout.str());
}
try {
idx1 = FileParserUtils::toUnsigned(text.substr(spos, 3));
spos += 3;
idx2 = FileParserUtils::toUnsigned(text.substr(spos, 3));
spos += 3;
bType = FileParserUtils::toUnsigned(text.substr(spos, 3));
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << text.substr(spos, 3) << "' to int on line "
<< line;
throw FileParseException(errout.str());
}
// adjust the numbering
idx1--;
idx2--;
Bond::BondType type;
Bond *res = nullptr;
switch (bType) {
case 1:
type = Bond::SINGLE;
res = new Bond;
break;
case 2:
type = Bond::DOUBLE;
res = new Bond;
break;
case 3:
type = Bond::TRIPLE;
res = new Bond;
break;
case 4:
type = Bond::AROMATIC;
res = new Bond;
break;
case 9:
type = Bond::DATIVE;
res = new Bond;
break;
case 0:
type = Bond::UNSPECIFIED;
res = new Bond;
BOOST_LOG(rdWarningLog)
<< "bond with order 0 found on line " << line
<< ". This is not part of the MDL specification." << std::endl;
break;
default:
type = Bond::UNSPECIFIED;
// it's a query bond of some type
res = new QueryBond;
if (bType == 8) {
BOND_NULL_QUERY *q;
q = makeBondNullQuery();
res->setQuery(q);
} else if (bType == 5) {
res->setQuery(makeSingleOrDoubleBondQuery());
res->setProp(common_properties::_MolFileBondQuery, 1);
} else if (bType == 6) {
res->setQuery(makeSingleOrAromaticBondQuery());
res->setProp(common_properties::_MolFileBondQuery, 1);
} else if (bType == 7) {
res->setQuery(makeDoubleOrAromaticBondQuery());
res->setProp(common_properties::_MolFileBondQuery, 1);
} else {
BOND_NULL_QUERY *q;
q = makeBondNullQuery();
res->setQuery(q);
BOOST_LOG(rdWarningLog)
<< "unrecognized query bond type, " << bType << ", found on line "
<< line << ". Using an \"any\" query." << std::endl;
}
break;
}
res->setBeginAtomIdx(idx1);
res->setEndAtomIdx(idx2);
res->setBondType(type);
res->setProp(common_properties::_MolFileBondType, bType);
if (text.size() >= 12 && text.substr(9, 3) != " 0") {
try {
stereo = FileParserUtils::toUnsigned(text.substr(9, 3));
switch (stereo) {
case 0:
res->setBondDir(Bond::NONE);
break;
case 1:
res->setBondDir(Bond::BEGINWEDGE);
break;
case 6:
res->setBondDir(Bond::BEGINDASH);
break;
case 3: // "either" double bond
res->setBondDir(Bond::EITHERDOUBLE);
res->setStereo(Bond::STEREOANY);
break;
case 4: // "either" single bond
res->setBondDir(Bond::UNKNOWN);
break;
}
res->setProp(common_properties::_MolFileBondStereo, stereo);
} catch (boost::bad_lexical_cast &) {
;
}
}
if (text.size() >= 18 && text.substr(15, 3) != " 0") {
try {
int topology = FileParserUtils::toInt(text.substr(15, 3));
if (topology) {
if (!res->hasQuery()) {
auto *qBond = new QueryBond(*res);
delete res;
res = qBond;
}
BOND_EQUALS_QUERY *q = makeBondIsInRingQuery();
switch (topology) {
case 1:
break;
case 2:
q->setNegation(true);
break;
default:
std::ostringstream errout;
errout << "Unrecognized bond topology specifier: " << topology
<< " on line " << line;
throw FileParseException(errout.str());
}
res->expandQuery(q);
}
} catch (boost::bad_lexical_cast &) {
;
}
}
if (text.size() >= 21 && text.substr(18, 3) != " 0") {
try {
int reactStatus = FileParserUtils::toInt(text.substr(18, 3));
res->setProp("molReactStatus", reactStatus);
} catch (boost::bad_lexical_cast &) {
;
}
}
return res;
} // namespace
void ParseMolBlockAtoms(std::istream *inStream, unsigned int &line,
unsigned int nAtoms, RWMol *mol, Conformer *conf,
bool strictParsing) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(mol, "bad molecule");
PRECONDITION(conf, "bad conformer");
for (unsigned int i = 1; i <= nAtoms; ++i) {
++line;
std::string tempStr = getLine(inStream);
if (inStream->eof()) {
throw FileParseException("EOF hit while reading atoms");
}
RDGeom::Point3D pos;
Atom *atom = ParseMolFileAtomLine(tempStr, pos, line, strictParsing);
unsigned int aid = mol->addAtom(atom, false, true);
conf->setAtomPos(aid, pos);
mol->setAtomBookmark(atom, i);
}
}
void ParseMolBlockBonds(std::istream *inStream, unsigned int &line,
unsigned int nBonds, RWMol *mol,
bool &chiralityPossible) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(mol, "bad molecule");
for (unsigned int i = 1; i <= nBonds; ++i) {
++line;
std::string tempStr = getLine(inStream);
if (inStream->eof()) {
throw FileParseException("EOF hit while reading bonds");
}
Bond *bond = ParseMolFileBondLine(tempStr, line);
// if we got an aromatic bond set the flag on the bond and the connected
// atoms
if (bond->getBondType() == Bond::AROMATIC) {
bond->setIsAromatic(true);
}
// if the bond might have chirality info associated with it, set a flag:
if (bond->getBondDir() != Bond::NONE &&
bond->getBondDir() != Bond::UNKNOWN) {
chiralityPossible = true;
}
// v2k has no way to set stereoCare on bonds, so set the property if both
// the beginning and end atoms have it set:
int care1 = 0;
int care2 = 0;
if (!bond->hasProp(common_properties::molStereoCare) &&
mol->getAtomWithIdx(bond->getBeginAtomIdx())
->getPropIfPresent(common_properties::molStereoCare, care1) &&
mol->getAtomWithIdx(bond->getEndAtomIdx())
->getPropIfPresent(common_properties::molStereoCare, care2)) {
if (care1 && care2) {
bond->setProp(common_properties::molStereoCare, 1);
}
}
mol->addBond(bond, true);
mol->setBondBookmark(bond, i);
}
}
bool checkAttachmentPointsAreValid(
const RWMol *mol, std::pair<const int, SubstanceGroup> &sgroup) {
bool res = true;
int nAtoms = static_cast<int>(mol->getNumAtoms());
std::vector<SubstanceGroup::AttachPoint> &attachPoints =
sgroup.second.getAttachPoints();
for (auto &attachPoint : attachPoints) {
if (attachPoint.lvIdx == nAtoms) {
const std::vector<unsigned int> &bonds = sgroup.second.getBonds();
if (bonds.size() == 1) {
const auto bond = mol->getBondWithIdx(bonds.front());
if (bond->getBeginAtomIdx() == attachPoint.aIdx ||
bond->getEndAtomIdx() == attachPoint.aIdx) {
attachPoint.lvIdx = bond->getOtherAtomIdx(attachPoint.aIdx);
}
}
}
if (attachPoint.lvIdx == nAtoms) {
BOOST_LOG(rdWarningLog)
<< "Could not infer missing lvIdx on malformed SAP line for SGroup "
<< sgroup.first << std::endl;
res = false;
}
}
return res;
}
bool ParseMolBlockProperties(std::istream *inStream, unsigned int &line,
RWMol *mol, bool strictParsing) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(mol, "bad molecule");
// older mol files can have an atom list block here
std::string tempStr = getLine(inStream);
++line;
// there is apparently some software out there that puts a
// blank line in mol blocks before the "M END". If we aren't
// doing strict parsing, deal with that here.
