Add support for parsing PubChem MMFF94 partial charges

Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Oct 31, 2024 · 15efe67 · 15efe67
1 parent 78e206c
commit 15efe67
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Showing 3 changed files with 25 additions and 4 deletions.
diff --git a/avogadro/io/fileformatmanager.cpp b/avogadro/io/fileformatmanager.cpp
@@ -294,6 +294,7 @@ FileFormatManager::FileFormatManager()
   addFormat(new OutcarFormat);
   addFormat(new PdbFormat);
   addFormat(new PoscarFormat);
+  addFormat(new SdfFormat);
   addFormat(new TrrFormat);
   addFormat(new TurbomoleFormat);
   addFormat(new XyzFormat);

diff --git a/avogadro/io/mdlformat.cpp b/avogadro/io/mdlformat.cpp
@@ -40,6 +40,25 @@ MdlFormat::MdlFormat() {}
 
 MdlFormat::~MdlFormat() {}
 
+void handlePartialCharges(Core::Molecule& mol, std::string data)
+{
+  // the string starts with the number of charges
+  // then atom index  charge
+  MatrixX charges(mol.atomCount(), 1);
+  std::istringstream iss(data);
+  size_t numCharges;
+  iss >> numCharges;
+  for (size_t i = 0; i < numCharges; ++i) {
+    size_t index;
+    Real charge;
+    iss >> index >> charge;
+    // prints with atom index 1, not zero
+    charges(index - 1, 0) = charge;
+  }
+
+  mol.setPartialCharges("MMFF94", charges);
+}
+
 bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
 {
   string buffer;
@@ -208,7 +227,11 @@ bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
       return true;
     if (inValue) {
       if (buffer.empty() && dataName.length() > 0) {
-        mol.setData(dataName, dataValue);
+        // check for partial charges
+        if (dataName == "PUBCHEM_MMFF94_PARTIAL_CHARGES")
+          handlePartialCharges(mol, dataValue);
+        else
+          mol.setData(dataName, dataValue);
         dataName.clear();
         dataValue.clear();
         inValue = false;

diff --git a/avogadro/io/sdfformat.h b/avogadro/io/sdfformat.h
@@ -56,9 +56,6 @@ class AVOGADROIO_EXPORT SdfFormat : public MdlFormat
 
   bool read(std::istream& in, Core::Molecule& molecule) override;
   bool write(std::ostream& out, const Core::Molecule& molecule) override;
-
-protected:
-  bool m_writeProperties = true;
 };
 
 } // namespace Io