Module _core_scoring_
Classes
APBSConfig
APBSConfigAP
APBSConfigCAP
APBSResult
APBSResultAP
APBSResultCAP
APBSWrapper
APBSWrapperAP
APBSWrapperCAP
AtomNeighbor
AtomNeighborAP
AtomNeighborCAP
AtomVDW
AtomVDWAP
AtomVDWCAP
BB_Pos
BB_PosAP
BB_PosCAP
CSA
CSAAP
CSACAP
CenHBPotential
CenHBPotentialAP
CenHBPotentialCAP
CenListInfo
CenListInfoAP
CenListInfoCAP
CenRotEnvPairPotential
CenRotEnvPairPotentialAP
CenRotEnvPairPotentialCAP
ChemicalShiftAnisotropy
ChemicalShiftAnisotropyAP
ChemicalShiftAnisotropyCAP
ContextGraph
ContextGraphAP
ContextGraphCAP
ContextGraphFactory
ContextGraphFactoryAP
ContextGraphFactoryCAP
ContextGraphType
DC
DCAP
DCCAP
DenseEnergyContainer
DenseEnergyContainerAP
DenseEnergyContainerCAP
DenseNeighborConstIterator
DenseNeighborConstIteratorAP
DenseNeighborConstIteratorCAP
DenseNeighborIterator
DenseNeighborIteratorAP
DenseNeighborIteratorCAP
DerivVectorPair
DerivVectorPairAP
DerivVectorPairCAP
DipolarCoupling
DipolarCouplingAP
DipolarCouplingCAP
DockingScoreFunction
DockingScoreFunctionAP
DockingScoreFunctionCAP
EMapVector
EMapVectorAP
EMapVectorCAP
Energies
EnergiesAP
EnergiesCAP
EnergyEdge
EnergyEdgeAP
EnergyEdgeCAP
EnergyGraph
EnergyGraphAP
EnergyGraphCAP
EnergyNode
EnergyNodeAP
EnergyNodeCAP
EnvPairPotential
EnvPairPotentialAP
EnvPairPotentialCAP
ExcludedResPredicate
ExcludedResPredicateAP
ExcludedResPredicateCAP
GenBornPoseInfo
GenBornPoseInfoAP
GenBornPoseInfoCAP
GenBornPotential
GenBornPotentialAP
GenBornPotentialCAP
GenBornResidueInfo
GenBornResidueInfoAP
GenBornResidueInfoCAP
GenBornRotamerSetInfo
GenBornRotamerSetInfoAP
GenBornRotamerSetInfoCAP
Hairpin
HairpinAP
HairpinCAP
Hairpins
HairpinsAP
HairpinsCAP
Helices
HelicesAP
HelicesCAP
IsProteinCAPredicate
IsProteinCAPredicateAP
IsProteinCAPredicateCAP
LREnergyContainer
LREnergyContainerAP
LREnergyContainerCAP
MembraneEmbed
MembraneEmbedAP
MembraneEmbedCAP
MembranePotential
MembranePotentialAP
MembranePotentialCAP
MembraneTopology
MembraneTopologyAP
MembraneTopologyCAP
Membrane_FAEmbed
Membrane_FAEmbedAP
Membrane_FAEmbedCAP
Membrane_FAPotential
Membrane_FAPotentialAP
Membrane_FAPotentialCAP
MinScoreScoreFunction
MinScoreScoreFunctionAP
MinScoreScoreFunctionCAP
MinimizationEdge
MinimizationEdgeAP
MinimizationEdgeCAP
MinimizationGraph
MinimizationGraphAP
MinimizationGraphCAP
MinimizationNode
MinimizationNodeAP
MinimizationNodeCAP
NeighborList
NeighborListAP
NeighborListCAP
OmegaTether
OmegaTetherAP
OmegaTetherCAP
OneToAllEnergyContainer
OneToAllEnergyContainerAP
OneToAllEnergyContainerCAP
OneToAllNeighborConstIterator
OneToAllNeighborConstIteratorAP
OneToAllNeighborConstIteratorCAP
OneToAllNeighborIterator
OneToAllNeighborIteratorAP
OneToAllNeighborIteratorCAP
PQR
PQRAP
PQRCAP
P_AA
P_AAAP
P_AACAP
PairEPotential
PairEPotentialAP
PairEPotentialCAP
PeptideBondedEnergyContainer
PeptideBondedEnergyContainerAP
PeptideBondedEnergyContainerCAP
PeptideBondedNeighborConstIterator
PeptideBondedNeighborConstIteratorAP
PeptideBondedNeighborConstIteratorCAP
PeptideBondedNeighborIterator
PeptideBondedNeighborIteratorAP
PeptideBondedNeighborIteratorCAP
PoissonBoltzmannPotential