if (!tempStr.size()) {
if (!strictParsing) {
tempStr = getLine(inStream);
++line;
} else {
std::ostringstream errout;
errout << "Problems encountered parsing Mol data, unexpected blank line "
"found at line "
<< line;
throw FileParseException(errout.str());
}
} else {
if (tempStr[0] != 'M' && tempStr[0] != 'A' && tempStr[0] != 'V' &&
tempStr[0] != 'G' && tempStr[0] != 'S') {
ParseOldAtomList(mol, std::string_view(tempStr.c_str()), line);
}
}
IDX_TO_SGROUP_MAP sGroupMap;
IDX_TO_STR_VECT_MAP dataFieldsMap;
bool fileComplete = false;
bool firstChargeLine = true;
unsigned int SCDcounter = 0;
unsigned int lastDataSGroup = 0;
std::ostringstream currentDataField;
std::string lineBeg = tempStr.substr(0, 6);
while (!inStream->eof() && !inStream->fail() && lineBeg != "M END" &&
tempStr.substr(0, 4) != "$$$$") {
if (tempStr[0] == 'A') {
line++;
std::string nextLine = getLine(inStream);
if (lineBeg != "M END") {
ParseAtomAlias(mol, tempStr, nextLine, line);
}
} else if (tempStr[0] == 'G') {
BOOST_LOG(rdWarningLog)
<< " deprecated group abbreviation ignored on line " << line
<< std::endl;
// we need to skip the next line, which holds the abbreviation:
line++;
tempStr = getLine(inStream);
} else if (tempStr[0] == 'V') {
ParseAtomValue(mol, tempStr, line);
} else if (lineBeg == "S SKP") {
int nToSkip = FileParserUtils::toInt(tempStr.substr(6, 3));
if (nToSkip < 0) {
std::ostringstream errout;
errout << "negative skip value " << nToSkip << " on line " << line;
throw FileParseException(errout.str());
}
for (unsigned int i = 0; i < static_cast<unsigned int>(nToSkip); ++i) {
++line;
tempStr = getLine(inStream);
}
} else if (lineBeg == "M ALS") {
ParseNewAtomList(mol, tempStr, line);
} else if (lineBeg == "M ISO") {
ParseIsotopeLine(mol, tempStr, line);
} else if (lineBeg == "M RGP") {
ParseRGroupLabels(mol, tempStr, line);
} else if (lineBeg == "M RBC") {
ParseRingBondCountLine(mol, tempStr, line);
} else if (lineBeg == "M SUB") {
ParseSubstitutionCountLine(mol, tempStr, line);
} else if (lineBeg == "M UNS") {
ParseUnsaturationLine(mol, tempStr, line);
} else if (lineBeg == "M CHG") {
ParseChargeLine(mol, tempStr, firstChargeLine, line);
firstChargeLine = false;
} else if (lineBeg == "M RAD") {
ParseRadicalLine(mol, tempStr, firstChargeLine, line);
firstChargeLine = false;
} else if (lineBeg == "M PXA") {
ParsePXALine(mol, tempStr, line);
/* SGroup parsing start */
} else if (lineBeg == "M STY") {
ParseSGroupV2000STYLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SST") {
ParseSGroupV2000SSTLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SLB") {
ParseSGroupV2000SLBLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SCN") {
ParseSGroupV2000SCNLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SDS") {
ParseSGroupV2000SDSLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SAL" || lineBeg == "M SBL" ||
lineBeg == "M SPA") {
ParseSGroupV2000VectorDataLine(sGroupMap, mol, tempStr, line,
strictParsing);
} else if (lineBeg == "M SMT") {
ParseSGroupV2000SMTLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SDI") {
ParseSGroupV2000SDILine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M CRS") {
std::ostringstream errout;
errout << "Unsupported SGroup subtype '" << lineBeg << "' on line "
<< line;
throw FileParseException(errout.str());
} else if (lineBeg == "M SBV") {
ParseSGroupV2000SBVLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SDT") {
ParseSGroupV2000SDTLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SDD") {
ParseSGroupV2000SDDLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SCD" || lineBeg == "M SED") {
ParseSGroupV2000SCDSEDLine(sGroupMap, dataFieldsMap, mol, tempStr, line,
strictParsing, SCDcounter, lastDataSGroup,
currentDataField);
} else if (lineBeg == "M SPL") {
ParseSGroupV2000SPLLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SNC") {
ParseSGroupV2000SNCLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SAP") {
ParseSGroupV2000SAPLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SCL") {
ParseSGroupV2000SCLLine(sGroupMap, mol, tempStr, line, strictParsing);
} else if (lineBeg == "M SBT") {
ParseSGroupV2000SBTLine(sGroupMap, mol, tempStr, line, strictParsing);
/* SGroup parsing end */
} else if (lineBeg == "M ZBO") {
ParseZBOLine(mol, tempStr, line);
} else if (lineBeg == "M ZCH") {
ParseZCHLine(mol, tempStr, line);
} else if (lineBeg == "M HYD") {
ParseHYDLine(mol, tempStr, line);
} else if (lineBeg == "M MRV") {
ParseMarvinSmartsLine(mol, tempStr, line);
} else if (lineBeg == "M APO") {
ParseAttachPointLine(mol, tempStr, line, strictParsing);
} else if (lineBeg == "M LIN") {
ParseLinkNodeLine(mol, tempStr, line);
}
line++;
tempStr = getLine(inStream);
lineBeg = tempStr.substr(0, 6);
}
if (tempStr[0] == 'M' && tempStr.substr(0, 6) == "M END") {
// All went well, make final updates to SGroups, and add them to Mol
for (auto &sgroup : sGroupMap) {
if (sgroup.second.getIsValid()) {
sgroup.second.setProp("DATAFIELDS", dataFieldsMap[sgroup.first]);
sgroup.second.setIsValid(checkAttachmentPointsAreValid(mol, sgroup));
}
if (sgroup.second.getIsValid()) {
addSubstanceGroup(*mol, sgroup.second);
} else {
std::ostringstream errout;
errout << "SGroup " << sgroup.first << " is invalid";
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog)
<< errout.str() << " and will be ignored" << std::endl;
}
}
}
fileComplete = true;
}
return fileComplete;
}
Atom *ParseV3000AtomSymbol(std::string_view token, unsigned int &line,
bool strictParsing) {
bool negate = false;
token = FileParserUtils::strip(token);
if (token.size() > 3 && (token[0] == 'N' || token[0] == 'n') &&
(token[1] == 'O' || token[1] == 'o') &&
(token[2] == 'T' || token[2] == 't')) {
negate = true;
token = token.substr(3, token.size() - 3);
token = FileParserUtils::strip(token);
}
std::unique_ptr<Atom> res;
if (token[0] == '[') {
// atom list:
if (token.back() != ']') {
std::ostringstream errout;
errout << "Bad atom token '" << token << "' on line: " << line;
throw FileParseException(errout.str());
}
token = token.substr(1, token.size() - 2);
std::vector<std::string> splitToken;
boost::split(splitToken, token, boost::is_any_of(","));
for (std::vector<std::string>::const_iterator stIt = splitToken.begin();
stIt != splitToken.end(); ++stIt) {
std::string_view stoken = *stIt;
std::string atSymb(FileParserUtils::strip(stoken));
if (atSymb.empty()) {
continue;
}
if (atSymb.size() == 2 && atSymb[1] >= 'A' && atSymb[1] <= 'Z') {
atSymb[1] = static_cast<char>(tolower(atSymb[1]));
}
int atNum = PeriodicTable::getTable()->getAtomicNumber(atSymb);
if (!res) {
res.reset(new QueryAtom(atNum));
} else {
res->expandQuery(makeAtomNumQuery(atNum), Queries::COMPOSITE_OR, true);
}
}
res->getQuery()->setNegation(negate);
} else {
if (negate) {
std::ostringstream errout;
errout << "NOT tokens only supported for atom lists. line " << line;
throw FileParseException(errout.str());
}
// it's a normal CTAB atom symbol:
// NOTE: "R" and "R0"-"R99" are not in the v3K CTAB spec, but we're going to
// support them anyway
bool isComplexQueryName =
std::find(complexQueries.begin(), complexQueries.end(), token) !=
complexQueries.end();
if (isComplexQueryName || token == "R" ||
(token[0] == 'R' && token >= "R0" && token <= "R99") || token == "R#" ||
token == "*") {
if (isComplexQueryName || token == "*") {
res.reset(new QueryAtom(0));
if (token == "*") {
// according to the MDL spec, these match anything
res->setQuery(makeAtomNullQuery());
} else if (isComplexQueryName) {
convertComplexNameToQuery(res.get(), token);
}
// queries have no implicit Hs:
res->setNoImplicit(true);
} else {
res.reset(new Atom(1));
res->setAtomicNum(0);
}
if (token[0] == 'R' && token >= "R0" && token <= "R99") {
auto rlabel = token.substr(1, token.length() - 1);
int rnumber;
try {
rnumber = boost::lexical_cast<int>(rlabel);
} catch (boost::bad_lexical_cast &) {
rnumber = -1;
}
if (rnumber >= 0) {
res->setIsotope(rnumber);
}
}
if (token[0] == 'R') {
// we used to skip R# here because that really should be handled by an
// RGP spec, but that turned out to not be permissive enough... <sigh>
setRGPProps(token, res.get());
}
} else if (token == "D") { // mol blocks support "D" and "T" as
// shorthand... handle that.
