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IMP Reference Guide
2.22.0
The Integrative Modeling Platform
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A CHARMM patch residue. More...
#include <IMP/atom/charmm_topology.h>
Inheritance diagram for IMP::atom::CHARMMPatch: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.
Definition at line 387 of file charmm_topology.h.
Public Member Functions | |
| CHARMMPatch (std::string type) | |
| Construct a new, empty patch residue. More... | |
| void | add_removed_atom (std::string name) |
| void | apply (CHARMMResidueTopology *res) const |
| Apply the patch to the residue, modifying its topology accordingly. More... | |
| void | apply (CHARMMResidueTopology *res1, CHARMMResidueTopology *res2) const |
| Apply the patch to the given pair of residues. More... | |
| unsigned int | get_number_of_removed_atoms () const |
| std::string | get_removed_atom (unsigned int i) const |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| 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::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| 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) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMResidueTopologyBase (std::string type) | |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase | |
| CHARMMAngles | angles_ |
| 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.
Definition at line 394 of file charmm_topology.h.
| 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. |
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::atom::CHARMMResidueTopologyBase.
Definition at line 425 of file charmm_topology.h.