From 8cee0b7a560c0206cb99e76d0fb475432de5de93 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 15 Jun 2023 08:56:54 +0200
Subject: [PATCH] fix: write charge in SDF writer
---
modules/io/src/mol/sdf_writer.cc | 25 ++++++++++++++++++++++++-
modules/io/tests/test_io_sdf.py | 22 ++++++++++++++++++++++
2 files changed, 46 insertions(+), 1 deletion(-)
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 8deaf9a78..e39444d0c 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -50,7 +50,12 @@ namespace {
<< format("%10.4f") % atom.GetPos()[1]
<< format("%10.4f ") % atom.GetPos()[2]
<< format("%-3s") % SDFAtomWriter::FormatEle(atom.GetElement())
- << " 0 0 0 0 0 0"
+ << " 0" // Mass difference
+ << format("%-3s") % SDFAtomWriter::FormatCharge(atom.GetCharge()) // Charge
+ << " 0" // Atom stereo parity
+ << " 0" // Hydrogen count + 1
+ << " 0" // Stereo care box
+ << " 0" // Valence
<< std::endl;
return true;
}
@@ -66,6 +71,24 @@ namespace {
}
return return_ele;
}
+
+ static String FormatCharge(const Real& chg) {
+ // Format charge according to https://doi.org/10.1021/ci00007a012
+ // 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1,
+ // 4 doublet (A), 5 = -1, 6 = -2, 7 = -3
+ // Doublet means radical. This function would never return 4.
+ if (chg == 0) {
+ return " 0";
+ }
+ else if (abs(chg) > 3) {
+ String msg = "SDF format only supports charges from -3 to +3, not %g";
+ throw IOException(str(format(msg) % chg));
+ }
+ else {
+ Real chg_sdf = 4 - chg;
+ return str(format("%3.0f") % chg_sdf);
+ }
+ }
private:
std::ostream& ostr_;
std::map<long, int>& atom_indices_;
diff --git a/modules/io/tests/test_io_sdf.py b/modules/io/tests/test_io_sdf.py
index 718ac0691..735158fc3 100644
--- a/modules/io/tests/test_io_sdf.py
+++ b/modules/io/tests/test_io_sdf.py
@@ -16,6 +16,28 @@ class TestSDF(unittest.TestCase):
ent = io.LoadSDF('testfiles/sdf/6d5w_rank1_crlf.sdf.gz')
self.assertEqual(len(ent.atoms), 21)
self.assertEqual(len(ent.bonds), 24)
+
+ def test_Charge(self):
+ ent = io.LoadSDF('testfiles/sdf/simple.sdf')
+ self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, 0)
+
+ # Write and read charges properly
+ for chg in range(-3, 4):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = chg
+ sdf_str = io.EntityToSDFStr(ent)
+ ent = io.SDFStrToEntity(sdf_str)
+ self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, chg)
+
+ # Only -3 to +3 is supported
+ # If M CHG is implemented the following tests can be removed
+ with self.assertRaises(Exception):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = 4
+ io.EntityToSDFStr(ent)
+
+ with self.assertRaises(Exception):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = -4
+ io.EntityToSDFStr(ent)
+
if __name__== '__main__':
from ost import testutils
--
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