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The topology of a complete CHARMM model.
This defines all of the segments (chains) in the model as CHARMMSegmentTopology objects, which in turn define the list of residues, the atoms in each residue, and their types and the connectivity between them.
A CHARMMTopology object can be created manually, in which case add_segment() can be called to add individual CHARMMSegmentTopology objects. In this way a new topology can be created, e.g. from protein primary sequence.
Alternatively, given an existing Hierarchy, e.g. as returned from read_pdb(), CHARMMParameters::create_topology() can be called to generate a new topology that corresponds to the primary sequence of the Hierarchy.
A new topology can be patched (apply_default_patches() or CHARMMPatch::apply()) to modify the simple chain of residues to account for modified residues, C- or N-termini special cases, disulfide bridges, etc.
Once a topology is created, it can be used to generate new particles which conform to that topology (create_hierarchy()), or to add topology information to an existing Hierarchy (e.g. add_atom_types(), add_bonds(), add_charges()).
Examples: structure from sequence
Inheritance diagram for IMP::atom::CHARMMTopology:Public Member Functions | |
| CHARMMTopology (const CHARMMParameters *force_field, std::string name="CHARMM topology %1%") | |
| void | add_atom_types (Hierarchy hierarchy) const |
| Add CHARMM atom types to the given Hierarchy using this topology. | |
| Particles | add_bonds (Hierarchy hierarchy) const |
| Add bonds to the given Hierarchy using this topology, and return them. | |
| void | add_charges (Hierarchy hierarchy) const |
| Add CHARMM charges to the given Hierarchy using this topology. | |
| void | add_coordinates (Hierarchy hierarchy) const |
| Add atom Cartesian coordinates to the given Hierarchy using this topology. | |
| Particles | add_dihedrals (Hierarchy hierarchy) const |
| Add dihedrals to the given Hierarchy using this topology, and return them. | |
| Particles | add_impropers (Hierarchy hierarchy) const |
| Add impropers to the given Hierarchy using this topology, and return them. | |
| void | add_missing_atoms (Hierarchy hierarchy) const |
| Add any missing atoms to the given Hierarchy using this topology. | |
| void | add_sequence (std::string sequence) |
| Add a sequence (as a string of one-letter codes) to the topology. | |
| void | apply_default_patches () |
| Call CHARMMSegmentTopology::apply_default_patches() for all segments. | |
| Hierarchy | create_hierarchy (Model *model) const |
| Create a new Hierarchy in the given model using this topology. | |
| const CHARMMParameters * | get_parameters () |
| void | setup_hierarchy (Hierarchy hierarchy) const |
| Make the Hierarchy conform with this topology. | |
| 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 CHARMMTopology * | get_from (IMP::base::Object *o) |
Segments | |
The topology contains a list of segments, one for each chain. | |
| void | remove_segment (CHARMMSegmentTopology *d) |
| template<class F > | |
| void | remove_segments_if (const F &f) |
| template<class List > | |
| void | remove_segments (List d) |
| template<class List > | |
| void | set_segments (List ps) |
| template<class List > | |
| void | set_segments_order (List ps) |
| unsigned int | add_segment (CHARMMSegmentTopology *obj) |
| template<class List > | |
| void | add_segments (List objs) |
| void | clear_segments () |
| unsigned int | get_number_of_segments () const |
| bool | get_has_segments () const |
| CHARMMSegmentTopology * | get_segment (unsigned int i) const |
| CHARMMSegmentTopologies | get_segments () const |
| void | reserve_segments (unsigned int sz) |
| CHARMMSegmentTopologyIterator | segments_begin () |
| CHARMMSegmentTopologyIterator | segments_end () |
| CHARMMSegmentTopologyConstIterator | segments_begin () const |
| CHARMMSegmentTopologyConstIterator | segments_end () const |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| void IMP::atom::CHARMMTopology::add_atom_types | ( | Hierarchy | hierarchy | ) | const |
Add CHARMM atom types to the given Hierarchy using this topology.
The primary sequence of the Hierarchy must match that of the topology.
Add bonds to the given Hierarchy using this topology, and return them.
The primary sequence of the Hierarchy must match that of the topology. Parameters for the bonds (ideal bond length, force constant) are extracted from the CHARMM parameter file, using the types of each atom (add_atom_types() must be called first, or the particles otherwise manually typed using CHARMMAtom::set_charmm_type()).