res.reset(new Atom(1));
res->setIsotope(2);
} else if (token == "T") { // mol blocks support "D" and "T" as
// shorthand... handle that.
res.reset(new Atom(1));
res->setIsotope(3);
} else if (token == "Pol" || token == "Mod") {
res.reset(new Atom(0));
res->setProp(common_properties::dummyLabel, std::string(token));
} else if (GenericGroups::genericMatchers.find(std::string(token)) !=
GenericGroups::genericMatchers.end()) {
res.reset(new QueryAtom(0));
res->setProp(common_properties::atomLabel, std::string(token));
} else {
std::string tcopy(token);
if (token.size() == 2 && token[1] >= 'A' && token[1] <= 'Z') {
tcopy[1] = static_cast<char>(tolower(token[1]));
}
res.reset(new Atom(0));
lookupAtomicNumber(res.get(), tcopy, strictParsing);
}
}
POSTCONDITION(res, "no atom built");
return res.release();
}
bool splitAssignToken(std::string_view token, std::string &prop,
std::string_view &val) {
auto equalsLoc = token.find("=");
if (equalsLoc == token.npos || equalsLoc != token.rfind("=")) {
return false;
}
prop = token.substr(0, equalsLoc);
boost::to_upper(prop);
val = token.substr(equalsLoc + 1);
return true;
}
template <class T>
void ParseV3000AtomProps(RWMol *mol, Atom *&atom, typename T::iterator &token,
const T &tokens, unsigned int &line,
bool strictParsing) {
PRECONDITION(mol, "bad molecule");
PRECONDITION(atom, "bad atom");
std::ostringstream errout;
while (token != tokens.end()) {
std::string prop;
std::string_view val;
if (!splitAssignToken(*token, prop, val)) {
errout << "Invalid atom property: '" << *token << "' for atom "
<< atom->getIdx() + 1 << " on line " << line << std::endl;
throw FileParseException(errout.str());
}
if (prop == "CHG") {
auto charge = FileParserUtils::toInt(val);
if (!atom->hasQuery()) {
atom->setFormalCharge(charge);
} else {
atom->expandQuery(makeAtomFormalChargeQuery(charge));
}
} else if (prop == "RAD") {
// FIX handle queries here
switch (FileParserUtils::toInt(val)) {
case 0:
break;
case 1:
atom->setNumRadicalElectrons(2);
break;
case 2:
atom->setNumRadicalElectrons(1);
break;
case 3:
atom->setNumRadicalElectrons(2);
break;
default:
errout << "Unrecognized RAD value " << val << " for atom "
<< atom->getIdx() + 1 << " on line " << line << std::endl;
throw FileParseException(errout.str());
}
} else if (prop == "MASS") {
// the documentation for V3000 CTABs says that this should contain the
// "absolute atomic weight" (whatever that means).
// Online examples seem to have integer (isotope) values and Marvin
// won't even read something that has a float. We'll go with the int
int v;
double dv;
try {
v = FileParserUtils::toInt(val);
} catch (boost::bad_lexical_cast &) {
try {
dv = FileParserUtils::toDouble(val);
v = static_cast<int>(floor(dv));
} catch (boost::bad_lexical_cast &) {
v = -1;
}
}
if (v < 0) {
errout << "Bad value for MASS :" << val << " for atom "
<< atom->getIdx() + 1 << " on line " << line << std::endl;
throw FileParseException(errout.str());
} else {
if (!atom->hasQuery()) {
atom->setIsotope(v);
} else {
atom->expandQuery(makeAtomIsotopeQuery(v));
}
}
} else if (prop == "CFG") {
auto cfg = FileParserUtils::toInt(val);
switch (cfg) {
case 0:
break;
case 1:
case 2:
case 3:
atom->setProp(common_properties::molParity, cfg);
break;
default:
errout << "Unrecognized CFG value : " << val << " for atom "
<< atom->getIdx() + 1 << " on line " << line << std::endl;
throw FileParseException(errout.str());
}
} else if (prop == "HCOUNT") {
if (val != "0") {
auto hcount = FileParserUtils::toInt(val);
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
if (hcount == -1) {
hcount = 0;
}
if (hcount > 0) {
ATOM_EQUALS_QUERY *oq = makeAtomImplicitHCountQuery(hcount);
auto nq = makeAtomSimpleQuery<ATOM_LESSEQUAL_QUERY>(
hcount, oq->getDataFunc(),
std::string("less_") + oq->getDescription());
atom->expandQuery(nq);
delete oq;
} else {
atom->expandQuery(makeAtomImplicitHCountQuery(0));
}
}
} else if (prop == "UNSAT") {
if (val == "1") {
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
atom->expandQuery(makeAtomUnsaturatedQuery());
}
} else if (prop == "RBCNT") {
if (val != "0") {
auto rbcount = FileParserUtils::toInt(val);
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
atom->setProp(common_properties::molRingBondCount, rbcount);
if (rbcount == -1) {
rbcount = 0;
} else if (rbcount == -2) {
// Ring bonds can only be counted during post processing
mol->setProp(common_properties::_NeedsQueryScan, 1);
rbcount = 0xDEADBEEF;
} else if (rbcount > 4) {
rbcount = 4;
}
atom->expandQuery(makeAtomRingBondCountQuery(rbcount));
}
} else if (prop == "VAL") {
if (val != "0") {
auto totval = FileParserUtils::toInt(val);
atom->setProp(common_properties::molTotValence, totval);
}
} else if (prop == "RGROUPS") {
ParseV3000RGroups(mol, atom, val, line);
// FIX
} else if (prop == "STBOX") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molStereoCare, ival);
}
} else if (prop == "SUBST") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molSubstCount, ival);
}
} else if (prop == "EXACHG") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molRxnExactChange, ival);
}
} else if (prop == "INVRET") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molInversionFlag, ival);
}
} else if (prop == "ATTCHPT") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
if (atom->hasProp(common_properties::molAttachPoint)) {
errout << "Multiple ATTCHPT values for atom " << atom->getIdx() + 1
<< " on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
errout.str(std::string());
}
} else {
atom->setProp(common_properties::molAttachPoint, ival);
}
}
} else if (prop == "ATTCHORD") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molAttachOrder, ival);
}
} else if (prop == "CLASS") {
atom->setProp(common_properties::molAtomClass, std::string(val));
} else if (prop == "SEQID") {
if (val != "0") {
auto ival = FileParserUtils::toInt(val);
atom->setProp(common_properties::molAtomSeqId, ival);
}
}
++token;
}
}
void tokenizeV3000Line(std::string_view line,
std::vector<std::string_view> &tokens) {
tokens.clear();
bool inQuotes = false, inParens = false;
unsigned int start = 0;
unsigned int pos = 0;
while (pos < line.size()) {
