Author: Jack Maguire
There are classes in protocols/jd3/dag_node_managers
that help us keep track of jobs that have been submitted and sort results.
There are a few different flavors of the NodeManager, but let's just use the most vanilla: the SimpleNodeManager
.
We have the opportunity to make decisions at this point about how many results we want to keep from DAG nodes 1 and 2. Let's arbitrarily say we want to keep the best half of the results from node 1 and best third of the results from node 2.
First off, we need to include the NodeManager forward header:
#include <protocols/jd3/dag_node_managers/NodeManager.fwd.hh>
We also have two new methods we need to declare:
protected:
void init_node_managers();
void count_num_jobs_for_nodes_1_and_2 (
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
);
And one new data member:
private:
utility::vector1< jd3::dag_node_managers::NodeManagerOP > node_managers_;
void
TutorialQueen::init_node_managers(){
using namespace jd3::dag_node_managers;
core::Size num_jobs_for_node1( 0 ), num_jobs_for_node2( 0 );
count_num_jobs_for_nodes_1_and_2( num_jobs_for_node1, num_jobs_for_node2 );
core::Size const num_results_to_keep_for_node1 = num_jobs_for_node1 / 2; //Let's keep half of the results
SimpleNodeManagerOP node1 = utility::pointer::make_shared< SimpleNodeManager >(
0, //Job offset
num_jobs_for_node1,
num_results_to_keep_for_node1
);
core::Size const num_results_to_keep_for_node2 = num_jobs_for_node2 / 3; //Let's keep half of the results
SimpleNodeManagerOP node2 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1, //Job offset
num_jobs_for_node2,
num_results_to_keep_for_node2
);
core::Size const num_jobs_for_node3 = num_results_to_keep_for_node1 + num_results_to_keep_for_node2;
core::Size const num_results_to_keep_for_node3 = num_jobs_for_node3; //Let's keep/dump all of the results
SimpleNodeManagerOP node3 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1 + num_jobs_for_node2, //Job offset
num_jobs_for_node3,
num_results_to_keep_for_node3
);
node_managers_.reserve( 3 );
node_managers_.push_back( node1 );
node_managers_.push_back( node2 );
node_managers_.push_back( node3 );
}
void
TutorialQueen::count_num_jobs_for_nodes_1_and_2(
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
) {
num_jobs_for_node_1 = 0;
num_jobs_for_node_2 = 0;
//vector has 1 element for each <Job> tag
utility::vector1< standard::PreliminaryLarvalJob > const & all_preliminary_larval_jobs = preliminary_larval_jobs();
for( standard::PreliminaryLarvalJob const & pl_job : all_preliminary_larval_jobs ){
core::pose::PoseOP pose = pose_for_inner_job( pl_job->inner_job );
num_jobs_for_node_1 += pose->chain_sequence( 1 ).length();
num_jobs_for_node_2 += pose->chain_sequence( 2 ).length();
}
}
Let's add our call to init_node_managers()
in initial_job_dag()
.
Take care to add this call AFTER determine_preliminary_job_list()
has already been called.
We also need a few more #include
's in the .cc file:
#include <protocols/jd3/dag_node_managers/NodeManager.hh>
#include <protocols/jd3/dag_node_managers/SimpleNodeManager.hh>
#include <core/pose/Pose.hh>
// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington CoMotion, email: license@uw.edu.
/// @file protocols/tutorial/TutorialQueen.hh
/// @author Jack Maguire, jackmaguire1444@gmail.com
#ifndef INCLUDED_protocols_tutorial_TutorialQueen_HH
#define INCLUDED_protocols_tutorial_TutorialQueen_HH
#include <protocols/tutorial/TutorialQueen.fwd.hh>
#include <protocols/jd3/standard/StandardJobQueen.hh>
#include <protocols/jd3/JobDigraph.fwd.hh>
#include <protocols/jd3/dag_node_managers/NodeManager.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
namespace protocols {
namespace tutorial {
class TutorialQueen: public jd3::standard::StandardJobQueen {
public:
//constructor
TutorialQueen();
//destructor
~TutorialQueen() override;
jd3::JobDigraphOP
initial_job_dag()
override;
void
parse_job_definition_tags(
utility::tag::TagCOP common_block_tags,
utility::vector1< jd3::standard::PreliminaryLarvalJob > const &
) override;
protected:
void init_node_managers();
void count_num_jobs_for_nodes_1_and_2 (
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
);
private:
core::Size num_input_structs_;
utility::vector1< jd3::dag_node_managers::NodeManagerOP > node_managers_;
};
} //tutorial
} //protocols
#endif
// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington CoMotion, email: license@uw.edu.
