diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 45b6aeca15ae479a8eea927407744ace12edc257..b45c8ac4639148a2f1b114c2c1da36452b0c9b6e 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -72,9 +72,9 @@ void SDFReader::Import(mol::EntityHandle& ent)
if (line_num<=4) {
ParseHeader(line, line_num, ent, editor);
- } else if (line_num<=atom_count_+4) {
+ } else if (version_ == "V2000" && line_num<=atom_count_+4) {
AddAtom(ParseAtom(line, line_num), line_num, ent, true, editor);
- } else if (line_num<=bond_count_+atom_count_+4) {
+ } else if (version_ == "V2000" && line_num<=bond_count_+atom_count_+4) {
AddBond(ParseBond(line, line_num), line_num, ent, editor);
} else if (boost::iequals(line.substr(0,2), "> ")) {
// parse data items
@@ -96,6 +96,8 @@ void SDFReader::Import(mol::EntityHandle& ent)
} else if (boost::iequals(line, "$$$$")) {
LOG_VERBOSE("MOLECULE " << curr_chain_.GetName() << " (" << chain_count_ << ") added.")
NextMolecule();
+ } else if (version_ == "V3000") {
+ ProcessV3000Line(line, ent, editor);
}
}
@@ -117,6 +119,9 @@ void SDFReader::ClearState(const boost::filesystem::path& loc)
atom_count_=0;
bond_count_=0;
line_num=0;
+ version_="";
+ v3000_bond_block_=false;
+ v3000_atom_block_=false;
}
void SDFReader::NextMolecule()
@@ -125,12 +130,15 @@ void SDFReader::NextMolecule()
atom_count_=0;
bond_count_=0;
line_num=0;
+ version_="";
+ v3000_bond_block_=false;
+ v3000_atom_block_=false;
curr_residue_ = ost::mol::ResidueHandle();
curr_chain_ = ost::mol::ChainHandle();
}
void SDFReader::ParseHeader(const String& line, int line_num,
- mol::EntityHandle& ent, mol::XCSEditor& editor)
+ mol::EntityHandle& ent, mol::XCSEditor& editor)
{
LOG_TRACE( "line: [" << line << "]" );
format chain_fmter("%05i_%s");
@@ -165,31 +173,40 @@ void SDFReader::ParseHeader(const String& line, int line_num,
throw IOException(str(format(msg) % line_num % line.length()));
}
String version_str=line.substr(34, 5);
- if (version_str != "V2000") {
+ if (version_str == "V2000" || version_str == "V3000") {
+ version_=version_str;
+ }
+ else {
String msg="Unsupported SDF version: %s.";
throw IOException(str(format(msg) % version_str));
}
+ // Counts will be overridden in V3000
String s_anum=line.substr(0,3);
- try {
- atom_count_=boost::lexical_cast<int>(boost::trim_copy(s_anum));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad counts line %d: Can't convert number of atoms"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_anum));
- }
String s_bnum=line.substr(3,3);
- try {
- bond_count_=boost::lexical_cast<int>(boost::trim_copy(s_bnum));
- } catch(boost::bad_lexical_cast&) {
- String msg="Bad counts line %d: Can't convert number of bonds"
- " '%s' to integral constant.";
- throw IOException(str(format(msg) % line_num % s_bnum));
- }
+ SetCounts(s_anum, s_bnum, line_num);
break;
}
}
}
+void SDFReader::SetCounts(const String& anum, const String bnum, int line_num)
+{
+ try {
+ atom_count_=boost::lexical_cast<int>(boost::trim_copy(anum));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad counts line %d: Can't convert number of atoms"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % anum));
+ }
+ try {
+ bond_count_=boost::lexical_cast<int>(boost::trim_copy(bnum));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad counts line %d: Can't convert number of bonds"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % bnum));
+ }
+}
+
SDFReader::atom_data SDFReader::ParseAtom(const String& line, int line_num)
{
@@ -217,7 +234,7 @@ SDFReader::atom_data SDFReader::ParseAtom(const String& line, int line_num)
}
void SDFReader::AddAtom(const atom_data& atom_tuple, int line_num, mol::EntityHandle& ent,
- bool hetatm, mol::XCSEditor& editor)
+ bool hetatm, mol::XCSEditor& editor)
{
int anum;
String s_posx, s_posy, s_posz, s_ele, s_charge;
@@ -295,7 +312,7 @@ SDFReader::bond_data SDFReader::ParseBond(const String& line, int line_num)
}
void SDFReader::AddBond(const bond_data& bond_tuple, int line_num, mol::EntityHandle& ent,
- mol::XCSEditor& editor)
+ mol::XCSEditor& editor)
{
String s_first_name, s_second_name, s_type;
tie(s_first_name, s_second_name, s_type) = bond_tuple;
@@ -340,4 +357,219 @@ void SDFReader::AddBond(const bond_data& bond_tuple, int line_num, mol::EntityHa
<< s_type << ") ");
}
+SDFReader::v3000_line_tokens SDFReader::TokenizeV3000Line(const String& line,
+ int line_num,
+ int num_posval)
+// Read whitespace-separated tokens from a V3000 line.
