ScoreType.hh

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// 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
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/// @file   core/scoring/ScoreType.hh
/// @brief  Score type enumeration
/// @author Phil Bradley


#ifndef INCLUDED_core_scoring_ScoreType_hh
#define INCLUDED_core_scoring_ScoreType_hh

#include <iostream>
#include <utility/vector1.hh>

namespace core {
namespace scoring {

  /////////////////////////////////////////////////////////////////////////////////
  /////// WARNING WARNING WARNING
  ///////
  /////// if you add a new ScoreType please also add its string name in ScoreTypeManager.cc
  ///////
  /////// WARNING WARNING WARNING
  /////////////////////////////////////////////////////////////////////////////////

/// @brief Type for looking up cached energies
/// I guess we could get rid of the fa_ prefix, except maybe for
/// fa_pair, to distinguish from std::pair and the centroid pair score...
enum ScoreType {

  /// begin short ranged ci2b scores -- these guys are cached
  /// in the energy graph -- when appropriate --
  /// they are reused between rounds of scoring.
  fa_atr = 1, //enumeration starts at 1 for indexing utility::vector1
  fa_rep,
  fa_sol,
  fa_intra_atr,
  fa_intra_rep,
  fa_intra_sol,
  fa_intra_RNA_base_phos_atr, //RNA specific score term
  fa_intra_RNA_base_phos_rep, //RNA specific score term
  fa_intra_RNA_base_phos_sol, //RNA specific score term
  lk_hack,
  lk_ball,
  lk_ball_iso,
  coarse_fa_atr,
  coarse_fa_rep,
  coarse_fa_sol,
  coarse_beadlj,
  mm_lj_intra_rep,
  mm_lj_intra_atr,
  mm_lj_inter_rep,
  mm_lj_inter_atr,
  mm_twist,      // could be lr 2benergy and not in energy graph
  mm_bend,       // could be lr 2benergy and not in energy graph
  mm_stretch,    // could be lr 2benergy and not in energy graph
  lk_costheta,
  lk_polar,
  lk_nonpolar,
  lk_polar_intra_RNA,    //RNA specific score term
  lk_nonpolar_intra_RNA, //RNA specific score term
//  csd_torsion, //commenting out until it is implemented
  hack_elec,
  hack_elec_bb_bb,
  hack_elec_bb_sc,
  hack_elec_sc_sc,
  h2o_hbond,
  dna_dr,
  dna_bp,
  dna_bs,
  peptide_bond,
  pcs, //Pseudocontact Shift Energy
  pcs2, //Pseudocontact Shift Energy version 2. Will replace pcs end of 2010

  fastsaxs,   // fastsaxs agreement using formulation of Stovgaard et al (BMC Bioinf. 2010)
  saxs_score, // centroid saxs asessment
  saxs_cen_score,
  saxs_fa_score, // full-atom SAXS score
  pddf_score, // score based on pairwise distance distribution function

  //pba Membrane all atom terms
  fa_mbenv,       // depth dependent reference term
  fa_mbsolv,      // burial+depth dependent term

  //Split out hack_elec for RNA.
  hack_elec_rna_phos_phos,
  hack_elec_rna_phos_sugr,
  hack_elec_rna_phos_base,
  hack_elec_rna_sugr_sugr,
  hack_elec_rna_sugr_base,
  hack_elec_rna_base_base,

  hack_elec_aro_aro,
  hack_elec_aro_all,
  hack_aro,

  rna_fa_atr_base,
  rna_fa_rep_base,
  rna_data_backbone, // Using chemical accessibility data for RNA.

