From af6f07b7feba19e9910a48725b529b1144e4a988 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 15 Jun 2023 11:08:40 +0200
Subject: [PATCH] feat: support for V2000 M CHG lines
---
modules/io/src/mol/sdf_reader.cc | 85 ++++++++++++++++++++++++
modules/io/src/mol/sdf_reader.hh | 7 ++
modules/io/tests/test_io_sdf.py | 7 ++
modules/io/tests/testfiles/sdf/m_chg.sdf | 19 ++++++
4 files changed, 118 insertions(+)
create mode 100644 modules/io/tests/testfiles/sdf/m_chg.sdf
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index ed53e5a0f..a64a46ec9 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -84,6 +84,8 @@ void SDFReader::Import(mol::EntityHandle& ent)
AddAtom(ParseAtom(line, line_num), line_num, ent, true, editor);
} else if (version_ == "V2000" && line_num<=bond_count_+atom_count_+4) {
AddBond(ParseBond(line, line_num), line_num, ent, editor);
+ } else if (version_ == "V2000" && boost::iequals(line.substr(0,6), "M CHG")) {
+ AddCharge(ParseMCharge(line, line_num), line_num, ent, editor);
} else if (boost::iequals(line.substr(0,2), "> ")) {
// parse data items
int data_header_start = line.find('<');
@@ -130,6 +132,7 @@ void SDFReader::ClearState(const boost::filesystem::path& loc)
version_="";
v3000_bond_block_=false;
v3000_atom_block_=false;
+ charges_reset_=false;
}
void SDFReader::NextMolecule()
@@ -141,6 +144,7 @@ void SDFReader::NextMolecule()
version_="";
v3000_bond_block_=false;
v3000_atom_block_=false;
+ charges_reset_=false;
curr_residue_ = ost::mol::ResidueHandle();
curr_chain_ = ost::mol::ChainHandle();
}
@@ -365,6 +369,87 @@ void SDFReader::AddBond(const bond_data& bond_tuple, int line_num, mol::EntityHa
<< s_type << ") ");
}
+
+void SDFReader::ResetCharges()
+// from doc of V2000 Atom Block:
+// > Retained for compatibility with older Ctabs, M CHG and M RAD lines take
+// > precedence.
+// Therefore we must reset all charges of the residue if we encounter an
+// M CHG line.
+{
+ LOG_DEBUG("Resetting all charges to 0.");
+ for (mol::AtomHandle & atom : curr_residue_.GetAtomList()) {
+ atom.SetCharge(0.0);
+ }
+ charges_reset_=true;
+}
+
+
+SDFReader::charge_data SDFReader::ParseMCharge(const String& line, int line_num)
+{
+
+ LOG_TRACE( "line: [" << line << "]" );
+
+ if (!charges_reset_) {
+ ResetCharges();
+ }
+
+ if(line.length()<15 || line.length()>17) {
+ // Handle the case where we have trailing space characters
+ if (line.length()>17 && boost::trim_copy(line.substr(17)) == "") {
+ LOG_DEBUG( "Ignoring trailing space" );
+ }
+ else {
+ String msg="Bad Charge line %d: Not correct number of characters on the"
+ " line: %i (should be between 15 and 17)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
+ }
+
+ String atom_index=line.substr(10,3);
+ String charge=line.substr(14,3);
+
+ return std::make_tuple(atom_index, charge);
+}
+
+ void SDFReader::AddCharge(const charge_data& charge_tuple, int line_num, mol::EntityHandle& ent,
+ mol::XCSEditor& editor)
+{
+ String s_atom_index, s_charge;
+ tie(s_atom_index, s_charge) = charge_tuple;
+
+ int atom_index;
+ Real charge;
+
+ try {
+ atom_index=boost::lexical_cast<int>(boost::trim_copy(s_atom_index));
+ if (atom_index > atom_count_) {
+ String msg="Bad charge line %d: Atom index"
+ " '%d' greater than number of atoms in the molecule (%d).";
