Separate

namespace lemon::separate

Separate entry frames into corresponding sub-frames.

Functions

template<typename Container>
void residues(const chemfiles::Frame &entry, const Container &accepted_residues, chemfiles::Frame &new_frame, const std::string &use_altloc = "A")

Copy residues from one frame into a second frame

Once a set of residues has been selected (and pruned), the residues of interest should be copied into a new frame so that they can written to disk separately. This function performs this action while taking care to copy the original connectivity of the residue.

Parameters

  • [in] entry: The original Frame from where the residues will be copied.

  • [in] accepted_residues: The residue IDs for the residues to be copied.

  • [inout] new_frame: The frame where the residues wil be copied to.

void protein_and_ligand(const chemfiles::Frame &entry, size_t ligand_id, double pocket_size, chemfiles::Frame &protein, chemfiles::Frame &ligand, const std::string &altloc = "A")

Separate a ligand and surrounding protein pocket into individual frames.

The environment surrounding a ligand in a protein defines the environment of that ligand. This function is meant to separate a ligand and relevent environment into separate *frame*s s that they can written to disk.

Parameters

  • [in] entry: The original Frame from where the residues will be copied.

  • [in] ligand_id: The residue ID for the ligand.

  • [in] pocket_size: The radius of the ligand environment copied into protein

  • [inout] protein: The frame where the protein residues wil be copied to.

  • [inout] ligand: The frame where the ligand residue will be copied to.

template<typename Container>
void protein_and_ligands(const chemfiles::Frame &entry, const Container &ligand_ids, double pocket_size, chemfiles::Frame &protein, chemfiles::Frame &ligand, const std::string &altloc = "A")

Separate ligands and surrounding protein pocket into individual frames.

The environment surrounding ligands in a protein defines the environment of those ligands. This function is meant to separate ligands and relevent environment into separate *frame*s s that they can written to disk.

Parameters

  • [in] entry: The original Frame from where the residues will be copied.

  • [in] ligand_ids: The residue IDs for the ligand.

  • [in] pocket_size: The radius of the ligand environment copied into protein

  • [inout] protein: The frame where the protein residues wil be copied to.

  • [inout] ligand: The frame where the ligand residue will be copied to.