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Rosetta 3.5
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Rosetta 3.5
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#include <ContactMap.hh>
Public Member Functions | |
| ContactMap () | |
| Default constructor. More... | |
| ContactMap (ContactMap const &) | |
| Copy constructor. More... | |
| ~ContactMap () | |
| Destructor. More... | |
| virtual moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual moves::MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| virtual void | parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &) |
| Processes options specified in xml-file and sets up the ContactMap. More... | |
| virtual void | apply (Pose &pose) |
| Process supplied pose. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| void | set_output_prefix (std::string prefix) |
| Setter functions for private class variables. More... | |
| void | set_distance_cutoff (core::Real cutoff) |
| void | parse_region_string (std::string, core::Size &, core::Size &, Pose const &) |
| : Parses region string end sets the boundaries accordingly More... | |
| void | reset () |
| Resets the movers n_poses_ variable and the counts of all contacts to 0. More... | |
| void | write_to_file (std::string filename="") |
| Output function that writes the ContactMap to the specified file. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| void | set_current_tag (std::string const &new_tag) |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | type (const std::string &type_in) |
| std::string | get_type () const |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual bool | reinitialize_for_each_job () const |
| this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Member Functions | |
| void | fill_contacts (core::Size region_begin, core::Size region_end, Pose const &pose) |
| Initializes ContactMap within a single region. More... | |
| void | fill_contacts (core::Size region_begin, core::Size region_end, core::Size seqpos_ligand, Pose const &pose) |
| Initializes ContactMap between a single region and a ligand. More... | |
| void | fill_contacts (core::Size region1_begin, core::Size region1_end, core::Size region2_begin, core::Size region2_end, Pose const &pose) |
| Initializes ContactMap between two separate regions. More... | |
Private Attributes | |
| utility::vector1< Contact > | contacts_ |
| Container for all AtomPairs included in the ContactMap. More... | |
| utility::vector1< core::Size > | output_matrix_ |
| Vector that maps the matrix position to the index of the contact in contacts_ Vector of size columns*rows with field(row, column) stored at (row-1)*[columns] + column. More... | |
| utility::vector1< std::string > | column_names_ |
| utility::vector1< std::string > | row_names_ |
| std::string | output_prefix_ |
| core::Size | n_poses_ |
| core::Real | distance_cutoff_ |
| core::Size | models_per_file_ |
| int value after how many models an output file will be generated More... | |
| bool | reset_count_ |
| bool value indicating whether the reset function will be called after file output More... | |
| bool | row_format_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More... | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Definition at line 42 of file ContactMap.hh.
| protocols::contact_map::ContactMap::ContactMap | ( | ) |
Default constructor.
Definition at line 81 of file ContactMap.cc.
Referenced by clone(), and fresh_instance().
| protocols::contact_map::ContactMap::ContactMap | ( | ContactMap const & | contact_map) |
Copy constructor.
Definition at line 93 of file ContactMap.cc.
| protocols::contact_map::ContactMap::~ContactMap | ( | ) |
Destructor.
Definition at line 109 of file ContactMap.cc.
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virtual |
Process supplied pose.
Implements protocols::moves::Mover.
Definition at line 358 of file ContactMap.cc.
References contacts_, protocols::nonlocal::current_job(), protocols::jd2::current_output_name(), core::kinematics::distance(), distance_cutoff_, protocols::jd2::JobDistributor::get_instance(), models_per_file_, n_poses_, output_prefix_, reset(), reset_count_, core::pose::Pose::residue(), write_to_file(), and protocols::kinmatch::xyz().
Referenced by test_move().
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virtual |
clone has to be overridden only if clone invocation is expected.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
Definition at line 113 of file ContactMap.cc.
References ContactMap().
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private |
Initializes ContactMap within a single region.
Definition at line 234 of file ContactMap.cc.
References column_names_, contacts_, core::sequence::end, core::chemical::ResidueType::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().
Referenced by parse_my_tag().
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Initializes ContactMap between a single region and a ligand.
Definition at line 282 of file ContactMap.cc.
