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If a chain ID is missing / invalid, skip (to read non-standard PDB) #647

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Jul 5, 2021
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If a chain ID is missing / invalid, skip (to read non-standard PDB) #647

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20 changes: 17 additions & 3 deletions avogadro/io/pdbformat.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
#include <avogadro/core/elements.h>
#include <avogadro/core/molecule.h>
#include <avogadro/core/residue.h>
#include <avogadro/core/unitcell.h>
#include <avogadro/core/utilities.h>
#include <avogadro/core/vector.h>

Expand All @@ -23,6 +24,7 @@ using Avogadro::Core::Molecule;
using Avogadro::Core::Residue;
using Avogadro::Core::startsWith;
using Avogadro::Core::trimmed;
using Avogadro::Core::UnitCell;

using std::getline;
using std::istringstream;
Expand Down Expand Up @@ -58,6 +60,20 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
}
}

// e.g. CRYST1 4.912 4.912 6.696 90.00 90.00 120.00 P1 1
// https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html
else if (startsWith(buffer, "CRYST1")) {
Real a = lexicalCast<Real>(buffer.substr(6, 9), ok);
Real b = lexicalCast<Real>(buffer.substr(15, 9), ok);
Real c = lexicalCast<Real>(buffer.substr(24, 9), ok);
Real alpha = lexicalCast<Real>(buffer.substr(33, 7), ok);
Real beta = lexicalCast<Real>(buffer.substr(40, 7), ok);
Real gamma = lexicalCast<Real>(buffer.substr(47, 8), ok);

Core::UnitCell* cell = new Core::UnitCell(a, b, c, alpha, beta, gamma);
mol.setUnitCell(cell);
}

else if (startsWith(buffer, "ATOM") || startsWith(buffer, "HETATM")) {
// First we initialize the residue instance
size_t residueId = lexicalCast<size_t>(buffer.substr(22, 4), ok);
Expand All @@ -78,9 +94,7 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)

char chainId = lexicalCast<char>(buffer.substr(21, 1), ok);
if (!ok) {
appendError("Failed to parse chain identifier: " +
buffer.substr(21, 1));
return false;
chainId = 'A'; // it's a non-standard "PDB"-like file
}

r = &mol.addResidue(residueName, currentResidueId, chainId);
Expand Down