+ throw IOException(str(format(msg) % line_num % atom_index % atom_count_));
+ } else if (atom_index < 1) {
+ String msg="Bad charge line %d: Atom index %d < 1.";
+ throw IOException(str(format(msg) % line_num % atom_index));
+ }
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad charge line %d: Can't convert atom index"
+ " '%s' to integral constant.";
+ throw IOException(str(format(msg) % line_num % s_atom_index));
+ }
+
+ try {
+ charge=boost::lexical_cast<Real>(boost::trim_copy(s_charge));
+ } catch(boost::bad_lexical_cast&) {
+ String msg="Bad charge line %d: Can't convert charge"
+ " '%s' to real number.";
+ throw IOException(str(format(msg) % line_num % s_charge));
+ }
+
+ curr_residue_.GetAtomList()[atom_index - 1].SetCharge(charge);
+
+ LOG_DEBUG("Setting charge of atom " << atom_index - 1 << " to " << charge);
+}
+
SDFReader::v3000_line_tokens SDFReader::TokenizeV3000Line(const String& line,
int line_num,
int num_posval)
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index f684a5325..f704462c2 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -47,6 +47,7 @@ public:
private:
typedef std::tuple<int, String, String, String, String, String> atom_data;
typedef std::tuple<String, String, String> bond_data;
+ typedef std::tuple<String, String> charge_data;
typedef std::tuple<std::vector<String>, std::map<String, String>> v3000_line_tokens;
boost::iostreams::filtering_stream<boost::iostreams::input>& GetLine(
@@ -68,6 +69,11 @@ private:
void AddBond(const bond_data& bond_tuple, int line_num, mol::EntityHandle& ent,
mol::XCSEditor& editor);
+ charge_data ParseMCharge(const String& line, int line_num);
+ void AddCharge(const charge_data& charge_tuple, int line_num, mol::EntityHandle& ent,
+ mol::XCSEditor& editor);
+ void ResetCharges();
+
// V3000 methods
v3000_line_tokens TokenizeV3000Line(const String& line, int line_num,
int num_posval);
@@ -94,6 +100,7 @@ private:
String version_;
bool v3000_atom_block_;
bool v3000_bond_block_;
+ bool charges_reset_;
};
}}
diff --git a/modules/io/tests/test_io_sdf.py b/modules/io/tests/test_io_sdf.py
index 735158fc3..5ca35b7fe 100644
--- a/modules/io/tests/test_io_sdf.py
+++ b/modules/io/tests/test_io_sdf.py
@@ -38,6 +38,13 @@ class TestSDF(unittest.TestCase):
ent.FindAtom("00001_Simple Ligand", 1, "6").charge = -4
io.EntityToSDFStr(ent)
+ def test_MChg(self):
+ ent = io.LoadSDF('testfiles/sdf/m_chg.sdf')
+ cl_at = ent.FindAtom("00001_Simple Ligand", 1, "6")
+ self.assertEqual(cl_at.charge, -1)
+ # Charge from atom line is ignored
+ n_at = ent.FindAtom("00001_Simple Ligand", 1, "1")
+ self.assertEqual(n_at.charge, 0)
if __name__== '__main__':
from ost import testutils
diff --git a/modules/io/tests/testfiles/sdf/m_chg.sdf b/modules/io/tests/testfiles/sdf/m_chg.sdf
new file mode 100644
index 000000000..e13bae5a7
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/m_chg.sdf
@@ -0,0 +1,19 @@
+Simple Ligand
+
+ Teststructure
+ 6 6 0 0 1 0 999 V2000
+ 0.0000 0.0000 0.0000 N 0 3 0 0 0 0
+ 1.0000 0.0000 0.0000 C 0 0 0 0 0 0
+ 0.0000 1.0000 0.0000 O 0 0 0 0 0 0
+ 1.0000 1.0000 0.0000 S 0 0 0 0 0 0
+ 2.0000 2.0000 0.0000 C 0 0 0 0 0 0
+ -1.0000 -1.0000 0.0000 Cl 0 0 0 0 0 0
+ 1 2 2 0 0 0
+ 1 3 1 0 0 0
+ 1 6 1 0 0 0
+ 2 4 1 0 0 0
+ 3 4 1 0 0 0
+ 4 5 3 0 0 0
+M CHG 1 6 -1
+M END
+$$$$
--
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