# ex_pdb_to_fasta¶

ads a PDB file and writes protein sequence(s) in FASTA format

## Categories:¶

• core::data::io::Pdb

## Program source:¶

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 #include #include #include /** @brief Reads a PDB file and writes protein sequence(s) in FASTA format. * * This is a simplified version of ap_pdb_to_fasta_ss.cc application * USAGE: * ex_pdb_to_fasta 5edw.pdb * * CATEGORIES: core::data::io::Pdb * KEYWORDS: PDB input */ int main(const int argc, const char *argv[]) { using namespace core::data::io; // Pdb and create_fasta_string lives there Pdb reader(argv[1], is_not_alternative, true); core::data::structural::Structure_SP strctr = (reader.create_structure(0)); // Iterate over all chains for (int ic = 0; ic < strctr->count_chains(); ++ic) std::cout << "> " << strctr->code() << (*strctr)[ic]->id() << "\n" // --- e.g. prints "> 2gb1 A" << (*strctr)[ic]->create_sequence()->sequence << "\n"; // --- prints the sequence itself }