Field.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/io/pdb/Field.cc
///
/// @brief Each line of a PDB file is a Record which is divided into Fields
/// @author Matthew O'Meara (mattjomeara@gmail.com)

#include <core/io/pdb/Field.hh>

// Utitility headers
#include <utility/tools/make_map.hh>


namespace core {
namespace io {
namespace pdb {


using std::string;
using std::ostream;

/// @brief various constructors - only for convenience.
Field::Field() :
  type(""),
  value(""),
  start(0),
  end(0)
{}

Field::Field(Size s, Size e) :
  type(""),
  value(""),
  start(s),
  end(e)
{}

Field::Field(string t, Size s, Size e) :
  type(t),
  value(""),
  start(s),
  end(e)
{}

/// @brief read field value from given string.
void
Field::getValueFrom(string source) {
  value = string(source.begin()+start-1, source.begin()+end);
}


/// @brief Debug output.
std::ostream&
operator <<(
  std::ostream &os,
  Field const & F
) {
  os << "[" << F.start << ", " <<  F.end << "]=" << F.value << "";
  return os;
}

/// @details static holder for collection of Fields.
RecordRef Field::PDB_Records_;

/// @details check if records table was init, init table otherwise
/// return reference to private static records collection
/// @remarks See http://www.wwpdb.org/docs.html#format for details.
RecordRef & Field::getRecordCollection()
{
  if( PDB_Records_.size() == 0 ) {
    PDB_Records_ = utility::tools::make_map<string, Record>(
      // Title Section
      "HEADER", utility::tools::make_map<string, Field>(
        "type",           Field( 1,  6),
        "classification", Field(11, 50),
        "depDate",        Field(51, 59),
        "idCode",         Field(63, 66) ),

      "TITLE ", utility::tools::make_map<string, Field>(
        "type",         Field( 1,  6),
        "continuation", Field( 9, 10),
        "title",        Field(11, 70) ),

      "COMPND", utility::tools::make_map<string, Field>(
        "type",         Field( 1,  6),
        "continuation", Field( 9, 10),
        "compound",     Field(11, 70) ),

      "KEYWDS", utility::tools::make_map<string, Field>(
        "type",         Field( 1,  6),
        "continuation", Field( 9, 10),
        "keywords",     Field(11, 70) ),

      "EXPDTA", utility::tools::make_map<string, Field>(
        "type",         Field( 1,  6),
        "continuation", Field( 9, 10),
        "technique",    Field(11, 70) ),

      "REMARK", utility::tools::make_map<string, Field>(
        "type",      Field( 1,  6),
        "remarkNum", Field( 8, 10),
        "value",     Field(12, 70) ), // non-standard name

      // Primary Structure Section

      // Heterogen Section
      "HETNAM", utility::tools::make_map<string, Field>(
        "type",         Field( 1,  6),
        "continuation", Field( 9, 10),
        "hetID",        Field(12, 14), // LString(3): HET identifier, right-justified
        "text",         Field(16, 70)  // String: chemical name
        ),

      // Secondary Structure Section

      // Connectivity Annotation Section
      "SSBOND", utility::tools::make_map<string, Field>(
        "type",     Field( 1,  6),
        "serNum",   Field( 8, 10), // Integer
        "CYS",      Field(12, 14),
        "chainID1", Field(16, 16), // Character
        "seqNum1",  Field(18, 21), // Integer
        "icode1",   Field(22, 22), // AChar
        "CYS",      Field(26, 28),
        "chainID2", Field(30, 30), // Character
        "seqNum2",  Field(32, 35), // Integer
        "icode2",   Field(36, 36), // AChar
        "sym1",     Field(60, 65), // SymOP
        "sym2",     Field(67, 72)  // SymOP
        ),
      "LINK  ", utility::tools::make_map<string, Field>(
        "type",     Field( 1,  6),
        "name1",    Field(13, 16), // Atom
        "altLoc1",  Field(17, 17), // Character
        "resName1", Field(18, 20), // Residue name
        "chainID1", Field(22, 22), // Character
        "resSeq1",  Field(23, 26), // Integer
        "iCode1",   Field(27, 27), // AChar
        "name2",    Field(43, 46), // Atom
        "altLoc2",  Field(47, 47), // Character
        "resName2", Field(48, 50), // Residue name
        "chainID2", Field(52, 52), // Character
        "resSeq2",  Field(53, 56), // Integer
        "iCode2",   Field(57, 57), // AChar
        "sym1",     Field(60, 65), // SymOP
        "sym2",     Field(67, 72), // SymOP
        "length",   Field(74, 78)  // Real(5.2)
        ),

      // Miscellaneous Features Section

      // Crystallographic & Coordinate Transformation Section

      // Coordinate Section
      "MODEL ", utility::tools::make_map<string, Field>(
        "type",   Field( 1,  6),
        "serial", Field( 7, 80) ),

      "ATOM  ", utility::tools::make_map<string, Field>(
        "type",       Field( 1,  6),
        "serial",     Field( 7, 11), // Integer
        "name",       Field(13, 16), // Atom
        "altLoc",     Field(17, 17), // Character
        "resName",    Field(18, 20), // Residue name
        "chainID",    Field(22, 22), // Character
        "resSeq",     Field(23, 26), // Integer
        "iCode",      Field(27, 27), // AChar
        "x",          Field(31, 38), // Real(8.3)
        "y",          Field(39, 46), // Real(8.3)
        "z",          Field(47, 54), // Real(8.3)
        "occupancy",  Field(55, 60), // Real(6.2)
        "tempFactor", Field(61, 66), // Real(6.2)
        //"segID",     Field(73, 76),
        "element",    Field(77, 78), // LString(2)
        "charge",     Field(79, 80)  // LString(2)
        ),
      "HETATM", utility::tools::make_map<string, Field>(
        "type",       Field( 1,  6),
        "serial",     Field( 7, 11), // Integer
        "name",       Field(13, 16), // Atom
        "altLoc",     Field(17, 17), // Character
        "resName",    Field(18, 20), // Residue name
        "chainID",    Field(22, 22), // Character
        "resSeq",     Field(23, 26), // Integer
        "iCode",      Field(27, 27), // AChar
        "x",          Field(31, 38), // Real(8.3)
        "y",          Field(39, 46), // Real(8.3)
        "z",          Field(47, 54), // Real(8.3)
        "occupancy",  Field(55, 60), // Real(6.2)
        "tempFactor", Field(61, 66), // Real(6.2)
        //"segID",     Field(73, 76),
        "element",    Field(77, 78), // LString(2)
        "charge",     Field(79, 80)  // LString(2)
        ),
      "TER   ", utility::tools::make_map<string, Field>(
        "type",    Field( 1,  6),
        "serial",  Field( 7, 11),
        "resName", Field(18, 20),
        "chainID", Field(22, 22),
        "resSeq",  Field(23, 26),
        "iCode",   Field(27, 27) ),

      // Connectivity Section

      // Bookkeeping Section

      // Unknown Type
      "UNKNOW", utility::tools::make_map<string, Field>(
        "type", Field( 1,  6),
        "info", Field( 7, 80) )
      );
  }
  return PDB_Records_;
}


/// @details Debug printing, serializing to Tracer like object.
std::ostream&
operator <<(std::ostream &os,Record const & R) {
  for(Record::const_iterator p=R.begin(); p!=R.end(); p++ ) {
    os << "<Record>{" << p->first << ":" << p->second
    << "}\n";
  }

  return os;
}


} // namespace
} // namespace
} // namespace