  //Carbon hydrogen bonds -- moved up here since they are currently context independent.
  ch_bond,
  ch_bond_bb_bb,
  ch_bond_sc_sc,
  ch_bond_bb_sc,

  /// proline closure energy
  pro_close,
  rama2b,

  vdw,     // centroid
  cenpack, // centroid

  cenpack_smooth,   //fpd  smooth cenpack
  cen_hb,           //fpd  centroid bb hbonding

  hybrid_vdw,     // hybrid centroid+fa

  // gaussian overlap
  gauss,


  rna_vdw,          // low res clash check for RNA
  rna_base_backbone,          // Bases to 2'-OH, phosphates, etc.
  rna_backbone_backbone,      // 2'-OH to 2'-OH, phosphates, etc.
  rna_repulsive,              // mainly phosphate-phosphate repulsion
  rna_base_pair_pairwise,    // Base-base interactions (Watson-Crick and non-Watson-Crick)
  rna_base_axis_pairwise,    // Force base normals to be parallel
  rna_base_stagger_pairwise, // Force base pairs to be in same plane.
  rna_base_stack_pairwise,   // Stacking interactions
  rna_base_stack_axis_pairwise,   // Stacking interactions should involve parallel bases.
  rna_data_base, // Using chemical accessibility data for RNA.

  //RNA stuff
  // This is a filtered version of the pairwise RNA low resolution terms above,
  //  disallows a base edge to form  more than one base pair, and
  //  disallows two bases to both stack and pair.
  // THIS IS NOT REALLY PAIR-WISE, but is calculated in a finalize_energy
  //  step at the end of a 2-body  score function (RNA_PairwiseLowResolutionEnergy.cc)
  rna_base_pair,    // Base-base interactions (Watson-Crick and non-Watson-Crick)
  rna_base_axis,    // Force base normals to be parallel
  rna_base_stagger, // Force base pairs to be in same plane.
  rna_base_stack,   // Stacking interactions
  rna_base_stack_axis,   // Stacking interactions should involve parallel bases.

  rna_mg, //knowledge-based term for mg(2+)/RNA interactions for use in low res modeling.
  rna_mg_rep, // ad-hoc, empirically validated term to prevent uncommon mg(2+)/atom interactions.
  rna_mg_indirect, //knowledge-based term for mg(2+)/RNA interactions for use in low res modeling.
  mg_chem_pot, // chemical potential ('mu') of instantiating an explicit mg(2+) ion. Actually a simple one-body term.

  // High resolution
  rna_torsion,       // RNA torsional potential.
  rna_sugar_close,   // constraints to keep RNA sugar closed, and with reasonably ideal geometry
  fa_stack,          // stacking interaction modeled as pairwise atom-atom interactions
  //  fa_stack_purine,          // stacking interaction modeled as pairwise atom-atom interactions FOR PURINE
  //  fa_stack_pyrimidine,          // stacking interaction modeled as pairwise atom-atom interactions FOR PYRIMIDINE
  fa_stack_aro,

  // DNA constraints-based torsional potentials
  dna_bb_torsion,
  dna_sugar_close,
  dna_base_distance,

  CI_geom_sol,           //Context independent version. Currently tested only for RNA case.
  CI_geom_sol_intra_RNA, //RNA specific score term

  fa_cust_pair_dist,  // custom short range 2b
  custom_atom_pair,


  // All the orbitals scoretypes
  orbitals_hpol,
  orbitals_haro,
  orbitals_orbitals,
  orbitals_hpol_bb,

  PyRosettaTwoBodyContextIndepenedentEnergy_first,
  PyRosettaTwoBodyContextIndepenedentEnergy_last = PyRosettaTwoBodyContextIndepenedentEnergy_first + 10,

  // for in-python runtime-defined methods: most inclusive positioning in the
  // score type enum: user may define any kind of energy method
  // However, the user may define only a single runtime defined method
  python,  // <-- Deprecated use PyRosettaEnergie* instead

  n_ci_2b_score_types = python, /// keep this guy at the end of the ci2b scores
  //end ci2b scores