PoissonBoltzmannPotentialAP
PoissonBoltzmannPotentialCAP
Predicate
PredicateAP
PredicateCAP
ProQPotential
ProQPotentialAP
ProQPotentialCAP
ProteinTorsion
RDC
RDCAP
RDCCAP
RDC_Rohl
RDC_RohlAP
RDC_RohlCAP
Rama2BOffset
Rama2BOffsetAP
Rama2BOffsetCAP
Rama2BOffsetTables
Ramachandran
Ramachandran2B
Ramachandran2BAP
Ramachandran2BCAP
RamachandranAP
RamachandranCAP
ResPairMinimizationData
ResPairMinimizationDataAP
ResPairMinimizationDataCAP
ResRangePredicate
ResRangePredicateAP
ResRangePredicateCAP
ResSingleMinimizationData
ResSingleMinimizationDataAP
ResSingleMinimizationDataCAP
ResidualDipolarCoupling
ResidualDipolarCouplingAP
ResidualDipolarCouplingCAP
ResidualDipolarCoupling_Rohl
ResidualDipolarCoupling_RohlAP
ResidualDipolarCoupling_RohlCAP
ResidueNblistData
ResidueNblistDataAP
ResidueNblistDataCAP
ResidueNeighborConstIterator
ResidueNeighborConstIteratorAP
ResidueNeighborConstIteratorCAP
ResidueNeighborIterator
ResidueNeighborIteratorAP
ResidueNeighborIteratorCAP
ResiduePairNeighborList
ResiduePairNeighborListAP
ResiduePairNeighborListCAP
SS_Info
SS_InfoAP
SS_InfoCAP
SS_Killhairpins_Info
SS_Killhairpins_InfoAP
SS_Killhairpins_InfoCAP
ScoreFunction
ScoreFunctionAP
ScoreFunctionCAP
ScoreFunctionFactory
ScoreFunctionFactoryAP
ScoreFunctionFactoryCAP
ScoreFunctionInfo
ScoreFunctionInfoAP
ScoreFunctionInfoCAP
ScoreType
ScoreTypeManager
ScoreTypeManagerAP
ScoreTypeManagerCAP
ScoringManager
ScoringManagerAP
ScoringManagerCAP
SecondaryStructurePotential
SecondaryStructurePotentialAP
SecondaryStructurePotentialCAP
SecondaryStructureWeights
SecondaryStructureWeightsAP
SecondaryStructureWeightsCAP
SelectedResPredicate
SelectedResPredicateAP
SelectedResPredicateCAP
SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase_T_core_chemical_ChemicalManager_TAP
SingletonBase_T_core_chemical_ChemicalManager_TCAP
SingletonBase_T_core_scoring_ScoringManager_T
SingletonBase_T_core_scoring_ScoringManager_TAP
SingletonBase_T_core_scoring_ScoringManager_TCAP
SmallAtNb
SmallAtNbAP
SmallAtNbCAP
SmoothEnvPairPotential
SmoothEnvPairPotentialAP
SmoothEnvPairPotentialCAP
SmoothScoreTermCoeffs
SmoothScoreTermCoeffsAP
SmoothScoreTermCoeffsCAP
Strands
StrandsAP
StrandsCAP
TMscore
TMscoreAP
TMscoreCAP
TMscoreStore
TMscoreStoreAP
TMscoreStoreCAP
TenANeighborEdge
TenANeighborEdgeAP
TenANeighborEdgeCAP
TenANeighborGraph
TenANeighborGraphAP
TenANeighborGraphCAP
TenANeighborNode
TenANeighborNodeAP
TenANeighborNodeCAP
TwelveANeighborEdge
TwelveANeighborEdgeAP
TwelveANeighborEdgeCAP
TwelveANeighborGraph
TwelveANeighborGraphAP
TwelveANeighborGraphCAP
TwelveANeighborNode
TwelveANeighborNodeAP
TwelveANeighborNodeCAP
UnfoldedStatePotential
UnfoldedStatePotentialAP
UnfoldedStatePotentialCAP
WaterAdductHBondPotential
WaterAdductHBondPotentialAP
WaterAdductHBondPotentialCAP