+// Tokens can be separated by any amount of whitespace.
+// The function is guaranteed to return exactly num_posval positional elements,
+// or throws an error. It returns any number of keyword elements with only
+// syntax checks (ie no checks if the keywords are correct, only well-formed).
+{
+ std::istringstream v30_stream(line);
+ std::vector<String> positional;
+ std::map<String, String> keywords;
+ String token;
+ bool keywords_reached = false;
+ size_t kw_equal_pos;
+ positional.reserve(num_posval);
+
+ while (v30_stream.tellg() != -1) {
+ std::getline(v30_stream, token, ' ');
+ if (token.empty()) {
+ continue;
+ }
+ kw_equal_pos = token.find('=');
+ if (kw_equal_pos != String::npos) {
+ keywords_reached = true;
+ }
+ if (keywords_reached) {
+ // Token can contain a list in round brackets
+ // We don't use them in OST so no fancy parsing, just capture them
+ // as a string keyword
+ if (token.find('(') == kw_equal_pos + 1) {
+ // Search for the closing bracket
+ while (token.find(')') == String::npos) {
+ String next_token;
+ std::getline(v30_stream, next_token, ' ');
+ token = token + " " + next_token;
+ }
+ }
+
+ // Check if keyword is well formed
+ if (token.size() < 3 // too short
+ || kw_equal_pos == String::npos // no =
+ || kw_equal_pos == 0 // no key (starts with =)
+ || kw_equal_pos == token.size() - 1 // no value (ends with =)
+ ) {
+ String msg="Bad V3000 keyword on line %d: '%s'.";
+ throw IOException(str(format(msg) % line_num % token));
+ }
+ String key = token.substr(0, kw_equal_pos);
+ String value = token.substr(kw_equal_pos + 1);
+ keywords.insert({key, value});
+ }
+ else {
+ positional.push_back(token);
+ }
+ }
+
+ int obtained_posval = positional.size();
+ if (obtained_posval != num_posval) {
+ String msg="Bad V3000 line %d: expected %d positional values, got %d.";
+ throw IOException(str(format(msg) % line_num % num_posval %
+ obtained_posval));
+ }
+
+ return std::make_tuple(positional, keywords);
+}
+
+String SDFReader::CleanupV3000Line(const String& line)
+// String cleanup and aggregation for V3000
+// Return a string with no "M V30 " and not ending with -
+{
+ String v30_line = line;
+ if (v30_line.substr(0, 7) != "M V30 ") {
+ String msg="Bad V3000 line %d: starts with '%s'.";
+ throw IOException(str(format(msg) % line_num % line.substr(0, 6)));
+ }
+
+ // Handle line continuation character -
+ while (v30_line.find("-") == v30_line.length()-1) {
+ // Read and append the next line
+ String next_line;
+ std::getline(in_,next_line);
+ ++line_num;
+ // std::getline removes EOL character but may leave a DOS CR (\r) in Unix
+ size_t cr_pos = next_line.find("\r");
+ if (cr_pos != String::npos) {
+ LOG_TRACE( "Remove CR@" << cr_pos);
+ next_line.erase(cr_pos);
+ }
+ // Ensure we have a valid line
+ if (next_line.substr(0, 7) != "M V30 ") {
+ String msg="Bad V3000 line %d: starts with '%s'.";
+ throw IOException(str(format(msg) % line_num % next_line.substr(0, 6)));
+ }
+ // All clear, add data
+ v30_line = v30_line.erase(v30_line.find("-")) + next_line.substr(7);
+ LOG_TRACE( "V3000 line: [" << v30_line << "]" );
+ }
+
+ // Cleanup the line
+ return v30_line.substr(7); // We previously ensured it starts with M V30
+}
+
+SDFReader::atom_data SDFReader::ParseV3000Atom(const String& line, int line_num)
+{
+ v3000_line_tokens tokens = TokenizeV3000Line(line, line_num, 6);
+ std::vector<String> posval;
+ std::map<String, String> keywords;
+ tie(posval, keywords) = tokens;
+
+ String s_anum = posval[0];
+ String atype = posval[1];
+ String posx = posval[2];
+ String posy = posval[3];
+ String posz = posval[4];
+
+ String chg;
+ try {
+ chg = keywords.at("CHG");
+ } catch(std::out_of_range&) {
+ chg = "0";
+ }
+
+ int anum;
+ try {
+ anum=boost::lexical_cast<int>(boost::trim_copy(s_anum));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad atom index '%s' on line %d.";
+ throw IOException(str(format(msg) % s_anum % line_num));
+ }
+
+ return std::make_tuple(anum, posx, posy, posz, atype, chg);
+}
+
+SDFReader::bond_data SDFReader::ParseV3000Bond(const String& line, int line_num)
+{
+ v3000_line_tokens tokens = TokenizeV3000Line(line, line_num, 4);
