From 1afc41923eaad02607f758da08770fa4b24fe2fa Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Tue, 15 Oct 2024 21:50:13 -0400
Subject: [PATCH] Fix up partial charges -- need to add after setting bonds

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/io/xyzformat.cpp | 25 ++++++++-----------------
 1 file changed, 8 insertions(+), 17 deletions(-)

diff --git a/avogadro/io/xyzformat.cpp b/avogadro/io/xyzformat.cpp
index 21378c9715..023fa5ceda 100644
--- a/avogadro/io/xyzformat.cpp
+++ b/avogadro/io/xyzformat.cpp
@@ -107,7 +107,6 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
       // we can safely assume species and pos are present
       if (tokens[i] == "charge") {
         chargeColumn = column;
-        std::cout << " found charges " << chargeColumn << std::endl;
       } else if (tokens[i] == "force" || tokens[i] == "forces") {
         forceColumn = column;
       } // TODO other properties (velocity, spin, selection, etc.)
@@ -169,18 +168,6 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
     return false;
   }
 
-  // set the charges
-  if (!charges.empty()) {
-    MatrixX chargesMatrix = MatrixX::Zero(mol.atomCount(), 1);
-    for (size_t i = 0; i < charges.size(); ++i) {
-      chargesMatrix(i, 0) = charges[i];
-    }
-    mol.setPartialCharges("From File", chargesMatrix);
-
-    std::cout << "Charges set " << charges.size() << " " << mol.atomCount()
-              << std::endl;
-  }
-
   // Do we have an animation?
   size_t numAtoms2;
   // check if the next frame has the same number of atoms
@@ -249,10 +236,14 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
     mol.perceiveBondOrders();
   }
 
-  // check partial charge types
-  auto types = mol.partialChargeTypes();
-  for (const auto& type : types) {
-    std::cout << "Partial charge type: " << type << std::endl;
+  // have to set the charges after creating bonds
+  // (since modifying bonds invalidates the partial charges)
+  if (!charges.empty()) {
+    MatrixX chargesMatrix = MatrixX::Zero(mol.atomCount(), 1);
+    for (size_t i = 0; i < charges.size(); ++i) {
+      chargesMatrix(i, 0) = charges[i];
+    }
+    mol.setPartialCharges("From File", chargesMatrix);
   }
 
   return true;