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Rosetta
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#include <apps/pilot/phil/capri15_scoring.hh>#include <apps/pilot/phil/loop_model.hh>#include <devel/dna/protocols.hh>#include <devel/dna/util.hh>#include <devel/dna/ProteinDNA_Relax.hh>#include <protocols/loops/loops_main.hh>#include <protocols/loops/Loops.hh>#include <protocols/frags/TorsionFragment.hh>#include <utility/excn/Exceptions.hh>#include <protocols/viewer/viewers.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/minimization_packing/RotamerTrialsMover.hh>#include <protocols/simple_moves/DME_FilterMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/minimization_packing/MinMover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/rigid_body_moves.hh>#include <core/scoring/LREnergyContainer.hh>#include <core/scoring/dna/setup.hh>#include <core/scoring/dna/base_geometry.hh>#include <core/scoring/dna/BasePartner.hh>#include <core/scoring/dna/DNA_BasePotential.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/scoring/func/Func.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/CoordinateConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/etable/Etable.hh>#include <core/scoring/AtomVDW.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/hbonds/hbonds.hh>#include <core/scoring/hbonds/HBondSet.hh>#include <core/types.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeSelector.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/AtomTypeSet.hh>#include <core/chemical/MMAtomTypeSet.hh>#include <core/chemical/AA.hh>#include <core/conformation/util.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueMatcher.hh>#include <core/pack/rotamer_trials.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/rotamer_set/RotamerCouplings.hh>#include <core/pack/rotamer_set/WaterPackingInfo.hh>#include <core/kinematics/FoldTree.hh>#include <protocols/viewer/visualize.hh>#include <core/kinematics/MoveMap.hh>#include <core/id/AtomID_Map.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <basic/options/util.hh>#include <basic/prof.hh>#include <basic/basic.hh>#include <core/id/SequenceMapping.hh>#include <core/sequence/util.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <numeric/xyzMatrix.hh>#include <numeric/xyz.functions.hh>#include <numeric/random/random.hh>#include <numeric/random/random_permutation.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <fstream>#include <iostream>#include <string>#include <set>#include <cstdlib>#include <sstream>#include <math.h>#include <basic/Tracer.hh>#include <basic/options/keys/OK.OptionKeys.gen.hh>#include <core/import_pose/import_pose.hh>#include <core/pose/util.hh>#include <core/util/SwitchResidueTypeSet.hh>Classes | |
| class | BondedRNA_Mover |
Typedefs | |
| typedef std::map< std::string, std::string > | SS_Map |
Functions | |
| void | capri15_relax (pose::Pose &pose, protocols::loops::Loops const &loops) |
| FWD DEC. More... | |
| ScoreFunctionOP | get_relax_scorefxn () |
| void | setup_sam_constraints_for_t033 (pose::Pose &pose) |
| SS_Map | get_t033_ss () |
| void | get_sequence_and_secstruct_from_dssp (std::string const &filename, std::string &sequence, std::string &secstruct) |
| std::string | filebase (std::string const &file) |
| id::SequenceMapping | trim_back_t033_pose (pose::Pose &pose) |
| void | setup_bonded_protein_rna_pose (pose::Pose &pose, pose::Pose rna_pose) |
| utility::vector1< DOF_ID > | get_bonded_rna_dof_ids (pose::Pose const &pose) |
| void | make_bonded_rna_move (pose::Pose &pose, Real const scale, bool const reorient) |
| ScoreFunctionOP | get_loop_scorefxn () |
| ScoreFunctionOP | get_loop_scorefxn_old () |
| ScoreFunctionOP | get_centroid_dock_scorefxn () |