  // Begin short-ranged, context dependent two-body energy method types.
  // These are also cached in the edges of the EnergyGraph.
  fa_pair, /// == fa_pair_pol_pol
  fa_pair_aro_aro,
  fa_pair_aro_pol,
  fa_pair_pol_pol,
  fa_plane,
  hbond_sr_bb,
  hbond_lr_bb,
  hbond_bb_sc,
  hbond_sr_bb_sc,
  hbond_lr_bb_sc,
  hbond_sc,
  hbond_intra,           //Currently effects only RNA

  PyRosettaTwoBodyContextDependentEnergy_first,
  PyRosettaTwoBodyContextDependentEnergy_last = PyRosettaTwoBodyContextDependentEnergy_first + 10,

  // protein-protein interface scores
  interface_dd_pair,

  // Geometric solvation
  geom_sol,
  geom_sol_intra_RNA,    //RNA specific score term
  occ_sol_fitted,
  occ_sol_fitted_onebody,
  occ_sol_exact,

  pair, // centroid
  cen_pair_smooth,  //fpd  smooth centroid pair
  Mpair,
  // sucker atom energy
  suck,

  //RNA stuff
  //Low resolution
  rna_rg,           // Radius of gyration for RNA

  // centroid interchain 1b (docking) scores
  interchain_pair,
  interchain_vdw,

  //
  // end short ranged two body scores
  n_shortranged_2b_score_types = interchain_vdw, // keep this guy at the end of the sr ci/cd 2b scores
  // 30 as of 1/7/2007 -- don't ever code using the literal "30", this is just a helpful count

  gb_elec,

  //Full atom disulfide terms
  dslf_ss_dst,
  dslf_cs_ang,
  dslf_ss_dih,
  dslf_ca_dih,
  dslf_cbs_ds,
  //Centroid disulfide terms
  dslfc_cen_dst,
  dslfc_cb_dst,
  dslfc_ang,
  dslfc_cb_dih,
  dslfc_bb_dih,
  //disulfide matching terms
  dslfc_rot,
  dslfc_trans,
  dslfc_RT,

  atom_pair_constraint,
  constant_constraint,
  coordinate_constraint,
  angle_constraint,
  dihedral_constraint,
  big_bin_constraint,
  dunbrack_constraint,
  site_constraint,
  metalhash_constraint, // Rigid body, metal binding constraints for centroid mode
  rna_bond_geometry, // deviations from ideal geometry

  rama,
  omega,
  fa_dun,
  fa_dun_dev,
  fa_dun_rot,
  fa_dun_semi,
  dna_chi,
  p_aa_pp,
  yhh_planarity,
  h2o_intra,
  ref,
  ref_nc,
  seqdep_ref,
  nmer_ref,
  nmer_pssm,
  envsmooth,
  e_pH,
  rna_bulge,
  mg_ref,  // chemical potential for mg(2+) ('reference weight' in Rosetta lingo)
  special_rot,

  // PB potential
  PB_elec,

  /// Whole structure energies
  /// centroid whole structure energies
  cen_env_smooth,   //fpd smooth centroid env
  cbeta_smooth,     //fpd smooth cbeta
  env,
  cbeta,
  DFIRE,
  Menv,
  Mcbeta,
  Menv_non_helix,
  Menv_termini,
  Menv_tm_proj,
  Mlipo,
  rg, // radius of gyration
  co, // contact order
  hs_pair,
  ss_pair,
  rsigma,
  sheet,
  burial, // informatic burial prediction
  abego,  // informatic torsion-bin prediction

  /// Whole structure energies, centroid score
  // secondary structure scores
  natbias_ss,
  natbias_hs,
  natbias_hh,
  natbias_stwist,

  /// amino acid composition score
  aa_cmp,

  dock_ens_conf, //conformer reference energies for docking

  csa,//NMR chemical shift anisotropy energy
  dc,//NMR dipolar coupling energy
  rdc,//NMR residual dipolar coupling energy
  rdc_segments, //fit alignment on multiple segments independently
  rdc_rohl,
  // end centroid whole structure energies
  holes,
  holes_decoy,
  holes_resl,
  holes_min,
  holes_min_mean,

    rna_chem_shift, //RNA NMR chemical shift pseudo-energy term

  dab_sasa, // classic 1.4A probe solvant accessible surface area
  dab_sev,  // solvent excluded volume -- volume of atoms inflated by 1.4A
  sa, // nonpolar contribution in GBSA

