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Fix panic if bond refers to missing atoms #25

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Fix panic if bond refers to missing atoms #25

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31 changes: 21 additions & 10 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -344,16 +344,27 @@ impl PDBFile {
for line in self.lines.iter() {
if line.starts_with("CONECT") {
// Extract ID of center atom
let center_index = *atom_id_to_index.get(&parse_number(&line[6..11])?).unwrap();
// Iterate over atom IDs bonded to center atom
for i in (11..31).step_by(5) {
match &parse_number(&line[i..i+5]) {
Ok(bonded_id) => bonds.push(
(center_index, *atom_id_to_index.get(bonded_id).unwrap())
),
// String is empty -> no further IDs
Err(_) => break
};
let center_index = atom_id_to_index.get(&parse_number(&line[6..11])?);
match center_index {
None => continue, // Atom ID is not in the AtomArray (probably removed altloc)
Some(center_index) => {
// Iterate over atom IDs bonded to center atom
for i in (11..31).step_by(5) {
match &parse_number(&line[i..i+5]) {
Ok(bonded_id) => {
let bonded_index = atom_id_to_index.get(bonded_id);
match bonded_index {
None => continue, // Atom ID is not in the AtomArray
Some(bonded_index) => {
bonds.push((*center_index, *bonded_index))
}
}
},
// String is empty -> no further IDs
Err(_) => break
};
}
}
}
}
}
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