| ScoreFunctionOP | get_centroid_dock_scorefxn_old () |
| protocols::loops::Loops | rebuild_trimmed_loops (pose::Pose &pose, std::string const &t033_seq, id::SequenceMapping const &mapping_from_t033_to_pose, SS_Map const &ss_map) |
| void | sample_rna_dofs_new (pose::Pose const &start_pose, std::string const &output_tag, Size const nstruct, std::string const &t033_seq, id::SequenceMapping const &mapping_from_t033_to_pose, SS_Map const &ss_map, bool const fa_relax) |
| void | capri_t033_centroid_trim_dock_test () |
| void | trim_dock_rebuild_relax_test_rhiju () |
| void | trim_dock_rebuild_relax_test () |
| Size | pose_pos_from_pdb_pos (int const pdb_pos, char const pdb_chain, pose::Pose const &pose) |
| void | setup_sam_constraints (pose::Pose &pose, id::SequenceMapping const &mapping_from_1p91A_to_pose, pose::Pose const &p91A_pose) |
| void | juke_sam_pos (pose::Pose &pose, id::SequenceMapping const &mapping_from_1p91A_to_pose, pose::Pose const &p91A_pose) |
| begins with full protein repack with soft soft rep, so can call immediately after core::util::switch_to_residue_type_set(FA) More... | |
| void | relax_test () |
| void | centroid_rescore_test () |
| void | diversify_sam_loop_test () |
| void | capri_t033_trim_dock_test () |
| void | capri_t033_loop_test () |
| char | map_sec (char const sec) |
| std::string | map_secstruct (std::string const &ss) |
| void | capri15_test () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("apps.pilot.phil.loop_model") |
| typedef std::map< std::string, std::string > SS_Map |
| void capri15_relax | ( | pose::Pose & | pose, |
| protocols::loops::Loops const & | loops | ||
| ) |
FWD DEC.
start with a docked, loop-rebuilt pose containing protein+sam+rna
– switch to fullatom residue set
– ramp up the repulsive
– scorefxn:
standard wts atompair constraints holding the sam capri15 scores
– dofs:
protein-SAM jump sam-rna dofs (6) protein chi angles
– moves: ( use nbr-atom dme filter as in zf-relax )
sam-jump move sam-rna dof move as in centroid docking, but with smaller scale loop small moves
References ObjexxFCL::abs(), test.T009_Exceptions::e, basic::options::OptionKeys::relax::energycut, get_bonded_rna_dof_ids(), get_relax_scorefxn(), create_a3b_hbs::i, loops::inner_cycles, numeric::log(), mc, vancomycin::min_mover, beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::dna::specificity::n_inner, basic::options::OptionKeys::dna::specificity::n_outer, create_a3b_hbs::nres, option, test.Workshop6test::pack_mover, beta_nonlocal::pose, ObjexxFCL::pow(), basic::prof_reset(), basic::prof_show(), oop_conformations::scorefxn, and test.Workshop5test::small_mover.
Referenced by relax_test(), and sample_rna_dofs_new().
| void capri15_test | ( | ) |
References utility::options::OptionKeys::options::exit, and get_t033_ss().
Referenced by my_main().
| void capri_t033_centroid_trim_dock_test | ( | ) |
Loops over starting structures, homology models for t033 including sam
References get_t033_ss(), create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::n_outer, basic::options::OptionKeys::dna::specificity::nloop, local::nstruct, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, sample_rna_dofs_new(), setup_bonded_protein_rna_pose(), setup_capri_data(), basic::options::start_files(), ObjexxFCL::string_of(), tag, test.G200_Module_Region::tf, and trim_back_t033_pose().
Referenced by my_main().
| void capri_t033_loop_test | ( | ) |
References utility::io::oc::cout, utility::options::OptionKeys::options::exit, lactamize::filename, full_protein_repack(), create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), oop_conformations::scorefxn, setup_frags_from_vall(), setup_loops_from_mapping(), and basic::options::start_file().
