sdf mol writer chg impl

CueMol · Sep 15, 2024 · 99732a7 · 99732a7
1 parent d3fafb4
commit 99732a7
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Showing 7 changed files with 92 additions and 15 deletions.
diff --git a/src/modules/importers/SDFMolReader.cpp b/src/modules/importers/SDFMolReader.cpp
@@ -144,7 +144,7 @@ void SDFMolReader::readCharge(const LString &str)
             continue;
         }
         auto aid = iter->second;
-        m_pMol->getAtom(aid)->setAtomPropReal("charge", ichg);
+        m_pMol->getAtom(aid)->setAtomPropReal("formal_charge", ichg);
 
         MB_DPRINTLN("SDFMolReader> atom %d set charge %d", aid, ichg);
     }

diff --git a/src/modules/importers/SDFMolWriter.cpp b/src/modules/importers/SDFMolWriter.cpp
@@ -8,6 +8,7 @@
 #include <modules/molstr/MolResidue.hpp>
 #include <modules/molstr/ResidIterator.hpp>
 #include <qlib/PrintStream.hpp>
+#include <algorithm>
 
 namespace importers {
 
@@ -138,6 +139,7 @@ void SDFMolWriter::writeResidue(const molstr::MolResiduePtr &presid,
     //   15.0880   10.7980   23.5470  N 0  3  0  4  0  4
     int index = 1;
     std::map<int, int> idmap;
+    std::map<int, int> chgmap;
     // for (auto iter = presid->atomBegin(); iter != presid->atomEnd(); ++iter, ++index) {
     for (int aid: atomset) {
         // auto aid = iter->second;
@@ -148,6 +150,17 @@ void SDFMolWriter::writeResidue(const molstr::MolResiduePtr &presid,
         // prs.formatln("%d", index);
         prs.formatln("%10.4f%10.4f%10.4f%3s  0  0  0  0  0  0  0  0  0  0  0  0",
                      pos.x(), pos.y(), pos.z(), elem.c_str());
+        if (patom->hasAtomProp("formal_charge")) {
+            auto typenm = patom->getPropTypeName("formal_charge");
+            if (typenm.equals("real")) {
+                double charge  = patom->getAtomPropReal("formal_charge");
+                MB_DPRINTLN("atom %d charge %f (%d)", aid, charge, int(charge));
+                chgmap.insert(std::pair<int, int>(aid, int(charge)));
+            }
+            else {
+                LOG_DPRINTLN("Warning: invalid atom charge type %s ignored", typenm.c_str());
+            }
+        }
         ++index;
     }
 
@@ -178,10 +191,38 @@ void SDFMolWriter::writeResidue(const molstr::MolResiduePtr &presid,
         prs.formatln("%3d%3d%3d  0", id1, id2, itype);
     }
 
+    writeChgLines(chgmap, prs);
+
     prs.println("M  END");
     prs.println("$$$$");
 
 }
 
+void SDFMolWriter::writeChgLines(const std::map<int, int> &chgmap,
+                                 qlib::PrintStream &prs)
+{
+    int nchg = chgmap.size();
+    if (nchg==0) {
+        return;
+    }
+
+    int nchg_lines = int(nchg / 8) + 1;
+    auto iter = chgmap.begin();
+    for (int i=0; i<nchg_lines; ++i) {
+        int nn8 = std::min(nchg, 8);
+        prs.format("M  CHG% 3d", nn8);
+        for (int j=0; j<8; ++j) {
+            if (iter == chgmap.end()) {
+                break;
+            }
+            const int aid = (iter->first) + 1;
+            const int chg = iter->second;
+            prs.format("% 4d% 4d", aid, chg);
+            ++iter;
+            --nchg;
+        }
+        prs.formatln("");
+    }
+}
 
 }  // namespace importers
diff --git a/src/modules/importers/SDFMolWriter.hpp b/src/modules/importers/SDFMolWriter.hpp
@@ -78,6 +78,8 @@ class IMPORTERS_API SDFMolWriter : public qsys::ObjWriter
     using ResBondMap = std::map<LString, std::deque<int>>;
     ResBondMap m_resBondMap;
     void writeResidue(const molstr::MolResiduePtr &presid, qlib::PrintStream &prs);
+
+    void writeChgLines(const std::map<int, int> &chgmap,qlib::PrintStream &prs);
 };
 