if (line[pos] == ' ' || line[pos] == '\t') {
if (start == pos) {
++start;
++pos;
} else if (!inQuotes && !inParens) {
tokens.push_back(line.substr(start, pos - start));
++pos;
start = pos;
} else {
++pos;
}
} else if (line[pos] == ')' && inParens) {
tokens.push_back(line.substr(start, pos - start + 1));
inParens = false;
++pos;
start = pos;
} else if (line[pos] == '(' && !inQuotes) {
inParens = true;
++pos;
} else if (line[pos] == '"' && !inParens) {
if (pos + 1 < line.size() && line[pos + 1] == '"') {
pos += 2;
} else if (inQuotes) {
// don't push on the quotes themselves
tokens.push_back(line.substr(start + 1, pos - start - 1));
++pos;
start = pos;
inQuotes = false;
} else {
++pos;
inQuotes = true;
}
} else {
++pos;
}
}
if (start != pos) {
tokens.push_back(line.substr(start, line.size() - start));
}
#if 0
std::cerr<<"tokens: ";
std::copy(tokens.begin(),tokens.end(),std::ostream_iterator<std::string>(std::cerr,"|"));
std::cerr<<std::endl;
#endif
}
bool calculate3dFlag(const RWMol &mol, const Conformer &conf,
bool chiralityPossible) {
int marked3d = 0;
if (mol.getPropIfPresent(common_properties::_3DConf, marked3d)) {
mol.clearProp(common_properties::_3DConf);
}
bool nonzeroZ = hasNonZeroZCoords(conf);
if (!nonzeroZ && marked3d == 1) {
// If we have no Z coordinates, mark the structure 2D if we see any
// 2D stereo markers, or stay as 3D if
if (chiralityPossible) {
BOOST_LOG(rdWarningLog)
<< "Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo "
"markers have been found, marking the mol as 2D."
<< std::endl;
return false;
}
return true;
} else if (marked3d == 0 && nonzeroZ) {
BOOST_LOG(rdWarningLog)
<< "Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. "
"Marking the mol as 3D."
<< std::endl;
return true;
}
return nonzeroZ;
}
void ParseV3000AtomBlock(std::istream *inStream, unsigned int &line,
unsigned int nAtoms, RWMol *mol, Conformer *conf,
bool strictParsing) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(nAtoms > 0, "bad atom count");
PRECONDITION(mol, "bad molecule");
PRECONDITION(conf, "bad conformer");
std::vector<std::string> splitLine;
auto inl = getV3000Line(inStream, line);
std::string_view tempStr = inl;
if (tempStr.length() < 10 || tempStr.substr(0, 10) != "BEGIN ATOM") {
std::ostringstream errout;
errout << "BEGIN ATOM line not found on line " << line;
throw FileParseException(errout.str());
}
for (unsigned int i = 0; i < nAtoms; ++i) {
inl = getV3000Line(inStream, line);
tempStr = inl;
auto trimmed = FileParserUtils::strip(tempStr);
std::vector<std::string_view> tokens;
std::vector<std::string_view>::iterator token;
tokenizeV3000Line(trimmed, tokens);
token = tokens.begin();
if (token == tokens.end()) {
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line" << line;
throw FileParseException(errout.str());
}
unsigned int molIdx = 0;
std::from_chars(token->data(), token->data() + token->size(), molIdx);
// start with the symbol:
++token;
if (token == tokens.end()) {
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
Atom *atom = ParseV3000AtomSymbol(*token, line, strictParsing);
// now the position;
RDGeom::Point3D pos;
++token;
if (token == tokens.end()) {
delete atom;
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
pos.x = atof(std::string(*token).c_str());
++token;
if (token == tokens.end()) {
delete atom;
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
pos.y = atof(std::string(*token).c_str());
++token;
if (token == tokens.end()) {
delete atom;
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
pos.z = atof(std::string(*token).c_str());
// the map number:
++token;
if (token == tokens.end()) {
delete atom;
std::ostringstream errout;
errout << "Bad atom line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
int mapNum = atoi(std::string(*token).c_str());
if (mapNum > 0) {
atom->setProp(common_properties::molAtomMapNumber, mapNum);
}
++token;
unsigned int aid = mol->addAtom(atom, false, true);
// additional properties this may change the atom,
// so be careful with it:
ParseV3000AtomProps(mol, atom, token, tokens, line, strictParsing);
mol->setAtomBookmark(atom, molIdx);
conf->setAtomPos(aid, pos);
}
inl = getV3000Line(inStream, line);
tempStr = inl;
if (tempStr.length() < 8 || tempStr.substr(0, 8) != "END ATOM") {
std::ostringstream errout;
errout << "END ATOM line not found on line " << line;
throw FileParseException(errout.str());
}
}
void ParseV3000BondBlock(std::istream *inStream, unsigned int &line,
unsigned int nBonds, RWMol *mol,
bool &chiralityPossible) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(nBonds > 0, "bad bond count");
PRECONDITION(mol, "bad molecule");
auto inl = getV3000Line(inStream, line);
std::string_view tempStr = inl;
if (tempStr.length() < 10 || tempStr.substr(0, 10) != "BEGIN BOND") {
throw FileParseException("BEGIN BOND line not found");
}
for (unsigned int i = 0; i < nBonds; ++i) {
inl = getV3000Line(inStream, line);
tempStr = inl;
tempStr = FileParserUtils::strip(tempStr);
std::vector<std::string_view> splitLine;
tokenizeV3000Line(tempStr, splitLine);
if (splitLine.size() < 4) {
std::ostringstream errout;
errout << "bond line " << line << " is too short";
throw FileParseException(errout.str());
}
Bond *bond;
unsigned int bondIdx = 0;
std::from_chars(splitLine[0].data(),
splitLine[0].data() + splitLine[0].size(), bondIdx);
unsigned int bType = 0;
std::from_chars(splitLine[1].data(),
splitLine[1].data() + splitLine[1].size(), bType);
unsigned int a1Idx = 0;
std::from_chars(splitLine[2].data(),
splitLine[2].data() + splitLine[2].size(), a1Idx);
unsigned int a2Idx = 0;
std::from_chars(splitLine[3].data(),
splitLine[3].data() + splitLine[3].size(), a2Idx);
switch (bType) {
case 1:
bond = new Bond(Bond::SINGLE);
break;
case 2:
bond = new Bond(Bond::DOUBLE);
break;
case 3:
bond = new Bond(Bond::TRIPLE);
break;
case 4:
bond = new Bond(Bond::AROMATIC);
bond->setIsAromatic(true);
break;
case 9:
bond = new Bond(Bond::DATIVE);
break;
case 10:
bond = new Bond(Bond::HYDROGEN);
break;
case 0:
bond = new Bond(Bond::UNSPECIFIED);
BOOST_LOG(rdWarningLog)
<< "bond with order 0 found on line " << line
<< ". This is not part of the MDL specification." << std::endl;
break;
default:
