/// \brief Escape residue name strings for use in PyMOL
str_vec pymol_tools::parse_residue_names_for_pymol(const residue_name_vec &arg_residue_names ///< The residue name strings to escape
) {
str_vec new_residue_names;
new_residue_names.reserve( arg_residue_names.size() );
for (const residue_name &the_residue_name : arg_residue_names) {
new_residue_names.push_back( parse_residue_name_for_pymol( the_residue_name ) );
}
return new_residue_names;
}
/// \brief TODOCUMENT
///
/// \relates residue_name_align_map
residue_name_align_map cath::align::detail::make_residue_name_align_map(const residue_name_vec &arg_residue_names ///< TODOCUMENT
) {
str_vec residue_name_strings;
residue_name_strings.reserve( arg_residue_names.size() );
for (const residue_name &the_residue_name : arg_residue_names) {
residue_name_strings.push_back( lexical_cast<string>( the_residue_name ) );
}
return residue_name_align_map( residue_name_strings );
}
/// \brief Convenience function for read_alignment_from_cath_ssap_legacy_format() to use
opt_aln_posn cath::align::search_for_residue_in_residue_names(const size_t &arg_pos, ///< TODOCUMENT
const residue_name_vec &arg_residue_names, ///< TODOCUMENT
const char &arg_amino_acid, ///< TODOCUMENT
const residue_name &arg_residue_name, ///< TODOCUMENT
ostream &/*arg_stderr*/ ///< TODOCUMENT
) {
const bool residue_is_present = ( arg_amino_acid != '0' );
if ( residue_is_present ) {
if (arg_pos >= arg_residue_names.size()) {
BOOST_THROW_EXCEPTION(runtime_error_exception("Counter has gone past end of list of residues whilst loading alignment"));
}
const auto res_itr = find(
common::cbegin( arg_residue_names ) + numeric_cast<ptrdiff_t>( arg_pos ),
common::cend ( arg_residue_names ),
arg_residue_name
);
if ( res_itr == common::cend( arg_residue_names ) ) {
cerr << "Residue names being searched:\n\n";
for (const residue_name &the_res_name : arg_residue_names) {
cerr << " " << the_res_name;
}
cerr << "\n" << endl;
BOOST_THROW_EXCEPTION(runtime_error_exception(
"Unable to find residue "
+ lexical_cast<string>( arg_residue_name )
+ " from alignment in list of residues, starting from position "
+ lexical_cast<string>( arg_pos )
));
}
const size_t new_pos = numeric_cast<size_t>( distance( common::cbegin( arg_residue_names ), res_itr ) );
if ( new_pos != arg_pos + 1 && ( new_pos != 0 || arg_pos != 0 ) ) {
const size_t jump = new_pos - (arg_pos + 1);
BOOST_LOG_TRIVIAL( warning ) << "Missing some residues whilst loading alignment: jumped "
<< jump
<< " position(s) from residue "
<< arg_residue_names[arg_pos]
<< " (in position "
<< arg_pos
<< ") to residue "
<< arg_residue_names[new_pos]
<< " (in position "
<< new_pos
<< ")";
}
return opt_aln_posn( new_pos );
}
return opt_aln_posn( none );
}