Referenced by my_main().
| void capri_t033_trim_dock_test | ( | ) |
References ObjexxFCL::abs(), vancomycin::CE, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::jumps::contact_score, utility::io::oc::cout, pyrosetta::create_score_function, utility::options::OptionKeys::options::exit, full_protein_repack(), numeric::random::gaussian(), create_a3b_hbs::i, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, option, PHI, pid(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, pose_pos_from_pdb_pos(), numeric::conversions::radians(), oop_conformations::scorefxn, basic::options::start_file(), ObjexxFCL::string_of(), and numeric::random::uniform().
Referenced by my_main().
| void centroid_rescore_test | ( | ) |
For calibrating the new centroid scores, rescore some models made with the old protocol
References utility::graph::Node::const_edge_list_end(), utility::io::oc::cout, create_a3b_hbs::f, get_loop_scorefxn(), utility::graph::Edge::get_node(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::score, oop_conformations::scorefxn, setup_capri_data(), basic::options::start_files(), and test.G200_Module_Region::tf.
Referenced by my_main().
| void diversify_sam_loop_test | ( | ) |
Diversify the conformation of the loop that passes beneath the SAM protocol: ** read 1P91A /w 1qao SAM ** read alignment for trimming, delete unaligned target residues, extend, apply ** setup loops file for the loop under SAM: "IFSPANY" in rlm2 sequence ** delete SAM ** convert to centroid ** centroid perturb ** convert to fullatom ** copy in SAM ** SAM-juke using Jim's constraints
** full protein repack
References utility::io::oc::cout, loops::cutpoint, lactamize::filename, create_a3b_hbs::i, juke_sam_pos(), ObjexxFCL::lead_zero_string_of(), demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), oop_conformations::scorefxn, setup_frags_from_vall(), and numeric::random::uniform().
Referenced by my_main().
| std::string filebase | ( | std::string const & | file | ) |
References evaluate_beta_mutants::file.
| utility::vector1< DOF_ID > get_bonded_rna_dof_ids | ( | pose::Pose const & | pose | ) |
This should be kept in sync with the next routine
References vancomycin::CE, create_a3b_hbs::i, PHI, and beta_nonlocal::pose.
Referenced by capri15_relax().
| ScoreFunctionOP get_centroid_dock_scorefxn | ( | ) |
Referenced by sample_rna_dofs_new().
| ScoreFunctionOP get_centroid_dock_scorefxn_old | ( | ) |
| ScoreFunctionOP get_loop_scorefxn | ( | ) |
References basic::options::OptionKeys::remodel::cbeta, env, options, pair, basic::options::OptionKeys::remodel::rama, basic::options::OptionKeys::remodel::rg, oop_conformations::scorefxn, and basic::options::OptionKeys::remodel::vdw.
Referenced by centroid_rescore_test(), rebuild_trimmed_loops(), and sample_rna_dofs_new().
| ScoreFunctionOP get_loop_scorefxn_old | ( | ) |
| ScoreFunctionOP get_relax_scorefxn | ( | ) |
References test.T220_AtomAtomPairEnergies::fa_elec, and oop_conformations::scorefxn.
Referenced by capri15_relax(), relax_test(), and sample_rna_dofs_new().
| void get_sequence_and_secstruct_from_dssp | ( | std::string const & | filename, |
| std::string & | sequence, | ||
| std::string & | secstruct | ||
| ) |
References data, lactamize::filename, getline(), ObjexxFCL::int_of(), line, make_symmdef_file_denovo::pos, numeric::sec(), secstruct(), and basic::options::OptionKeys::relax::sequence.
Referenced by get_t033_ss().
| SS_Map get_t033_ss | ( | ) |
Returns a map from type to ss, indexed by: "1p91A", "psipred", "sam_stride", "sam_dssp"
References get_sequence_and_secstruct_from_dssp(), create_a3b_hbs::i, map_secstruct(), numeric::sec(), and basic::options::OptionKeys::relax::sequence.
