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Functions
core::io::carbohydrates Namespace Reference

Functions

utility::vector1< std::pair
< core::uint, std::string > > 
sugar_modifications_from_suffix (std::string const &suffix)
 Parse sugar code suffixes to extract a list of sugar modifications with their corresponding positions. More...
 
std::string residue_gws_string (core::pose::Pose const &pose, core::uint const seqpos)
 Read a CFG structure from a GWS-formatted string and load into a pose. More...
 
std::string residue_range_gws_string (core::pose::Pose const &pose, core::uint const begin, core::uint const end)
 Return a GWS-formatted string for each carbohydrate residue in the given sequence range, including branches. More...
 
std::string chain_gws_string (core::pose::Pose const &pose, core::uint const chain_id)
 Return a GWS-formatted string for the given carbohydrate chain, including branches. More...
 
void dump_gws_chain (core::pose::Pose const &pose, core::uint const chain_id, std::string const &filename)
 Write the GlycoWorkbench structure file for the given pose chain to <filename>. More...
 
void dump_gws (core::pose::Pose const &pose, std::string const &filename)
 Write the GlycoWorkbench structure file for all carbohydrate chains of the given pose to <filename>. More...
 
core::uint char_to_int (char const char_in)
 Given a char, parse it as an integer. More...
 

Function Documentation

std::string core::io::carbohydrates::chain_gws_string ( core::pose::Pose const &  pose,
core::uint const  chain_id 
)
core::uint core::io::carbohydrates::char_to_int ( char const  char_in)

Given a char, parse it as an integer.

Returns 0 for anything outside of the range 1-9.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by sugar_modifications_from_suffix().

void core::io::carbohydrates::dump_gws ( core::pose::Pose const &  pose,
std::string const &  filename 
)

Write the GlycoWorkbench structure file for all carbohydrate chains of the given pose to <filename>.

Chains that are branches are only output once, as a part of their parent chain.

References chain_gws_string(), core::pose::Pose::conformation(), core::sequence::end, core::pose::Pose::glycan_tree_set(), core::conformation::Residue::is_carbohydrate(), core::chemical::ResidueType::is_lipid(), core::conformation::membrane::out, core::pose::Pose::residue(), core::io::TR(), and core::conformation::Residue::type().

void core::io::carbohydrates::dump_gws_chain ( core::pose::Pose const &  pose,
core::uint const  chain_id,
std::string const &  filename 
)

Write the GlycoWorkbench structure file for the given pose chain to <filename>.

If the given chain is a glycan, this function writes a GWS file describing the CFG "structure" of that glycan. If the chain contains branch-point residues, attached branches are also included in the output.

References chain_gws_string(), and core::io::TR().

std::string core::io::carbohydrates::residue_gws_string ( core::pose::Pose const &  pose,
core::uint const  seqpos 
)

Read a CFG structure from a GWS-formatted string and load into a pose.

The GWS format for (1->4)-beta-D-Galactopyranosyl, e.g., is "--4b1D-Gal,p". (Question marks are used for cases where information is not known or not applicable.)

Read the first CFG structure from a GWS file and load into a pose. Read all CFG structures from a GWS file and load into poses. Create a pose from a GWS file. Return a GWS-formatted string for the given carbohydrate residue.

References core::pose::Pose::glycan_tree_set(), core::conformation::Residue::is_ligand(), core::conformation::membrane::out, and core::pose::Pose::residue().

Referenced by residue_range_gws_string().

std::string core::io::carbohydrates::residue_range_gws_string ( core::pose::Pose const &  pose,
core::uint const  begin,
core::uint const  end 
)

Return a GWS-formatted string for each carbohydrate residue in the given sequence range, including branches.

This function is used recursively to handle branching. Branching in GWS format uses parentheses following the residue to which the branch is attached.

References core::sequence::end, core::conformation::Residue::is_upper_terminus(), core::conformation::membrane::out, core::pose::Pose::residue(), and residue_gws_string().

Referenced by chain_gws_string().

utility::vector1< std::pair< core::uint, std::string > > core::io::carbohydrates::sugar_modifications_from_suffix ( std::string const &  suffix)

Parse sugar code suffixes to extract a list of sugar modifications with their corresponding positions.

Returns
A list of pairs of positions and modifications.

References char_to_int(), and core::io::TR().

Referenced by core::pose::residue_types_from_saccharide_sequence_recursive().