Module _protocols_comparative_modeling_

    protocols/comparative_modeling/util.hh:108

    C++ signature :
        protocols::comparative_modeling::AlignmentSet alignments_from_cmd_line()

Returns: AlignmentSet :

bounded_loops_from_alignment( (int)num_residues, (int)min_size, (SequenceAlignment)alignment, (Loops)unaligned_regions) -> None :
    Identifies consecutive stretches of unaligned residues by scanning
    the alignment. Each unaligned region is guaranteed to have length at least
    <min_size>. Aligned regions share this property as well, and can be obtained
    by calling the invert() method on the output parameter <unaligned_regions>.
    

    C++ signature :
        void bounded_loops_from_alignment(unsigned long,unsigned long,core::sequence::SequenceAlignment,boost::shared_ptr<protocols::loops::Loops> {lvalue})

    Initiates LoopRelaxThreadingMover using the job distributor (jd2)
    

    C++ signature :
        void cm_main()

Returns: None :

gather_coords( (Pose)model, (Pose)native, (SequenceAlignment)aln, (int)natoms, (object)p1a, (object)p2a [, (str)atom_name='CA']) -> None :
    protocols/comparative_modeling/coord_util.hh:35

    C++ signature :
        void gather_coords(core::pose::Pose,core::pose::Pose,core::sequence::SequenceAlignment,int {lvalue},ObjexxFCL::FArray2D<double> {lvalue},ObjexxFCL::FArray2D<double> {lvalue} [,std::string='CA'])

initialize_ss( (Pose)pose) -> None :
    protocols/comparative_modeling/util.hh:95

    C++ signature :
        void initialize_ss(core::pose::Pose {lvalue})

loops_are_closed( (Pose)pose) -> bool :
    protocols/comparative_modeling/util.hh:100

    C++ signature :
        bool loops_are_closed(core::pose::Pose {lvalue})

loops_from_alignment( (int)nres, (SequenceAlignment)aln, (int)min_loop_size) -> Loops :
    protocols/comparative_modeling/util.hh:36

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> loops_from_alignment(unsigned long,core::sequence::SequenceAlignment,unsigned long)

loops_from_transitive_alignments( (int)nres1, (SequenceAlignment)aln1, (int)nres2, (SequenceAlignment)aln2, (int)min_loop_size) -> Loops :
    protocols/comparative_modeling/util.hh:54

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> loops_from_transitive_alignments(unsigned long,core::sequence::SequenceAlignment,unsigned long,core::sequence::SequenceAlignment,unsigned long)

pick_loops_chainbreak( (Pose)query_pose, (int)min_loop_size) -> Loops :
    protocols/comparative_modeling/util.hh:65

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> pick_loops_chainbreak(core::pose::Pose {lvalue},unsigned long)

pick_loops_unaligned( (int)nres, (vector1_Size)unaligned_residues, (int)min_loop_size) -> Loops :
    protocols/comparative_modeling/util.hh:60

    C++ signature :
        boost::shared_ptr<protocols::loops::Loops> pick_loops_unaligned(unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >,unsigned long)

poses_from_cmd_line( (vector1_string)fn_list) -> object :
    protocols/comparative_modeling/util.hh:105

    C++ signature :
        std::map<std::string, core::pose::Pose, std::less<std::string>, std::allocator<std::pair<std::string const, core::pose::Pose> > > poses_from_cmd_line(utility::vector1<std::string, std::allocator<std::string> >)

randomize_selected_atoms( (Pose)query_pose, (AtomID_Map_T_bool_T)selected) -> None :
    protocols/comparative_modeling/util.hh:113

    C++ signature :
        void randomize_selected_atoms(core::pose::Pose {lvalue},core::id::AtomID_Map<bool>)

rebuild_loops_until_closed( (Pose)query_pose, (int)min_loop_size, (int)max_times, (str)loop_mover_name) -> None :
    protocols/comparative_modeling/util.hh:72

    C++ signature :
        void rebuild_loops_until_closed(core::pose::Pose {lvalue},unsigned long,unsigned long,std::string)

steal_ligands( (Pose)dest_pose, (Pose)source_pose_in, (NamedAtomID)anchor_atom_dest, (NamedAtomID)anchor_atom_source, (object)ligand_indices) -> None :
    Function for stealing ligands from a given Pose
    and adding them to source_pose.
    : The parameters are: @arg dest_pose Pose to which
    ligands are added.
    @arg source_pose_in Pose from which ligands and orientations
    are taken.
    @arg anchor_atom_dest anchor atom providing reference in
    dest_pose for ligand orientation.
    @arg anchor_atom_source anchor atom providing reference in
    source_pose for ligand orientation.
    @arg ligand_indices list of AtomID entries for ligand, one per
    ligand. Ligand orientation is determined by orientation between
    anchor_atom_source and each ligand AtomID.
    

    C++ signature :
        void steal_ligands(core::pose::Pose {lvalue},core::pose::Pose,core::id::NamedAtomID,core::id::NamedAtomID,utility::vector1<core::id::NamedAtomID, std::allocator<core::id::NamedAtomID> >)

    protocols/comparative_modeling/util.hh:98

    C++ signature :
        utility::vector1<core::pose::Pose, std::allocator<core::pose::Pose> > templates_from_cmd_line()

Returns: vector1_Pose :