Referenced by capri15_test(), capri_t033_centroid_trim_dock_test(), trim_dock_rebuild_relax_test(), and trim_dock_rebuild_relax_test_rhiju().
| void juke_sam_pos | ( | pose::Pose & | pose, |
| id::SequenceMapping const & | mapping_from_1p91A_to_pose, | ||
| pose::Pose const & | p91A_pose | ||
| ) |
begins with full protein repack with soft soft rep, so can call immediately after core::util::switch_to_residue_type_set(FA)
References pyrosetta::create_score_function, full_protein_repack(), beta_nonlocal::mm, beta_nonlocal::pose, oop_conformations::scorefxn, and setup_sam_constraints().
Referenced by diversify_sam_loop_test().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().
| void make_bonded_rna_move | ( | pose::Pose & | pose, |
| Real const | scale, | ||
| bool const | reorient | ||
| ) |
References ObjexxFCL::abs(), erraser_analysis::angle1, erraser_analysis::angle2, erraser_analysis::bond1, vancomycin::CE, numeric::random::gaussian(), create_a3b_hbs::i, PHI, beta_nonlocal::pose, numeric::conversions::radians(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, and numeric::random::uniform().
Referenced by BondedRNA_Mover::apply(), and sample_rna_dofs_new().
| char map_sec | ( | char const | sec | ) |
References utility::io::oc::cout, and numeric::sec().
Referenced by map_secstruct().
| std::string map_secstruct | ( | std::string const & | ss | ) |
References create_a3b_hbs::i, map_sec(), and challenge::ss.
Referenced by get_t033_ss().
| void* my_main | ( | void * | ) |
References capri15_test(), capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), centroid_rescore_test(), diversify_sam_loop_test(), utility::options::OptionKeys::options::exit, SmotifHasher::mode, option, relax_test(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), and value.
Referenced by main().
| Size pose_pos_from_pdb_pos | ( | int const | pdb_pos, |
| char const | pdb_chain, | ||
| pose::Pose const & | pose | ||
| ) |
Silly helper function
References basic::Tracer::Fatal, create_a3b_hbs::i, basic::options::OptionKeys::dna::specificity::pdb_pos, beta_nonlocal::pose, TR, and utility_exit.
Referenced by capri_t033_trim_dock_test(), and setup_sam_constraints().
| protocols::loops::Loops rebuild_trimmed_loops | ( | pose::Pose & | pose, |
| std::string const & | t033_seq, | ||
| id::SequenceMapping const & | mapping_from_t033_to_pose, | ||
| SS_Map const & | ss_map | ||
| ) |
Take a trimmed, docked model and add the loops
References get_loop_scorefxn(), create_a3b_hbs::i, basic::options::OptionKeys::cluster::loops, option, beta_nonlocal::pose, setup_capri_data(), setup_frags_from_vall(), setup_loops_from_mapping(), and test.G200_Module_Region::tf.
Referenced by sample_rna_dofs_new().
| void relax_test | ( | ) |
read in a full-length model from recent simulations
make chemical bond modifications
setup foldtree:: attach sam by jump, attach rna by bond from sam
read alignment_for_trimming, setup an extended, trimmed mapping from 1p91a pdb to pose
setup loops from this mapping
References capri15_relax(), utility::io::oc::cout, create_a3b_hbs::f, get_relax_scorefxn(), create_a3b_hbs::i, basic::options::OptionKeys::cluster::loops, create_a3b_hbs::nres, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, setup_capri_data(), setup_loops_from_mapping(), basic::options::start_file(), and test.G200_Module_Region::tf.
Referenced by my_main().
| void sample_rna_dofs_new | ( | pose::Pose const & | start_pose, |
| std::string const & | output_tag, | ||
| Size const | nstruct, | ||
| std::string const & | t033_seq, | ||
| id::SequenceMapping const & | mapping_from_t033_to_pose, | ||
| SS_Map const & | ss_map, | ||
| bool const | fa_relax | ||
| ) |
Doesnt do any modifying of protein or rna internal coords Just attaches rna to protein at sam and does random sampling of protein-RNA dofs
References capri15_relax(), utility::io::oc::cout, lactamize::filename, full_protein_repack(), get_centroid_dock_scorefxn(), get_loop_scorefxn(), get_relax_scorefxn(), create_a3b_hbs::i, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, make_bonded_rna_move(), mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::cm::nn, local::nstruct, drrafter_rna::output_tag, beta_nonlocal::pose, rebuild_trimmed_loops(), retrieve_capri_data_from_pose(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, setup_sam_constraints_for_t033(), and ObjexxFCL::string_of().