// it's a query bond of some type
bond = new QueryBond;
if (bType == 8) {
BOND_NULL_QUERY *q;
q = makeBondNullQuery();
bond->setQuery(q);
} else if (bType == 5) {
bond->setQuery(makeSingleOrDoubleBondQuery());
bond->setProp(common_properties::_MolFileBondQuery, 1);
} else if (bType == 6) {
bond->setQuery(makeSingleOrAromaticBondQuery());
bond->setProp(common_properties::_MolFileBondQuery, 1);
} else if (bType == 7) {
bond->setQuery(makeDoubleOrAromaticBondQuery());
bond->setProp(common_properties::_MolFileBondQuery, 1);
} else {
BOND_NULL_QUERY *q;
q = makeBondNullQuery();
bond->setQuery(q);
BOOST_LOG(rdWarningLog)
<< "unrecognized query bond type, " << bType << ", found on line "
<< line << ". Using an \"any\" query." << std::endl;
}
break;
}
bond->setProp(common_properties::_MolFileBondType, bType);
// additional bond properties:
unsigned int lPos = 4;
std::ostringstream errout;
while (lPos < splitLine.size()) {
std::string prop;
std::string_view val;
if (!splitAssignToken(splitLine[lPos], prop, val)) {
errout << "bad bond property '" << splitLine[lPos] << "' on line "
<< line;
throw FileParseException(errout.str());
}
if (prop == "CFG") {
unsigned int cfg = 0;
std::from_chars(val.data(), val.data() + val.size(), cfg);
switch (cfg) {
case 0:
break;
case 1:
bond->setBondDir(Bond::BEGINWEDGE);
chiralityPossible = true;
break;
case 2:
if (bType == 1) {
bond->setBondDir(Bond::UNKNOWN);
} else if (bType == 2) {
bond->setBondDir(Bond::EITHERDOUBLE);
bond->setStereo(Bond::STEREOANY);
}
break;
case 3:
bond->setBondDir(Bond::BEGINDASH);
chiralityPossible = true;
break;
default:
errout << "bad bond CFG " << val << "' on line " << line;
throw FileParseException(errout.str());
}
bond->setProp(common_properties::_MolFileBondCfg, cfg);
} else if (prop == "TOPO") {
if (val != "0") {
if (!bond->hasQuery()) {
auto *qBond = new QueryBond(*bond);
delete bond;
bond = qBond;
}
BOND_EQUALS_QUERY *q = makeBondIsInRingQuery();
if (val == "1") {
// nothing
} else if (val == "2") {
q->setNegation(true);
} else {
errout << "bad bond TOPO " << val << "' on line " << line;
throw FileParseException(errout.str());
}
bond->expandQuery(q);
}
} else if (prop == "RXCTR") {
int reactStatus = FileParserUtils::toInt(val);
bond->setProp(common_properties::molReactStatus, reactStatus);
} else if (prop == "STBOX") {
bond->setProp(common_properties::molStereoCare, std::string(val));
} else if (prop == "ENDPTS") {
bond->setProp(common_properties::_MolFileBondEndPts, std::string(val));
} else if (prop == "ATTACH") {
bond->setProp(common_properties::_MolFileBondAttach, std::string(val));
}
++lPos;
}
bond->setBeginAtomIdx(mol->getAtomWithBookmark(a1Idx)->getIdx());
bond->setEndAtomIdx(mol->getAtomWithBookmark(a2Idx)->getIdx());
mol->addBond(bond, true);
mol->setBondBookmark(bond, bondIdx);
// set the stereoCare property on the bond if it's not set already and
// both the beginning and end atoms have it set:
int care1 = 0;
int care2 = 0;
if (!bond->hasProp(common_properties::molStereoCare) &&
mol->getAtomWithIdx(bond->getBeginAtomIdx())
->getPropIfPresent(common_properties::molStereoCare, care1) &&
mol->getAtomWithIdx(bond->getEndAtomIdx())
->getPropIfPresent(common_properties::molStereoCare, care2)) {
if (care1 == care2) {
bond->setProp(common_properties::molStereoCare, care1);
}
}
}
inl = getV3000Line(inStream, line);
tempStr = inl;
if (tempStr.length() < 8 || tempStr.substr(0, 8) != "END BOND") {
std::ostringstream errout;
errout << "END BOND line not found at line " << line;
throw FileParseException(errout.str());
}
}
// The documentation about MRV_COORDINATE_BOND_TYPE in
// https://docs.chemaxon.com/display/docs/chemaxon-specific-information-in-mdl-mol-files.md
// seems to be wrong: it says the only data field in this group contains the
// index for the coordinate atom. But behavior in Marvin Sketch seems to
// indicate that it references the bond index instead (see
// https://github.com/rdkit/rdkit/issues/4473)
void processMrvCoordinateBond(RWMol &mol, const SubstanceGroup &sg) {
std::vector<std::string> dataFields;
if (sg.getPropIfPresent("DATAFIELDS", dataFields)) {
if (dataFields.empty()) {
BOOST_LOG(rdWarningLog)
<< "ignoring MRV_COORDINATE_BOND_TYPE SGroup without data fields."
<< std::endl;
return;
}
auto coordinate_bond_idx =
FileParserUtils::toUnsigned(dataFields[0], true) - 1;
if (dataFields.size() > 1) {
BOOST_LOG(rdWarningLog) << "ignoring extra data fields in "
"MRV_COORDINATE_BOND_TYPE SGroup for bond "
<< coordinate_bond_idx << '.' << std::endl;
}
Bond *old_bond = nullptr;
try {
old_bond = mol.getBondWithIdx(coordinate_bond_idx);
} catch (const Invar::Invariant &) {
BOOST_LOG(rdWarningLog)
<< "molecule does not contain a bond matching the "
"MRV_COORDINATE_BOND_TYPE SGroup for bond "
<< coordinate_bond_idx << ", ignoring." << std::endl;
return;
}
if (!old_bond || old_bond->getBondType() != Bond::BondType::UNSPECIFIED) {
BOOST_LOG(rdWarningLog)
<< "MRV_COORDINATE_BOND_TYPE SGroup with value "
<< coordinate_bond_idx
<< " does not reference a query bond, ignoring." << std::endl;
return;
}
Bond new_bond(Bond::BondType::DATIVE);
auto preserveProps = true;
auto keepSGroups = true;
mol.replaceBond(coordinate_bond_idx, &new_bond, preserveProps, keepSGroups);
}
}
void processSMARTSQ(RWMol &mol, const SubstanceGroup &sg) {
std::string field;
if (sg.getPropIfPresent("QUERYOP", field) && field != "=") {
BOOST_LOG(rdWarningLog) << "unrecognized QUERYOP '" << field
<< "' for SMARTSQ. Query ignored." << std::endl;
return;
}
std::vector<std::string> dataFields;
if (!sg.getPropIfPresent("DATAFIELDS", dataFields) || dataFields.empty()) {
BOOST_LOG(rdWarningLog)
<< "empty FIELDDATA for SMARTSQ. Query ignored." << std::endl;
return;
}
if (dataFields.size() > 1) {
BOOST_LOG(rdWarningLog)
<< "multiple FIELDDATA values for SMARTSQ. Taking the first."
<< std::endl;
}
const std::string &sma = dataFields[0];
if (sma.empty()) {
BOOST_LOG(rdWarningLog)
<< "Skipping empty SMARTS value for SMARTSQ." << std::endl;
return;
}
for (auto aidx : sg.getAtoms()) {
auto at = mol.getAtomWithIdx(aidx);
std::unique_ptr<RWMol> m;
try {
m.reset(SmartsToMol(sma));
} catch (...) {
// Is this ever used?
