IMP
2.0.0
The Integrative Modeling Platform
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A CHARMM patch residue. More...
#include <IMP/atom/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... | |
virtual void | do_show (std::ostream &out) const |
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 | |
virtual void | clear_caches () |
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. 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) |
Related Functions | |
(Note that these are not member functions.) | |
typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMPatch > > | CHARMMPatchesTemp |
Related Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMResidueTopologyBase > > | CHARMMResidueTopologyBasesTemp |
Related Functions inherited from IMP::base::Object | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Additional Inherited Members | |
Protected Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase | |
CHARMMResidueTopologyBase (std::string type) | |
Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase | |
CHARMMAngles | angles_ |
base::Vector< CHARMMAtomTopology > | atoms_ |
CHARMMBonds | bonds_ |
CHARMMDihedrals | dihedrals_ |
CHARMMDihedrals | impropers_ |
CHARMMInternalCoordinates | internal_coordinates_ |
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 373 of file charmm_topology.h.
IMP::atom::CHARMMPatch::CHARMMPatch | ( | std::string | type | ) |
To get an existing patch, use CHARMMParameters::get_patch() instead.
Definition at line 379 of file charmm_topology.h.
void IMP::atom::CHARMMPatch::apply | ( | CHARMMResidueTopology * | res | ) | const |
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 |
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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related |
Pass a set of objects.
Definition at line 413 of file charmm_topology.h.