/// @file protocols/tutorial/TutorialQueen.cc
/// @author Jack Maguire, jackmaguire1444@gmail.com
#include <protocols/tutorial/TutorialQueen.hh>
#include <protocols/jd3/JobDigraph.hh>
#include <protocols/jd3/dag_node_managers/NodeManager.hh>
#include <protocols/jd3/dag_node_managers/SimpleNodeManager.hh>
#include <utility/pointer/memory.hh>
#include <core/pose/Pose.hh>
#include <basic/Tracer.hh>
static basic::Tracer TR( "protocols.tutorial.TutorialQueen" );
using namespace protocols::jd3;
namespace protocols {
namespace tutorial {
//Constructor
TutorialQueen::TutorialQueen() :
StandardJobQueen()
{}
//Destructor
TutorialQueen::~TutorialQueen()
{}
JobDigraphOP
TutorialQueen::initial_job_dag() {
//you need to call this for the standard job queen to initialize
determine_preliminary_job_list();
init_node_managers();
JobDigraphOP dag = utility::pointer::make_shared< JobDigraph >( 3 );
dag->add_edge( 1, 3 );
dag->add_edge( 2, 3 );
return dag;
}
void
TutorialQueen::parse_job_definition_tags(
utility::tag::TagCOP common_block_tags,
utility::vector1< standard::PreliminaryLarvalJob > const & prelim_larval_jobs
){
num_input_structs_ = prelim_larval_jobs.size();
}
void
TutorialQueen::init_node_managers(){
using namespace jd3::dag_node_managers;
core::Size num_jobs_for_node1( 0 ), num_jobs_for_node2( 0 );
count_num_jobs_for_nodes_1_and_2( num_jobs_for_node1, num_jobs_for_node2 );
core::Size const num_results_to_keep_for_node1 = num_jobs_for_node1 / 2; //Let's keep half of the results
SimpleNodeManagerOP node1 = utility::pointer::make_shared< SimpleNodeManager >(
0, //Job offset
num_jobs_for_node1,
num_results_to_keep_for_node1
);
core::Size const num_results_to_keep_for_node2 = num_jobs_for_node2 / 3; //Let's keep half of the results
SimpleNodeManagerOP node2 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1, //Job offset
num_jobs_for_node2,
num_results_to_keep_for_node2
);
core::Size const num_jobs_for_node3 = num_results_to_keep_for_node1 + num_results_to_keep_for_node2;
core::Size const num_results_to_keep_for_node3 = num_jobs_for_node3; //Let's keep/dump all of the results
SimpleNodeManagerOP node3 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1 + num_jobs_for_node2, //Job offset
num_jobs_for_node3,
num_results_to_keep_for_node3
);
node_managers_.reserve( 3 );
node_managers_.push_back( node1 );
node_managers_.push_back( node2 );
node_managers_.push_back( node3 );
}
void
TutorialQueen::count_num_jobs_for_nodes_1_and_2(
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
) {
num_jobs_for_node_1 = 0;
num_jobs_for_node_2 = 0;
//vector has 1 element for each <Job> tag
utility::vector1< standard::PreliminaryLarvalJob > const & all_preliminary_larval_jobs = preliminary_larval_jobs();
for( standard::PreliminaryLarvalJob const & pl_job : all_preliminary_larval_jobs ){
core::pose::PoseOP pose = pose_for_inner_job( pl_job.inner_job );
num_jobs_for_node_1 += pose->chain_sequence( 1 ).length();
num_jobs_for_node_2 += pose->chain_sequence( 2 ).length();
}
}
} //tutorial
} //protocols