}
if (!m || !m->getNumAtoms()) {
BOOST_LOG(rdWarningLog)
<< "SMARTS for SMARTSQ '" << sma
<< "' could not be parsed or has no atoms. Ignoring it." << std::endl;
return;
}
if (!at->hasQuery()) {
QueryAtom qAt(*at);
int oidx = at->getIdx();
mol.replaceAtom(oidx, &qAt);
at = mol.getAtomWithIdx(oidx);
}
QueryAtom::QUERYATOM_QUERY *query = nullptr;
if (m->getNumAtoms() == 1) {
query = m->getAtomWithIdx(0)->getQuery()->copy();
} else {
query = new RecursiveStructureQuery(m.release());
}
at->setQuery(query);
at->setProp(common_properties::MRV_SMA, sma);
at->setProp(common_properties::_MolFileAtomQuery, 1);
}
}
void processMrvImplicitH(RWMol &mol, const SubstanceGroup &sg) {
std::vector<std::string> dataFields;
if (sg.getPropIfPresent("DATAFIELDS", dataFields)) {
for (const auto &df : dataFields) {
if (df.substr(0, 6) == "IMPL_H") {
auto val = FileParserUtils::toInt(df.substr(6));
for (auto atIdx : sg.getAtoms()) {
if (atIdx < mol.getNumAtoms()) {
// if the atom has aromatic bonds to it, then set the explicit
// value, otherwise skip it.
auto atom = mol.getAtomWithIdx(atIdx);
bool hasAromaticBonds = false;
for (auto bndI :
boost::make_iterator_range(mol.getAtomBonds(atom))) {
auto bnd = (mol)[bndI];
if (bnd->getIsAromatic() ||
bnd->getBondType() == Bond::AROMATIC) {
hasAromaticBonds = true;
break;
}
}
if (hasAromaticBonds) {
atom->setNumExplicitHs(val);
} else {
BOOST_LOG(rdWarningLog)
<< "MRV_IMPLICIT_H SGroup on atom without aromatic "
"bonds, "
<< atIdx << ", ignored." << std::endl;
}
} else {
BOOST_LOG(rdWarningLog)
<< "bad atom index, " << atIdx
<< ", found in MRV_IMPLICIT_H SGroup. Ignoring it."
<< std::endl;
}
}
}
}
}
}
void processZBO(RWMol &mol, const SubstanceGroup &sg) {
for (auto bidx : sg.getBonds()) {
auto bond = mol.getBondWithIdx(bidx);
bond->setBondType(Bond::BondType::ZERO);
}
}
void processZCH(RWMol &mol, const SubstanceGroup &sg) {
RDUNUSED_PARAM(mol);
std::vector<std::string> dataFields;
if (sg.getPropIfPresent("DATAFIELDS", dataFields)) {
if (dataFields.empty()) {
BOOST_LOG(rdWarningLog)
<< "ignoring ZCHG SGroup without data fields." << std::endl;
return;
}
for (const auto &df : dataFields) {
std::string trimmed = boost::trim_copy(df);
std::vector<std::string> splitLine;
boost::split(splitLine, trimmed, boost::is_any_of(";"),
boost::token_compress_off);
const auto &aids = sg.getAtoms();
if (splitLine.size() < aids.size()) {
BOOST_LOG(rdWarningLog)
<< "DATAFIELDS in ZCH SGroup is shorter than the number of atoms in the SGroup. Ignoring it."
<< std::endl;
continue;
}
for (auto i = 0u; i < aids.size(); ++i) {
auto aid = aids[i];
auto atom = mol.getAtomWithIdx(aid);
auto val = 0;
if (!splitLine[i].empty()) {
val = FileParserUtils::toInt(splitLine[i]);
}
atom->setFormalCharge(val);
}
}
}
}
void processHYD(RWMol &mol, const SubstanceGroup &sg) {
std::vector<std::string> dataFields;
if (sg.getPropIfPresent("DATAFIELDS", dataFields)) {
if (dataFields.empty()) {
BOOST_LOG(rdWarningLog)
<< "ignoring HYD SGroup without data fields." << std::endl;
return;
}
for (const auto &df : dataFields) {
std::string trimmed = boost::trim_copy(df);
std::vector<std::string> splitLine;
boost::split(splitLine, trimmed, boost::is_any_of(";"),
boost::token_compress_off);
const auto &aids = sg.getAtoms();
if (splitLine.size() < aids.size()) {
BOOST_LOG(rdWarningLog)
<< "DATAFIELDS in HYD SGroup is shorter than the number of atoms in the SGroup. Ignoring it."
<< std::endl;
continue;
}
for (auto i = 0u; i < aids.size(); ++i) {
auto aid = aids[i];
auto atom = mol.getAtomWithIdx(aid);
auto val = 0;
if (!splitLine[i].empty()) {
val = FileParserUtils::toInt(splitLine[i]);
}
atom->setProp("_ZBO_H", true);
atom->setNumExplicitHs(val);
}
}
}
}
// process (and remove) SGroups which modify the structure
// and which we can unambiguously apply
void processSGroups(RWMol *mol) {
std::vector<unsigned int> sgsToRemove;
unsigned int sgIdx = 0;
for (auto &sg : getSubstanceGroups(*mol)) {
if (sg.getProp<std::string>("TYPE") == "DAT") {
std::string field;
if (sg.getPropIfPresent("FIELDNAME", field)) {
if (field == "MRV_COORDINATE_BOND_TYPE") {
// V2000 support for coordinate bonds
processMrvCoordinateBond(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
} else if (field == "MRV_IMPLICIT_H") {
// CXN extension to specify implicit Hs, used for aromatic rings
processMrvImplicitH(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
} else if (field == "ZBO") {
// RDKit extension for zero-order bonds
processZBO(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
} else if (field == "ZCH") {
// RDKit extension for charge on atoms involved in zero-order bonds
processZCH(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
} else if (field == "HYD") {
// RDKit extension for hydrogen-count on atoms involved in
// zero-order bonds
processHYD(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
}
}
if (sg.getPropIfPresent("QUERYTYPE", field) &&
(field == "SMARTSQ" || field == "SQ")) {
processSMARTSQ(*mol, sg);
sgsToRemove.push_back(sgIdx);
continue;
}
}
++sgIdx;
}
// now remove the S groups we processed, we saved indices so do this in
// backwards
auto &sgs = getSubstanceGroups(*mol);
for (auto it = sgsToRemove.rbegin(); it != sgsToRemove.rend(); ++it) {
sgs.erase(sgs.begin() + *it);
}
}
void ProcessMolProps(RWMol *mol) {
PRECONDITION(mol, "no molecule");
// we have to loop the ugly way because we may need to actually replace an
// atom
for (unsigned int aidx = 0; aidx < mol->getNumAtoms(); ++aidx) {
auto atom = mol->getAtomWithIdx(aidx);
int ival = 0;
if (atom->getPropIfPresent(common_properties::molSubstCount, ival) &&
ival != 0) {
if (!atom->hasQuery()) {
atom = QueryOps::replaceAtomWithQueryAtom(mol, atom);
}
bool gtQuery = false;
if (ival == -1) {
ival = 0;
} else if (ival == -2) {
// as drawn
ival = atom->getDegree();
} else if (ival >= 6) {
// 6 or more
gtQuery = true;
}
if (!gtQuery) {
atom->expandQuery(makeAtomExplicitDegreeQuery(ival));
} else {
// create a temp query the normal way so that we can be sure to get
// the description right
std::unique_ptr<ATOM_EQUALS_QUERY> tmp{
makeAtomExplicitDegreeQuery(ival)};
atom->expandQuery(makeAtomSimpleQuery<ATOM_LESSEQUAL_QUERY>(
ival, tmp->getDataFunc(),
std::string("less_") + tmp->getDescription()));
}
}
if (atom->getPropIfPresent(common_properties::molTotValence, ival) &&
ival != 0 && !atom->hasProp("_ZBO_H")) {
atom->setNoImplicit(true);
if (ival == 15 // V2000
|| ival == -1 // v3000
) {
atom->setNumExplicitHs(0);
} else {
if (atom->getExplicitValence() > ival) {
BOOST_LOG(rdWarningLog)
<< "atom " << atom->getIdx() << " has specified valence (" << ival
