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A CHARMM patch residue.
Patch residues are similar to regular residues, except that they are used to modify an existing residue. Any atoms they contain replace or add to those in the residue; they can also remove atoms. Atom names are as for regular residues, except for patches that affect two residues (e.g. DISU, LINK) in which each atom contains a 1 or 2 prefix (plus an optional colon) to identify the residue which will be patched; for example, both 1:CA and 1CA identify the CA atom in the first residue.
Inheritance diagram for IMP::atom::CHARMMPatch:Public Member Functions | |
| CHARMMPatch (std::string type) | |
| Construct a new, empty patch residue. | |
| void | add_removed_atom (std::string name) |
| void | apply (CHARMMResidueTopology *res) const |
| Apply the patch to the residue, modifying its topology accordingly. | |
| void | apply (CHARMMResidueTopology *res1, CHARMMResidueTopology *res2) const |
| Apply the patch to the given pair of residues. | |
| unsigned int | get_number_of_removed_atoms () const |
| std::string | get_removed_atom (unsigned int i) const |
| Public Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| void | add_angle (const CHARMMAngle &bond) |
| void | add_atom (const CHARMMAtomTopology &atom) |
| void | add_bond (const CHARMMBond &bond) |
| void | add_dihedral (const CHARMMDihedral &bond) |
| void | add_improper (const CHARMMDihedral &bond) |
| void | add_internal_coordinate (const CHARMMInternalCoordinate &ic) |
| const CHARMMAngle & | get_angle (unsigned int index) const |
| const CHARMMAtomTopology & | get_atom (unsigned int i) const |
| const CHARMMAtomTopology & | get_atom (AtomType type) const |
| const CHARMMAtomTopology & | get_atom (std::string name) const |
| const CHARMMBond & | get_bond (unsigned int index) const |
| const CHARMMDihedral & | get_dihedral (unsigned int index) const |
| const CHARMMDihedral & | get_improper (unsigned int index) const |
| const CHARMMInternalCoordinate & | get_internal_coordinate (unsigned int index) const |
| unsigned int | get_number_of_angles () const |
| unsigned int | get_number_of_atoms () const |
| unsigned int | get_number_of_bonds () const |
| unsigned int | get_number_of_dihedrals () const |
| unsigned int | get_number_of_impropers () const |
| unsigned int | get_number_of_internal_coordinates () const |
| std::string | get_type () const |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Static Public Member Functions | |
| static CHARMMPatch * | get_from (IMP::base::Object *o) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMResidueTopologyBase (std::string type) | |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMAngles | angles_ |
| base::Vector< CHARMMAtomTopology > | atoms_ |
| CHARMMBonds | bonds_ |
| CHARMMDihedrals | dihedrals_ |
| CHARMMDihedrals | impropers_ |
| CHARMMInternalCoordinates | internal_coordinates_ |
| IMP::atom::CHARMMPatch::CHARMMPatch | ( | std::string | type | ) |
Construct a new, empty patch residue.
To get an existing patch, use CHARMMParameters::get_patch() instead.
| void IMP::atom::CHARMMPatch::apply | ( | CHARMMResidueTopology * | res | ) | const |
Apply the patch to the residue, modifying its topology accordingly.
IMP prohibits this. To allow an already-patched residue to be re-patched, first call CHARMMResidueTopology::set_patched(false). | void IMP::atom::CHARMMPatch::apply | ( | CHARMMResidueTopology * | res1, |
| CHARMMResidueTopology * | res2 | ||
| ) | const |
Apply the patch to the given pair of residues.
This can only be used for special two-residue patches, such as DISU or LINK. In a two-residue patch, each atom has a 1: or 2: prefix to identify the residue it refers to.
| ValueException | if the patch is not a two-residue patch. |