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//
// Copyright (C) 2016 Novartis Institutes for BioMedical Research
//
// @@ 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 <map>
#include "StructChecker.h"
namespace RDKit {
namespace StructureCheck {
static const char* flags[] = {
"BAD_MOLECULE",
"ALIAS_CONVERSION_FAILED",
"STEREO_ERROR",
"STEREO_FORCED_BAD",
"ATOM_CLASH",
"ATOM_CHECK_FAILED",
"SIZE_CHECK_FAILED",
"", // reserved error = 0x0080,
"TRANSFORMED",
"FRAGMENTS_FOUND",
"EITHER_WARNING",
"DUBIOUS_STEREO_REMOVED",
"RECHARGED",
"STEREO_TRANSFORMED",
"TEMPLATE_TRANSFORMED",
"TAUTOMER_TRANSFORMED",
};
// Converts structure property flags to a comma seperated string
std::string StructChecker::StructureFlagsToString(unsigned f) {
std::string s;
for (unsigned bit = 0; bit < 16; bit++) {
if (0 != (f & (1 << bit))) {
if (!s.empty()) s += ",";
s += flags[bit];
}
}
return s;
}
// Converts a comma seperated string to a StructureFlag unsigned integer
class FMap : public std::map<std::string, unsigned> {
public:
FMap() {
for (unsigned bit = 0; bit < 16; bit++)
if (*flags[bit]) (*this)[std::string(flags[bit])] = (1 << bit);
}
};
unsigned StructChecker::StringToStructureFlags(const std::string& str) {
static const FMap fmap; // map name string to StructureFlags enum value
unsigned int f = 0;
const char* token = str.c_str();
while (*token) {
while (*token && *token <= ' ') // skip whitespaces (<tab>|<space>...)
token++;
unsigned len = 0;
while (token[len] && !(token[len] == ',' || token[len] <= ' ')) len++;
if (0 == len) continue;
std::string name(token, len);
auto it = fmap.find(name);
if (fmap.end() != it) f |= it->second;
while (token[len] &&
(token[len] == ',' || token[len] <= ' ')) // skip delimeter
len++;
token += len;
}
return f;
// there is no way to return syntax error in input string
}
} // namespace StructureCheck
} // namespace RDKit
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