 }  // namespace importers
diff --git a/src/modules/molstr/MolAtom.hpp b/src/modules/molstr/MolAtom.hpp
@@ -285,6 +285,9 @@ namespace molstr {
 */
   public:
 
+    bool hasAtomProp(const LString &propnm) const {
+        return hasDynProp(propnm);
+    }
     bool getAtomProp(const LString &propnm, qlib::LVariant &presult) const {
       return getDynProp(propnm, presult);
     }

diff --git a/src/qlib/LPropContainer.cpp b/src/qlib/LPropContainer.cpp
@@ -16,6 +16,13 @@ LDynPropContainer::~LDynPropContainer()
 {
 }
 
+bool LDynPropContainer::hasDynProp(const LString &propnm) const
+{
+    DynPropTab::const_iterator i = m_props.find(propnm);
+    if (m_props.end()==i)
+        return false; // not found!!
+    return true;
+}
 
 bool LDynPropContainer::getDynProp(const LString &propnm, qlib::LVariant &presult) const
 {

diff --git a/src/qlib/LPropContainer.hpp b/src/qlib/LPropContainer.hpp
@@ -32,6 +32,7 @@ namespace qlib {
 
   public:
 
+    bool hasDynProp(const LString &propnm) const;
     bool getDynProp(const LString &propnm, qlib::LVariant &presult) const;
     bool setDynProp(const LString &propnm, const qlib::LVariant &pvalue);
     bool removeDynProp(const LString &propnm);

diff --git a/tests/importers_tests/test_sdf_reader.py b/tests/importers_tests/test_sdf_reader.py
@@ -23,45 +23,68 @@ def test_sdf_reader(test_data_path):
     assert nbonds == 40
 
 
-def test_sdf_reader_chg(test_data_path):
+@pytest.fixture
+def mol_from_sdf(test_data_path):
     svc = cuemol.getService("StreamManager")
     reader = svc.createHandler("sdf", 0)
-    print(f"{reader=}")
-
-    test_sdf_file = test_data_path / "test_chg1.sdf"
+    test_sdf_file = test_data_path / "test1.sdf"
     reader.setPath(str(test_sdf_file))
     obj = reader.createDefaultObj()
     reader.attach(obj)
     reader.read()
     reader.detach()
+    return obj
 
 
-@pytest.fixture
-def mol_from_sdf(test_data_path):
+def test_sdf_writer(mol_from_sdf, tmp_path):
+    svc = cuemol.getService("StreamManager")
+    writer = svc.createHandler("sdf", 1)
+    print(f"{writer=}")
+
+    out_file = tmp_path / "test.sdf"
+    writer.setPath(str(out_file))
+    writer.attach(mol_from_sdf)
+    writer.write()
+    writer.detach()
+
+    with out_file.open() as f:
+        result = f.readlines()
+        # result = f.read()
+
+    assert len(result) == 83
+    assert result[3].rstrip() == " 37 40  0  0  0  0  0  0  0  0999 V2000"
+    assert result[81].rstrip() == "M  END"
+    assert result[82].rstrip() == "$$$$"
+
+
+def test_sdf_chg(test_data_path, tmp_path):
     svc = cuemol.getService("StreamManager")
     reader = svc.createHandler("sdf", 0)
-    test_sdf_file = test_data_path / "test1.sdf"
+    print(f"{reader=}")
+
+    test_sdf_file = test_data_path / "test_chg1.sdf"
     reader.setPath(str(test_sdf_file))
     obj = reader.createDefaultObj()
     reader.attach(obj)
     reader.read()
     reader.detach()
-    return obj
 
+    ###
 
-def test_sdf_writer(mol_from_sdf, tmp_path):
-    svc = cuemol.getService("StreamManager")
     writer = svc.createHandler("sdf", 1)
     print(f"{writer=}")
 
     out_file = tmp_path / "test.sdf"
     writer.setPath(str(out_file))
-    writer.attach(mol_from_sdf)
+    writer.attach(obj)
     writer.write()
     writer.detach()
 
     with out_file.open() as f:
         result = f.readlines()
-        # result = f.read()
-    for i in result:
-        print(i.rstrip())
+
+    assert len(result) == 128
+    assert result[3].rstrip() == " 59 62  0  0  0  0  0  0  0  0999 V2000"
+    assert result[125].rstrip() == "M  CHG  1  17   1"
+    assert result[126].rstrip() == "M  END"
+    assert result[127].rstrip() == "$$$$"