  // centroid interhcain 1b (docking) scores -- Demonstrate that these improve performance or remove them
  interchain_env,
  interchain_contact,
  //

  chainbreak,
  linear_chainbreak,
  overlap_chainbreak,
  distance_chainbreak,
  dof_constraint,

  cart_bonded,  // cartesian bonded potential
  cart_bonded_angle,  // cartesian bonded potential
  cart_bonded_length,  // cartesian bonded potential
  cart_bonded_torsion,  // cartesian bonded potential

  //Neighbor Vector solvation approximation
  neigh_vect,
  neigh_count,
  neigh_vect_raw,



  //Symmetry bonus
  symE_bonus,

  //Implicit Ligand interactions (symmetry)
  sym_lig,

  // Other energies.

  // packing score energy
  pack_stat,

  // model-quality metrics.
  rms,


  // for ResidueConstraint
  res_type_constraint,

  // Residue Type linking constraint
  res_type_linking_constraint,

  // for PocketConstraint
  pocket_constraint,

  // for BackboneStubConstraint
  backbone_stub_constraint,

  surface,
  p_aa,
  unfolded,

  // fit-to-density scores
  elec_dens_fast,
  elec_dens_window,
  elec_dens_whole_structure_ca,
  elec_dens_whole_structure_allatom,
  elec_dens_atomwise,

  // patterson correlation
  patterson_cc,

  hpatch,
  //membrane environment smooth
  Menv_smooth,

  PyRosettaEnergy_first,
  PyRosettaEnergy_last = PyRosettaEnergy_first + 10,

  // etc etc
  // Why is there a total score?
  total_score,

  /// This element marks the end of the active score types.  Elements in the enumeration
  /// up to this point will have space allocated for them in the EnergyMap object.  Elements
  /// past this point are considered inactive and will not have space allocated for them.
  /// If you wish to use an inactive score type, you must move that score type into its appropriate
  /// position in the ScoreType enumeration (described above) and then recompile.
  /// Inactive score types must still have their names included in the ScoreTypeManager's
  /// string-to-score-type map.
  n_score_types = total_score,

  /// This element marks the very end of the score type enumeration.  Elements between
  /// the n_score_types element and this element are considered inactive.  They may not
  /// be used by any EnergyMethod or they will result in an out-of-bounds write and
  /// unexpected behavior.  To use an inactived score type, the score type must be moved
  /// to an earlier position in this enumeration, and the program must be recompiled.
  /// Keep this guy last.
  end_of_score_type_enumeration = total_score
};


typedef utility::vector1< ScoreType > ScoreTypes;

/// @brief Returns the ScoreType titled  <name>
///
/// example(s):
///     score_type_from_name("fa_sol")
/// See also:
///     ScoreFunction
///     ScoreType
///     Energies
///     Energies.residue_total_energies
///     name_from_score_type
ScoreType
score_type_from_name( std::string const & name );

/// @brief Returns the name of the ScoreType  <score_type>
///
/// example(s):
///     name_from_score_type(fa_sol)
/// See also:
///     ScoreFunction
///     ScoreType
///     Energies
///     Energies.residue_total_energies
///     score_type_from_name
std::string
name_from_score_type( ScoreType  score_type );

  /// @brief input operator for ScoreType enum type
std::istream & operator >>( std::istream & is, ScoreType & t );
  /// @brief output operator for ScoreType enum type
std::ostream & operator <<( std::ostream & os, ScoreType const & t );

  /// @brief output operator for ScoreTypes list
std::ostream & operator <<( std::ostream & os, ScoreTypes const & score_types );

} // namespace scoring
} // namespace core


#endif