Referenced by capri_t033_centroid_trim_dock_test(), trim_dock_rebuild_relax_test(), and trim_dock_rebuild_relax_test_rhiju().
| void setup_bonded_protein_rna_pose | ( | pose::Pose & | pose, |
| pose::Pose | rna_pose | ||
| ) |
References create_a3b_hbs::i, and beta_nonlocal::pose.
Referenced by capri_t033_centroid_trim_dock_test(), trim_dock_rebuild_relax_test(), and trim_dock_rebuild_relax_test_rhiju().
| void setup_sam_constraints | ( | pose::Pose & | pose, |
| id::SequenceMapping const & | mapping_from_1p91A_to_pose, | ||
| pose::Pose const & | p91A_pose | ||
| ) |
References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, pid(), beta_nonlocal::pose, and pose_pos_from_pdb_pos().
Referenced by juke_sam_pos(), and setup_sam_constraints_for_t033().
| void setup_sam_constraints_for_t033 | ( | pose::Pose & | pose | ) |
References create_a3b_hbs::i, basic::init(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and setup_sam_constraints().
Referenced by sample_rna_dofs_new().
| id::SequenceMapping trim_back_t033_pose | ( | pose::Pose & | pose | ) |
centroid score for docking / loop building:
"cyan" experimental data reward RNA contacts to conserved residues in protein
for the latter, seems like we need an alignment to t033_.fasta ? In case we've done some trimming??
K/R centroid contacts to phosphate backbone OP2/OP1 S/T/N/Q centroid contacts to phosphate backbone OP2/OP1 D/E/H centroid contacts to O2'
vdw/hybrid vdw
backbone O to O2' backbone N to OP2, OP1
distance between SAM CE and rGU N1
Sets up a trimmed t033 protein using the 1p91 structure with 1qao SAM in place and rna added
Given a pose with protein + SAM + rna, does random re-orientation and slide into contact to get distribution of docked conformations
Trims back a full-length t033 protein+sam pose to include only aligned residues Used for trimming Rhiju's homology models back to only the aligned positions
References create_a3b_hbs::i, basic::options::OptionKeys::cm::min_loop_size, beta_nonlocal::pose, TR, and basic::Tracer::Warning.
Referenced by capri_t033_centroid_trim_dock_test(), and trim_dock_rebuild_relax_test_rhiju().
| void trim_dock_rebuild_relax_test | ( | ) |
Loops over the loop-diversified models Each one has t033 sequence plus SAM minus unaligned residues
MISNOMER AS WE ARE NOT DOING RELAX (NIGHT BEFORE TARGET IS DUE)
References get_t033_ss(), create_a3b_hbs::i, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::cm::nn, local::nstruct, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::random::random_permutation(), numeric::random::rg(), sample_rna_dofs_new(), setup_bonded_protein_rna_pose(), setup_capri_data(), basic::options::start_files(), ObjexxFCL::string_of(), tag, and test.G200_Module_Region::tf.
Referenced by my_main().
| void trim_dock_rebuild_relax_test_rhiju | ( | ) |
References get_t033_ss(), create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, sample_rna_dofs_new(), setup_bonded_protein_rna_pose(), setup_capri_data(), basic::options::start_files(), ObjexxFCL::string_of(), tag, test.G200_Module_Region::tf, and trim_back_t033_pose().
Referenced by my_main().
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static |
Referenced by pose_pos_from_pdb_pos(), and trim_back_t033_pose().
1.9.1