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Enhance PDB File Import to Support Trajectory Data in Avogadro #1659

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Enhance PDB File Import to Support Trajectory Data in Avogadro #1659

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19 changes: 10 additions & 9 deletions avogadro/io/pdbformat.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -58,14 +58,12 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)

while (getline(in, buffer)) { // Read Each line one by one

if (startsWith(buffer, "ENDMDL")) {
if (coordSet == 0) {
mol.setCoordinate3d(mol.atomPositions3d(), coordSet++);
positions.reserve(mol.atomCount());
} else {
mol.setCoordinate3d(positions, coordSet++);
positions.clear();
}
if (startsWith(buffer, "ENDMDL")) {
// Ensure positions array is not empty before creating a new frame
if (!positions.empty()) {
mol.setCoordinate3d(positions, coordSet++);
positions.clear(); // Clear positions after adding them as a frame
}
}

// e.g. CRYST1 4.912 4.912 6.696 90.00 90.00 120.00 P1 1
Expand Down Expand Up @@ -245,7 +243,10 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
}
}
} // End while loop

if (!positions.empty()) {
// This handles the last set of positions if the file doesn't end with ENDMDL
mol.setCoordinate3d(positions, coordSet);
}
int count = mol.coordinate3dCount() ? mol.coordinate3dCount() : 1;
for (int c = 0; c < count; ++c) {
for (char l : altLocs) {
Expand Down