References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::conformation::Residue::atoms(), column_names_, contacts_, core::sequence::end, core::chemical::ResidueType::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().
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private |
Initializes ContactMap between two separate regions.
Definition at line 321 of file ContactMap.cc.
References column_names_, contacts_, core::chemical::ResidueType::name1(), core::conformation::Residue::name3(), output_matrix_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), row_names_, and protocols::contact_map::ContactPartner::string_rep().
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virtual |
this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
Definition at line 117 of file ContactMap.cc.
References ContactMap().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 121 of file ContactMap.cc.
References protocols::contact_map::ContactMapCreator::mover_name().
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virtual |
Processes options specified in xml-file and sets up the ContactMap.
Reimplemented from protocols::moves::Mover.
Definition at line 126 of file ContactMap.cc.
References distance_cutoff_, fill_contacts(), models_per_file_, core::pose::Pose::n_residue(), output_prefix_, parse_region_string(), reset_count_, row_format_, set_distance_cutoff(), and set_output_prefix().
| void protocols::contact_map::ContactMap::parse_region_string | ( | std::string | region_def, |
| core::Size & | region_begin, | ||
| core::Size & | region_end, | ||
| Pose const & | pose | ||
| ) |
: Parses region string end sets the boundaries accordingly
Parses region definition string end sets the boundaries accordingly.
: Possible formats for the region definition are "<int seqpos>" (e.g '12'), "<int begin>-<int end>" (e.g. '1-10') or "<char chainID>"(e.g. 'A')
Definition at line 186 of file ContactMap.cc.
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::get_chain_id_from_chain(), and core::pose::Pose::n_residue().
Referenced by parse_my_tag().
| void protocols::contact_map::ContactMap::reset | ( | void | ) |
Resets the movers n_poses_ variable and the counts of all contacts to 0.
Definition at line 401 of file ContactMap.cc.
References contacts_, and n_poses_.
Referenced by apply().
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inline |
Definition at line 72 of file ContactMap.hh.
References distance_cutoff_.
Referenced by parse_my_tag().
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inline |
Setter functions for private class variables.
Definition at line 71 of file ContactMap.hh.
References output_prefix_.
Referenced by parse_my_tag().
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inlinevirtual |
: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying
Reimplemented from protocols::moves::Mover.
Definition at line 66 of file ContactMap.hh.
References apply().
| void protocols::contact_map::ContactMap::write_to_file | ( | std::string | filename = "") |
Output function that writes the ContactMap to the specified file.
Definition at line 409 of file ContactMap.cc.
References column_names_, contacts_, n_poses_, output_matrix_, output_prefix_, row_format_, and row_names_.
Referenced by apply().
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Definition at line 96 of file ContactMap.hh.
Referenced by fill_contacts(), and write_to_file().
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Container for all AtomPairs included in the ContactMap.
Definition at line 92 of file ContactMap.hh.
Referenced by apply(), fill_contacts(), reset(), and write_to_file().
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Definition at line 100 of file ContactMap.hh.
Referenced by apply(), parse_my_tag(), and set_distance_cutoff().
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int value after how many models an output file will be generated
Definition at line 102 of file ContactMap.hh.
Referenced by apply(), and parse_my_tag().
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Definition at line 99 of file ContactMap.hh.
Referenced by apply(), reset(), and write_to_file().
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Vector that maps the matrix position to the index of the contact in contacts_ Vector of size columns*rows with field(row, column) stored at (row-1)*[columns] + column.
Definition at line 95 of file ContactMap.hh.
Referenced by fill_contacts(), and write_to_file().
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Definition at line 98 of file ContactMap.hh.
Referenced by apply(), parse_my_tag(), set_output_prefix(), and write_to_file().
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bool value indicating whether the reset function will be called after file output
Definition at line 104 of file ContactMap.hh.
Referenced by apply(), and parse_my_tag().
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Definition at line 105 of file ContactMap.hh.
Referenced by parse_my_tag(), and write_to_file().
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Definition at line 97 of file ContactMap.hh.
Referenced by fill_contacts(), and write_to_file().
1.8.4