<< ") smaller than the drawn valence "
<< atom->getExplicitValence() << "." << std::endl;
atom->setNumExplicitHs(0);
} else {
atom->setNumExplicitHs(ival - atom->getExplicitValence());
}
}
}
atom->clearProp(common_properties::molTotValence);
}
processSGroups(mol);
}
} // namespace
namespace FileParserUtils {
bool ParseV3000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
Conformer *&conf, bool &chiralityPossible,
unsigned int &nAtoms, unsigned int &nBonds,
bool strictParsing, bool expectMEND) {
PRECONDITION(inStream, "bad stream");
PRECONDITION(mol, "bad molecule");
std::string tempStr;
std::vector<std::string> splitLine;
bool fileComplete = false;
tempStr = getV3000Line(inStream, line);
boost::to_upper(tempStr);
if (tempStr.length() < 10 || tempStr.substr(0, 10) != "BEGIN CTAB") {
std::ostringstream errout;
errout << "BEGIN CTAB line not found on line " << line;
throw FileParseException(errout.str());
}
tempStr = getV3000Line(inStream, line);
boost::to_upper(tempStr);
if (tempStr.size() < 8 || tempStr.substr(0, 7) != "COUNTS ") {
std::ostringstream errout;
errout << "Bad counts line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
std::string trimmed =
boost::trim_copy(tempStr.substr(7, tempStr.length() - 7));
boost::split(splitLine, trimmed, boost::is_any_of(" \t"),
boost::token_compress_on);
if (splitLine.size() < 2) {
std::ostringstream errout;
errout << "Bad counts line : '" << tempStr << "' on line " << line;
throw FileParseException(errout.str());
}
nAtoms = FileParserUtils::toUnsigned(splitLine[0]);
nBonds = FileParserUtils::toUnsigned(splitLine[1]);
conf = new Conformer(nAtoms);
unsigned int nSgroups = 0, n3DConstraints = 0, chiralFlag = 0;
if (splitLine.size() > 2) {
nSgroups = FileParserUtils::toUnsigned(splitLine[2]);
}
if (splitLine.size() > 3) {
n3DConstraints = FileParserUtils::toUnsigned(splitLine[3]);
}
if (splitLine.size() > 4) {
chiralFlag = FileParserUtils::toUnsigned(splitLine[4]);
}
mol->setProp(common_properties::_MolFileChiralFlag, chiralFlag);
if (nAtoms) {
ParseV3000AtomBlock(inStream, line, nAtoms, mol, conf, strictParsing);
}
if (nBonds) {
ParseV3000BondBlock(inStream, line, nBonds, mol, chiralityPossible);
}
tempStr = getV3000Line(inStream, line);
// do link nodes:
boost::to_upper(tempStr);
while (tempStr.length() > 8 && tempStr.substr(0, 8) == "LINKNODE") {
boost::to_upper(tempStr);
// if the line has nothing on it we just ignore it
if (tempStr.size() > 9) {
std::string existing = "";
if (mol->getPropIfPresent(common_properties::molFileLinkNodes,
existing)) {
existing += "|";
}
existing += tempStr.substr(9); // skip the "LINKNODE "
mol->setProp(common_properties::molFileLinkNodes, existing);
}
tempStr = getV3000Line(inStream, line);
}
if (nSgroups) {
boost::to_upper(tempStr);
if (tempStr.length() < 12 || tempStr.substr(0, 12) != "BEGIN SGROUP") {
std::ostringstream errout;
errout << "BEGIN SGROUP line not found on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
} else {
tempStr =
ParseV3000SGroupsBlock(inStream, line, nSgroups, mol, strictParsing);
boost::to_upper(tempStr);
if (tempStr.length() < 10 || tempStr.substr(0, 10) != "END SGROUP") {
std::ostringstream errout;
errout << "END SGROUP line not found on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
} else {
tempStr = getV3000Line(inStream, line);
}
}
}
while (tempStr.length() > 5 && tempStr.substr(0, 5) == "BEGIN") {
if (tempStr.length() > 15 && tempStr.substr(6, 10) == "COLLECTION") {
tempStr = parseEnhancedStereo(inStream, line, mol);
} else {
// skip blocks we don't know how to read
BOOST_LOG(rdWarningLog) << "skipping block at line " << line << ": '"
<< tempStr << "'" << std::endl;
while (tempStr.length() < 3 || tempStr.substr(0, 3) != "END") {
tempStr = getV3000Line(inStream, line);
}
tempStr = getV3000Line(inStream, line);
}
}
if (n3DConstraints) {
BOOST_LOG(rdWarningLog)
<< "3D constraint information in mol block ignored at line " << line
<< std::endl;
boost::to_upper(tempStr);
if (tempStr.length() < 11 || tempStr.substr(0, 11) != "BEGIN OBJ3D") {
std::ostringstream errout;
errout << "BEGIN OBJ3D line not found on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
}
for (unsigned int i = 0; i < n3DConstraints; ++i) {
tempStr = getV3000Line(inStream, line);
}
tempStr = getV3000Line(inStream, line);
boost::to_upper(tempStr);
if (tempStr.length() < 9 || tempStr.substr(0, 9) != "END OBJ3D") {
std::ostringstream errout;
errout << "END OBJ3D line not found on line " << line;
if (strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
} else {
tempStr = getV3000Line(inStream, line);
}
}
boost::to_upper(tempStr);
if (tempStr.length() < 8 || tempStr.substr(0, 8) != "END CTAB") {
if (strictParsing) {
throw FileParseException("END CTAB line not found");
} else {
BOOST_LOG(rdWarningLog) << "END CTAB line not found." << std::endl;
}
}
if (expectMEND) {
tempStr = getLine(inStream);
++line;
if (tempStr[0] == 'M' && tempStr.substr(0, 6) == "M END") {
fileComplete = true;
}
} else {
fileComplete = true;
}
auto is3d = calculate3dFlag(*mol, *conf, chiralityPossible);
conf->set3D(is3d);
mol->addConformer(conf, true);
conf = nullptr;
return fileComplete;
}
bool ParseV2000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
Conformer *&conf, bool &chiralityPossible,
unsigned int &nAtoms, unsigned int &nBonds,
bool strictParsing) {
conf = new Conformer(nAtoms);
if (nAtoms == 0) {
conf->set3D(false);
} else {
ParseMolBlockAtoms(inStream, line, nAtoms, mol, conf, strictParsing);
}
ParseMolBlockBonds(inStream, line, nBonds, mol, chiralityPossible);
auto is3d = calculate3dFlag(*mol, *conf, chiralityPossible);
conf->set3D(is3d);
mol->addConformer(conf, true);
conf = nullptr;
bool fileComplete =
ParseMolBlockProperties(inStream, line, mol, strictParsing);
return fileComplete;
}
void finishMolProcessing(
RWMol *res, bool chiralityPossible,
const RDKit::v2::FileParsers::MolFileParserParams &params) {
if (!res) {
return;
}
res->clearAllAtomBookmarks();
res->clearAllBondBookmarks();
if (params.expandAttachmentPoints) {
MolOps::expandAttachmentPoints(*res);
}
// calculate explicit valence on each atom:
for (auto atom : res->atoms()) {
atom->calcExplicitValence(false);
}
// postprocess mol file flags
ProcessMolProps(res);
// update the chirality and stereo-chemistry
//
// NOTE: we detect the stereochemistry before sanitizing/removing
// hydrogens because the removal of H atoms may actually remove
// the wedged bond from the molecule. This wipes out the only
// sign that chirality ever existed and makes us sad... so first
// perceive chirality, then remove the Hs and sanitize.
