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Implement the two deprecations that were planned for the 2020.09 release cycle (#3047)

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* Deprecation: planned removal of .message() and .getMessage() methods

* Deprecation: planned removal of old MolHash code

* document deprecations

* output the diffs when the psql tests fail

* remove .message() from SWIG wrappers

note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway

* typo
This commit is contained in:
Greg Landrum
2020-04-01 14:30:07 +02:00
committed by GitHub
parent cf031c2f7e
commit 5712176605
126 changed files with 1172 additions and 22492 deletions
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82
Code/GraphMol/StructChecker/StructCheckerOptions.cpp
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@@ -93,15 +93,15 @@ static const char
// used in unit test
bool StringToAugmentedAtom(const char *str, AugmentedAtom &aa) {
/*
* The syntax of a augmented atom string is as follows:
*
* <AAString> ::= ['@'|'!@'] <Atom Symbol> [<Charge>]
* {'(' <Bond Symbol> <Atom Symbol> [<Charge>] ')'}.
* Bond symbols and charge descriptors are defined in the symbol tables
* 'bond_to_string' and 'charge_to_string'.
* '@' means central atom is in ring, '!@' means central atom is not in ring,
*omitting means any topography could match.
*/
* The syntax of a augmented atom string is as follows:
*
* <AAString> ::= ['@'|'!@'] <Atom Symbol> [<Charge>]
* {'(' <Bond Symbol> <Atom Symbol> [<Charge>] ')'}.
* Bond symbols and charge descriptors are defined in the symbol tables
* 'bond_to_string' and 'charge_to_string'.
* '@' means central atom is in ring, '!@' means central atom is not in ring,
*omitting means any topography could match.
*/
size_t i;
aa.ShortName = str;
@@ -185,8 +185,8 @@ bool StringToAugmentedAtom(const char *str, AugmentedAtom &aa) {
return false;
}
if (!isalpha(*str)) { /* there must be an atom symbol */
BOOST_LOG(rdErrorLog) << "syntax error '" << str
<< "'\nthere must be an atom symbol.\n";
BOOST_LOG(rdErrorLog)
<< "syntax error '" << str << "'\nthere must be an atom symbol.\n";
return false;
}
@@ -260,10 +260,10 @@ bool StringToAugmentedAtom(const char *str, AugmentedAtom &aa) {
static bool ReadAugmentedAtoms(const std::string &path,
std::vector<AugmentedAtom> &atoms) {
/*
* '*.chk' and '*.aci' files loader
* Only the portion of the strings between the two '"' characters is used,
* other characters are regarded as comments.
*/
* '*.chk' and '*.aci' files loader
* Only the portion of the strings between the two '"' characters is used,
* other characters are regarded as comments.
*/
FILE *fp = fopen(path.c_str(), "r");
if (!fp) {
BOOST_LOG(rdErrorLog) << "could not open file '" << path << "'\n"
@@ -308,20 +308,20 @@ static bool ReadAugmentedAtoms(const std::string &path,
while (s[len] >= ' ' && s[len] != '"') len++;
s[len] = '\0'; // == atom_string
if (!StringToAugmentedAtom(s, atoms[i])) {
BOOST_LOG(rdErrorLog) << "unsuccessful AA parsing of " << i + 1 << " "
<< str << "\n";
BOOST_LOG(rdErrorLog)
<< "unsuccessful AA parsing of " << i + 1 << " " << str << "\n";
fclose(fp);
return false;
}
} else { // incorrect text line
BOOST_LOG(rdErrorLog) << "unsuccessful AA parsing of " << i + 1 << " "
<< str << "\n";
BOOST_LOG(rdErrorLog)
<< "unsuccessful AA parsing of " << i + 1 << " " << str << "\n";
fclose(fp);
return false;
}
} else if (ferror(fp)) {
BOOST_LOG(rdErrorLog) << "unsuccessful AA parsing of " << i + 1 << " "
<< str << "\n";
BOOST_LOG(rdErrorLog)
<< "unsuccessful AA parsing of " << i + 1 << " " << str << "\n";
fclose(fp);
return false;
}
@@ -334,16 +334,16 @@ static bool ReadAAPairs(
const std::string &path,
std::vector<std::pair<AugmentedAtom, AugmentedAtom>> &trans_pairs) {
/*
* '*.trn' file loader
* Reads file and constructs an array of pairs of augmented atom
* descriptions. The first one being the search pattern and the second
* one the target pattern.
* The function expects the number of augmented atom description pairs
* on the first line and the strings corresponding to the data structures
* on the n following lines.
* Only the portion of the strings between the two '"' characters is used,
* other characters are regarded as comments.
*/
* '*.trn' file loader
* Reads file and constructs an array of pairs of augmented atom
* descriptions. The first one being the search pattern and the second
* one the target pattern.
* The function expects the number of augmented atom description pairs
* on the first line and the strings corresponding to the data structures
* on the n following lines.
* Only the portion of the strings between the two '"' characters is used,
* other characters are regarded as comments.
*/
FILE *fp = fopen(path.c_str(), "r");
if (!fp) {
BOOST_LOG(rdErrorLog) << "could not open file '" << path << "'\n"
@@ -389,8 +389,8 @@ static bool ReadAAPairs(
s[len] = '\0'; // == atom_string
if (!StringToAugmentedAtom(s, trans_pairs[i].first)) {
BOOST_LOG(rdErrorLog) << "unsuccessful translation of " << str
<< "\n";
BOOST_LOG(rdErrorLog)
<< "unsuccessful translation of " << str << "\n";
fclose(fp);
return false;
}
@@ -406,8 +406,8 @@ static bool ReadAAPairs(
s[len] = '\0'; // == atom_string
if (!StringToAugmentedAtom(s, trans_pairs[i].second)) {
BOOST_LOG(rdErrorLog) << "unsuccessful translation of " << str
<< "\n";
BOOST_LOG(rdErrorLog)
<< "unsuccessful translation of " << str << "\n";
fclose(fp);
return false;
}
@@ -597,9 +597,9 @@ bool StructCheckerOptions::loadTautomerData(const std::string &path) {
if (str.length() >= 4 && 0 == strcmp(str.c_str(), "$MOL")) {
RWMol *molTo = MolDataStreamToMol(in, line);
if (!molTo) {
BOOST_LOG(rdErrorLog) << "RD-file corrupted. " << path
<< " line " << line
<< "\n"; // log error
BOOST_LOG(rdErrorLog)
<< "RD-file corrupted. " << path << " line " << line
<< "\n"; // log error
return false;
}
// ?? MakeHydrogensImplicit()
@@ -612,8 +612,8 @@ bool StructCheckerOptions::loadTautomerData(const std::string &path) {
}
} while (!in.eof());
} else {
BOOST_LOG(rdErrorLog) << "unsupported file type. " << path
<< "\n"; // log error
BOOST_LOG(rdErrorLog)
<< "unsupported file type. " << path << "\n"; // log error
return false;
}
} catch (std::exception &ex) {
@@ -661,7 +661,7 @@ void StructCheckerOptions::parseTautomerData(
}
//--------------------------------------------------------------------------
bool loadChargeDataTables(const std::string& path) {
bool loadChargeDataTables(const std::string &path) {
// TODO: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
RDUNUSED_PARAM(path);
/*