+ std::vector<String> posval;
+ tie(posval, std::ignore) = tokens;
+
+ String btype = posval[1];
+ String s_first_name = posval[2];
+ String s_second_name = posval[3];
+
+ return std::make_tuple(s_first_name, s_second_name, btype);
+}
+
+std::tuple<String, String> SDFReader::ParseV3000Counts(const String& line, int line_num)
+{
+ v3000_line_tokens tokens = TokenizeV3000Line(line, line_num, 5);
+ std::vector<String> posval;
+ tie(posval, std::ignore) = tokens;
+
+ String anum = posval[0];
+ String bnum = posval[1];
+
+ return std::make_tuple(anum, bnum);
+}
+
+void SDFReader::VerifyV3000Counts()
+{
+ int actual_atom_count = curr_residue_.GetAtomCount();
+ int actual_bond_count = curr_residue_.GetBondCount();
+ if (actual_atom_count != atom_count_) {
+ String msg="Bad counts for molecule ending on line %d: "
+ "expected %d atoms, got %d.";
+ throw IOException(str(format(msg) % line_num % atom_count_ %
+ actual_atom_count));
+ }
+ if (actual_bond_count != bond_count_) {
+ String msg="Bad counts for molecule ending on line %d: "
+ "expected %d bonds, got %d.";
+ throw IOException(str(format(msg) % line_num % bond_count_ %
+ actual_bond_count));
+ }
+}
+
+void SDFReader::ProcessV3000Line(const String& line,
+ mol::EntityHandle& ent,
+ mol::XCSEditor& editor)
+{
+ if (line.substr(0, 6) == "M END") {
+ VerifyV3000Counts();
+ return;
+ }
+ String v30_line = CleanupV3000Line(line);
+
+ if (v30_line.substr(0, 6) == "COUNTS") {
+ String anum, bnum;
+ std::tie(anum, bnum) = ParseV3000Counts(v30_line.substr(7), line_num);
+ SetCounts(anum, bnum, line_num);
+ }
+ else if (v30_line.substr(0, 10) == "BEGIN ATOM") {
+ v3000_atom_block_=true;
+ }
+ else if (v30_line.substr(0, 8) == "END ATOM") {
+ v3000_atom_block_=false;
+ }
+ else if (v30_line.substr(0, 10) == "BEGIN BOND") {
+ v3000_bond_block_=true;
+ }
+ else if (v30_line.substr(0, 8) == "END BOND") {
+ v3000_bond_block_=false;
+ }
+ else if (v3000_atom_block_) {
+ AddAtom(ParseV3000Atom(v30_line, line_num), line_num, ent, true, editor);
+ }
+ else if (v3000_bond_block_) {
+ AddBond(ParseV3000Bond(v30_line, line_num), line_num, ent, editor);
+ }
+ else {
+ LOG_TRACE( "ignoring line: [" << v30_line << "]" );
+ }
+}
+
}}
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index 7863fb7840fda692e60fa5e3a9c6cbc09e396953..ad8a6fff86954fbf5897090201fdda07284e3eb1 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -47,20 +47,33 @@ public:
private:
typedef std::tuple<int, String, String, String, String, String> atom_data;
typedef std::tuple<String, String, String> bond_data;
+ typedef std::tuple<std::vector<String>, std::map<String, String>> v3000_line_tokens;
void ClearState(const boost::filesystem::path& loc);
void NextMolecule();
void ParseHeader(const String& line, int line_num, mol::EntityHandle& ent,
mol::XCSEditor& editor);
+ void SetCounts(const String& anum, const String bnum, int line_num);
+ atom_data ParseAtom(const String& line, int line_num);
void AddAtom(const atom_data& atom_tuple, int line_num, mol::EntityHandle& ent,
bool hetatm, mol::XCSEditor& editor);
- atom_data ParseAtom(const String& line, int line_num);
+ bond_data ParseBond(const String& line, int line_num);
void AddBond(const bond_data& bond_tuple, int line_num, mol::EntityHandle& ent,
mol::XCSEditor& editor);
- bond_data ParseBond(const String& line, int line_num);
+
+ // V3000 methods
+ v3000_line_tokens TokenizeV3000Line(const String& line, int line_num,
+ int num_posval);
+ String CleanupV3000Line(const String& line);
+ void ProcessV3000Line(const String& line, mol::EntityHandle& ent,
+ mol::XCSEditor& editor);
+ atom_data ParseV3000Atom(const String& line, int line_num);
+ bond_data ParseV3000Bond(const String& line, int line_num);
+ std::tuple<String, String> ParseV3000Counts(const String& line, int line_num);
+ void VerifyV3000Counts();
String curr_chain_name_;
mol::ResidueKey curr_res_key_;
@@ -74,6 +87,9 @@ private:
boost::filesystem::ifstream infile_;
std::istream& instream_;
boost::iostreams::filtering_stream<boost::iostreams::input> in_;
+ String version_;
+ bool v3000_atom_block_;
+ bool v3000_bond_block_;
};
}}