pdb.hpp

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// Copyright 2017 Global Phasing Ltd.
//
// Read the PDB file format and store it in Structure.
//
// Based on the format spec:
// https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
// + support for two-character chain IDs (columns 21 and 22)
// + read segment ID (columns 73-76)
// + read hybrid-36 serial numbers (http://cci.lbl.gov/hybrid_36/)
// + hybrid-36 sequence id for sequences longer than 9999 (no such examples)
// + allow for longer REMARK lines (up to 120 characters)
 
#ifndef GEMMI_PDB_HPP_
#define GEMMI_PDB_HPP_
 
#include "input.hpp"    // for FileStream
#include "model.hpp"    // for Structure, ...
 
namespace gemmi {
 
inline bool is_record_type4(const char* s, const char* record) {
  return ialpha4_id(s) == ialpha4_id(record);
}
inline bool is_record_type3(const char* s, const char* record) {
  return (ialpha4_id(s) & ~0xf) == ialpha4_id(record);
}
 
GEMMI_DLL std::vector<Op> read_remark_290(const std::vector<std::string>& raw_remarks);
 
GEMMI_DLL Structure read_pdb_from_stream(AnyStream& line_reader,
                                         const std::string& source,
                                         PdbReadOptions options);
 
inline Structure read_pdb_file(const std::string& path,
                               PdbReadOptions options={}) {
  FileStream stream(path.c_str(), "rb");
  return read_pdb_from_stream(stream, path, options);
}
 
inline Structure read_pdb_from_memory(const char* data, size_t size,
                                      const std::string& name,
                                      PdbReadOptions options={}) {
  MemoryStream stream{data, size};
  return read_pdb_from_stream(stream, name, options);
}
 
inline Structure read_pdb_string(const std::string& str,
                                 const std::string& name,
                                 PdbReadOptions options={}) {
  return read_pdb_from_memory(str.c_str(), str.length(), name, options);
}
 
template<typename T>
inline Structure read_pdb(T&& input, PdbReadOptions options={}) {
  return read_pdb_from_stream(*input.create_stream(), input.path(), options);
}
 
} // namespace gemmi
#endif