If no parameters are defined for a given bond, the bond is created with zero stiffness, such that the bond can still be excluded from nonbonded interactions but BondSingletonScore will not score it.
Note that typically CHARMM defines bonds and impropers (see add_impropers()) but angles and dihedrals are auto-generated from the existing bond graph (see CHARMMParameters::create_angles() and CHARMMParameters::create_dihedrals()).
The list of newly-created Bond particles can be passed to a StereochemistryPairFilter to exclude bonded particles from nonbonded interactions, or to a BondSingletonScore to score each bond.
| void IMP::atom::CHARMMTopology::add_charges | ( | Hierarchy | hierarchy | ) | const |
| void IMP::atom::CHARMMTopology::add_coordinates | ( | Hierarchy | hierarchy | ) | const |
Add atom Cartesian coordinates to the given Hierarchy using this topology.
The primary sequence of the Hierarchy must match that of the topology.
This method can be used to add missing coordinates (e.g. of hydrogens
or sidechains, such as those added by add_missing_atoms()), or to
generate a starting conformation for a new Hierarchy (e.g. generated
by create_hierarchy()). On exit, all atoms will have coordinates.
- Cartesian coordinates for any atoms that are not currently core::XYZ
particles are generated using internal coordinates that relate them
to particles that do have XYZ coordinates.
- For each segment (chain), if no atoms have coordinates but a triplet
of atoms can be found where theit internal distances and angle can be
determined from internal coordinates, these three atoms will be
placed to seed the generation procedure. For the first segment, the
atoms will be placed on the xy plane with the first atom at the origin.
For subsequent segments, the first atom is placed offset by (2.,2.,2.)
from the last atom in the previous segment.
- If any atoms cannot be placed using either method, their coordinates
are assigned randomly to lie near atoms that are near in sequence or,
if no such atoms exist, near the segment origin.
\note It is valid to specify internal coordinates in a CHARMM topology
file that leave the angles or distances unspecified. This function
will attempt to fill in this missing information using CHARMM atom
types and the parameter file. Thus, better results will be obtained
if add_atom_types() is called before this function, and the
CHARMMParameters object used contains parameter information.
Add dihedrals to the given Hierarchy using this topology, and return them.
The primary sequence of the Hierarchy must match that of the topology.
Typically, dihedrals are auto-generated from the existing bond graph (see CHARMMParameters::create_dihedrals()) rather than using this function. \return a list of the generated Dihedral decorators. \see add_bonds().
Add impropers to the given Hierarchy using this topology, and return them.
The primary sequence of the Hierarchy must match that of the topology.
The list of newly-created Dihedral particles can be passed to a ImproperSingletonScore to score each improper dihedral. \return a list of the generated Dihedral decorators. \see add_bonds().
| void IMP::atom::CHARMMTopology::add_missing_atoms | ( | Hierarchy | hierarchy | ) | const |
Add any missing atoms to the given Hierarchy using this topology.
Missing atoms are defined as those present in the topology but not in the hierarchy. Newly-added atoms are assigned CHARMM types, but no coordinates (use add_coordinates() to add them). The primary sequence of the Hierarchy must match that of the topology.
| void IMP::atom::CHARMMTopology::add_sequence | ( | std::string | sequence | ) |
Add a sequence (as a string of one-letter codes) to the topology.
The sequence can contain amino-acid one-letter codes and '/' characters to denote the start of a new segment. The empty string simply adds a new segment that contains no residues.
| ValueException | if an invalid one-letter code is passed. |
| void IMP::atom::CHARMMTopology::apply_default_patches | ( | ) |
Call CHARMMSegmentTopology::apply_default_patches() for all segments.
Create a new Hierarchy in the given model using this topology.
The hierarchy contains chains, residues and atoms as defined in the topology. Note, however, that none of the generated atoms is given coordinates. Chains are labeled 'A', 'B' etc. Residues are numbered from 1 within each chain.
| void IMP::atom::CHARMMTopology::setup_hierarchy | ( | Hierarchy | hierarchy | ) | const |
Make the Hierarchy conform with this topology.
The hierarchy is modified if necessary so that each residue contains the same set of atoms as defined in the CHARMM topology, and any atoms missing coordinates are assigned them.
This is equivalent to calling add_atom_types(), add_missing_atoms(), remove_charmm_untyped_atoms(), and add_coordinates() in that order.