//
const Conformer &conf = res->getConformer();
if (chiralityPossible || conf.is3D()) {
if (!conf.is3D()) {
DetectAtomStereoChemistry(*res, &conf);
} else {
res->updatePropertyCache(false);
MolOps::assignChiralTypesFrom3D(*res, conf.getId(), true);
}
}
Atropisomers::detectAtropisomerChirality(*res, &conf);
// now that atom stereochem has been perceived, the wedging
// information is no longer needed, so we clear
// single bond dir flags:
MolOps::clearSingleBondDirFlags(*res);
if (params.sanitize) {
if (params.removeHs) {
// Bond stereo detection must happen before H removal, or
// else we might be removing stereogenic H atoms in double
// bonds (e.g. imines). But before we run stereo detection,
// we need to run mol cleanup so don't have trouble with
// e.g. nitro groups. Sadly, this a;; means we will find
// run both cleanup and ring finding twice (a fast find
// rings in bond stereo detection, and another in
// sanitization's SSSR symmetrization).
unsigned int failedOp = 0;
MolOps::sanitizeMol(*res, failedOp, MolOps::SANITIZE_CLEANUP);
MolOps::detectBondStereochemistry(*res);
MolOps::removeHs(*res, false, false);
} else {
MolOps::sanitizeMol(*res);
MolOps::detectBondStereochemistry(*res);
}
MolOps::assignStereochemistry(*res, true, true, true);
} else {
MolOps::detectBondStereochemistry(*res);
}
if (res->hasProp(common_properties::_NeedsQueryScan)) {
res->clearProp(common_properties::_NeedsQueryScan);
QueryOps::completeMolQueries(res);
}
}
} // namespace FileParserUtils
namespace v2 {
namespace FileParsers {
//------------------------------------------------
//
// Read a molecule from a stream
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMolDataStream(std::istream &inStream,
unsigned int &line,
const MolFileParserParams &params) {
std::string tempStr;
bool fileComplete = false;
bool chiralityPossible = false;
Utils::LocaleSwitcher ls;
// mol name
line++;
tempStr = getLine(inStream);
if (inStream.eof()) {
return nullptr;
}
auto res = std::make_unique<RWMol>();
res->setProp(common_properties::_Name, tempStr);
// info
line++;
tempStr = getLine(inStream);
res->setProp("_MolFileInfo", tempStr);
if (tempStr.length() >= 22) {
std::string dimLabel = tempStr.substr(20, 2);
// Unless labelled as 3D we assume 2D
if (dimLabel == "3d" || dimLabel == "3D") {
res->setProp(common_properties::_3DConf, 1);
}
}
// comments
line++;
tempStr = getLine(inStream);
res->setProp("_MolFileComments", tempStr);
unsigned int nAtoms = 0, nBonds = 0, nLists = 0, chiralFlag = 0, nsText = 0,
nRxnComponents = 0;
int nReactants = 0, nProducts = 0, nIntermediates = 0;
(void)nLists; // read from the file but unused
(void)nsText;
(void)nRxnComponents;
(void)nReactants;
(void)nProducts;
(void)nIntermediates;
// counts line, this is where we really get started
line++;
tempStr = getLine(inStream);
if (tempStr.size() < 6) {
if (res) {
res = nullptr;
}
std::ostringstream errout;
errout << "Counts line too short: '" << tempStr << "' on line" << line;
throw FileParseException(errout.str());
}
unsigned int spos = 0;
// this needs to go into a try block because if the lexical_cast throws an
// exception we want to catch throw a different exception
try {
nAtoms = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
spos = 3;
nBonds = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
spos = 6;
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '" << tempStr.substr(spos, 3)
<< "' to unsigned int on line " << line;
throw FileParseException(errout.str());
}
try {
spos = 6;
if (tempStr.size() >= 9) {
nLists = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 12;
if (tempStr.size() >= spos + 3) {
chiralFlag = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 15;
if (tempStr.size() >= spos + 3) {
nsText = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 18;
if (tempStr.size() >= spos + 3) {
nRxnComponents =
FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 21;
if (tempStr.size() >= spos + 3) {
nReactants = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 24;
if (tempStr.size() >= spos + 3) {
nProducts = FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
spos = 27;
if (tempStr.size() >= spos + 3) {
nIntermediates =
FileParserUtils::toUnsigned(tempStr.substr(spos, 3), true);
}
} catch (boost::bad_lexical_cast &) {
// some SD files (such as some from NCI) lack all the extra information
// on the header line, so ignore problems parsing there.
}
unsigned int ctabVersion = 2000;
if (tempStr.size() > 35) {
if (tempStr.size() < 39 || tempStr[34] != 'V') {
std::ostringstream errout;
errout << "CTAB version string invalid at line " << line;
if (params.strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
} else if (tempStr.substr(34, 5) == "V3000") {
ctabVersion = 3000;
} else if (tempStr.substr(34, 5) != "V2000") {
std::ostringstream errout;
errout << "Unsupported CTAB version: '" << tempStr.substr(34, 5)
<< "' at line " << line;
if (params.strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
}
}
res->setProp(common_properties::_MolFileChiralFlag, chiralFlag);
Conformer *conf = nullptr;
try {
if (ctabVersion == 2000) {
fileComplete = FileParserUtils::ParseV2000CTAB(
&inStream, line, res.get(), conf, chiralityPossible, nAtoms, nBonds,
params.strictParsing);
} else {
if (nAtoms != 0 || nBonds != 0) {
std::ostringstream errout;
errout << "V3000 mol blocks should have 0s in the initial counts line. "
"(line: "
<< line << ")";
if (params.strictParsing) {
throw FileParseException(errout.str());
} else {
BOOST_LOG(rdWarningLog) << errout.str() << std::endl;
}
}
fileComplete = FileParserUtils::ParseV3000CTAB(
&inStream, line, res.get(), conf, chiralityPossible, nAtoms, nBonds,
params.strictParsing);
}
} catch (MolFileUnhandledFeatureException &e) {
// unhandled mol file feature, show an error
res.reset();
delete conf;
conf = nullptr;
BOOST_LOG(rdErrorLog) << " Unhandled CTAB feature: '" << e.what()
<< "'. Molecule skipped." << std::endl;
if (!inStream.eof()) {
tempStr = getLine(inStream);
}
++line;
while (!inStream.eof() && !inStream.fail() &&
tempStr.substr(0, 6) != "M END" && tempStr.substr(0, 4) != "$$$$") {
tempStr = getLine(inStream);
++line;
}
fileComplete = !inStream.eof() || tempStr.substr(0, 6) == "M END" ||
tempStr.substr(0, 4) == "$$$$";
} catch (FileParseException &e) {
// catch our exceptions and throw them back after cleanup
delete conf;
conf = nullptr;
throw e;
}
if (!fileComplete) {
delete conf;
conf = nullptr;
std::ostringstream errout;
errout
<< "Problems encountered parsing Mol data, M END missing around line "
<< line;
throw FileParseException(errout.str());
}
if (res) {
FileParserUtils::finishMolProcessing(res.get(), chiralityPossible, params);
}
return res;
}
//------------------------------------------------
//
// Read a molecule from a string
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMolBlock(const std::string &molBlock,
const MolFileParserParams &params) {
std::istringstream inStream(molBlock);
unsigned int line = 0;
return MolFromMolDataStream(inStream, line, params);
}
//------------------------------------------------
//
// Read a molecule from a file
//
//------------------------------------------------
std::unique_ptr<RWMol> MolFromMolFile(const std::string &fName,
const MolFileParserParams &params) {
std::ifstream inStream(fName.c_str());
if (!inStream || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
if (!inStream.eof()) {
unsigned int line = 0;
return MolFromMolDataStream(inStream, line, params);
} else {
return std::unique_ptr<RWMol>();
}
}
} // namespace FileParsers
} // namespace v2
} // namespace RDKit
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