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| RemodelEnzdesCstModule (protocols::forge::remodel::RemodelData external_data) |
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| ~RemodelEnzdesCstModule () override |
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void | apply (core::pose::Pose &pose) |
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void | blueprint_cst_definition (core::pose::Pose &pose) |
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void | enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn) |
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void | use_backbone_only_blocks () |
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void | use_all_blocks () |
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| EnzConstraintIO (core::chemical::ResidueTypeSetCOP src_restype_set) |
| @ brief constructor for EnzConstraintIO class, builds up function types More...
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| ~EnzConstraintIO () override |
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EnzConstraintIOCOP | get_self_ptr () const |
| self pointers More...
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EnzConstraintIOOP | get_self_ptr () |
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EnzConstraintIOCAP | get_self_weak_ptr () const |
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EnzConstraintIOAP | get_self_weak_ptr () |
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void | read_enzyme_cstfile (std::string fname) |
| reads the enzyme cstfile and for each block of residue residue constraints, creates a new More...
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void | initialize_with_mcfi_list (utility::vector1< MatchConstraintFileInfoListOP > mcfi_list_vec) |
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toolbox::match_enzdes_util::MatchConstraintFileInfoListCOP | mcfi_list (core::Size block) const |
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core::Size | num_mcfi_lists () const |
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void | add_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, bool accept_blocks_missing_header) |
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void | add_constraints_to_pose_for_block_without_clearing_and_header_processing (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, core::Size cst_block) const |
| BE CAREFUL when using this function, it generates constraints. More...
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void | add_pregenerated_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const |
| convenience function that will add constraints to the pose if they have More...
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void | remove_constraints_from_pose (core::pose::Pose &pose, bool const keep_covalent, bool const fail_on_constraints_missing) const |
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void | remove_constraints_from_pose_for_block (core::pose::Pose &pose, core::Size cst_block, bool const fail_on_constraints_missing) const |
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void | remove_position_from_template_res_for_block (core::pose::Pose &pose, core::Size pos, core::Size cst_block) const |
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void | remove_position_from_template_res (core::pose::Pose &pose, core::Size pos) const |
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void | process_pdb_header (core::pose::Pose &pose, bool accept_missing_blocks) |
| reads the residue numbers that the constraints will be applied to. More...
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bool | contains_position (core::pose::Pose const &pose, core::Size const seqpos) const |
| are constraints specified for this position? More...
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bool | is_backbone_only_cst (core::pose::Pose const &pose, core::Size const seqpos) const |
| are the constraints specified at this position mediated through backbone interactions only? More...
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void | update_pdb_remarks_for_backbone_params (core::pose::Pose &pose) const |
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utility::vector1< std::string > | allowed_res_name3_at_position (core::pose::Pose const &pose, core::Size const seqpos) const |
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void | show_cst_definitions () const |
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void | remap_resid (core::id::SequenceMapping const &smap) |
| changing the constrained residues if the sequence length changes More...
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void | set_position_for_missing_res_in_parameter_block (core::pose::Pose &pose, core::Size cst_block, core::Size respos) const |
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void | clear_active_pose_constraints_for_block (core::pose::Pose &pose, core::Size cst_block) const |
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void | set_external_position_for_resA_in_parameter_block (core::Size cst_block, core::Size respos) |
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void | set_external_position_for_resB_in_parameter_block (core::Size cst_block, core::Size respos) |
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EnzConstraintParametersCOP | enz_cst_params (core::Size block) const |
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utility::vector1
< EnzConstraintParametersCOP > | enz_cst_params_missing_in_pose (core::pose::Pose const &pose) const |
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utility::vector1< core::Size > | ordered_constrained_positions (core::pose::Pose const &pose) const |
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core::Size | mcfi_lists_size () const |
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core::Size | enz_cst_params_size () |
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utility::vector1< std::pair
< core::Size, core::Size >
> const & | target_downstream_res () const |
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