__CPP_CenListInfo__
__CPP_ChemicalShiftAnisotropy__
__CPP_DenseEnergyContainer__
__CPP_DenseNeighborConstIterator__
__CPP_DenseNeighborIterator__
__CPP_DipolarCoupling__
__CPP_DockingScoreFunction__
__CPP_Energies__
__CPP_EnergyEdge__
__CPP_EnergyGraph__
__CPP_EnergyNode__
__CPP_ExcludedResPredicate__
__CPP_GenBornPoseInfo__
__CPP_GenBornRotamerSetInfo__
__CPP_IsProteinCAPredicate__
__CPP_LREnergyContainer__
__CPP_MembraneEmbed__
__CPP_MembranePotential__
__CPP_MembraneTopology__
__CPP_Membrane_FAEmbed__
__CPP_Membrane_FAPotential__
__CPP_MinScoreScoreFunction__
__CPP_MinimizationEdge__
__CPP_MinimizationGraph__
__CPP_MinimizationNode__
__CPP_OneToAllEnergyContainer__
__CPP_OneToAllNeighborConstIterator__
__CPP_OneToAllNeighborIterator__
__CPP_PeptideBondedEnergyContainer__
__CPP_PeptideBondedNeighborConstIterator__
__CPP_PeptideBondedNeighborIterator__
__CPP_Predicate__
__CPP_ResRangePredicate__
__CPP_ResidualDipolarCoupling_Rohl__
__CPP_ResidualDipolarCoupling__
__CPP_ResidueNblistData__
__CPP_ResiduePairNeighborList__
__CPP_SS_Info__
__CPP_SS_Killhairpins_Info__
__CPP_ScoreFunction__
__CPP_SelectedResPredicate__
__CPP_TenANeighborEdge__
__CPP_TenANeighborNode__
__CPP_TwelveANeighborEdge__
__CPP_TwelveANeighborNode__
min_pair_data
min_single_data
Functions
CA_gdtmm
CA_gdttm
CA_maxsub
CA_rmsd
CA_rmsd_symmetric
MembraneEmbed_from_pose
MembraneTopology_from_pose
Membrane_FAEmbed_from_pose
all_atom_rmsd
all_atom_rmsd_nosuper
all_scatom_rmsd_nosuper
automorphic_rmsd
bb_rmsd
bb_rmsd_including_O
calc_atom_masks
calc_per_atom_sasa
calc_per_atom_sasa_sc
calc_per_res_hydrophobic_sasa
calc_total_sasa
calpha_superimpose_pose
compute_bb_centroid
compute_bb_radius
compute_jump_rmsd
compute_sc_centroid
compute_sc_radius
create_score_function
create_score_function_ws_patch
create_shuffle_map_recursive_rms
eval_atom_derivatives_for_minedge
eval_atom_derivatives_for_minnode
eval_bbbb_sr2b_energies
eval_bbsc_sr2b_energies
eval_dof_deriv_for_minnode
eval_res_onebody_energies_for_minnode
eval_res_pair_energy_for_minedge
eval_scsc_sr2b_energies
eval_weighted_atom_derivatives_for_minedge
eval_weighted_dof_deriv_for_minnode
eval_weighted_res_onebody_energies_for_minnode
eval_weighted_res_pair_energy_for_minedge
find_weights_file
gdtha
gdtsc
get_2way_orientation
get_angles
get_masks
get_num_bytes
get_orientation
get_overlap
get_score_function
get_score_functionName
get_score_function_legacy
input_sasa_dats
interpolate_value_and_deriv
invert_exclude_residues
is_heavyatom
is_ligand_heavyatom
is_ligand_heavyatom_residues
is_nbr_atom
is_non_peptide_heavy_atom
is_polymer_heavyatom
is_protein_CA
is_protein_CA_or_CB
is_protein_backbone
is_protein_backbone_including_O
is_protein_sidechain_heavyatom
is_scatom
name_from_score_type
native_CA_gdtmm
native_CA_rmsd
nbr_atom_rmsd
non_peptide_heavy_atom_RMSD
nonconst_MembraneEmbed_from_pose
nonconst_MembraneTopology_from_pose
nonconst_Membrane_FAEmbed_from_pose
normalizing_area
residue_sc_rmsd_no_super
retrieve_CSA_from_pose
retrieve_DC_from_pose
retrieve_RDC_ROHL_from_pose
retrieve_RDC_from_pose
rms_at_all_corresponding_atoms
rms_at_corresponding_atoms
rms_at_corresponding_atoms_no_super
rms_at_corresponding_heavy_atoms
score_type_from_name
setup_matching_CA_atoms
setup_matching_atoms_with_given_names
setup_matching_heavy_atoms
setup_matching_protein_backbone_heavy_atoms
store_CSA_in_pose
store_DC_in_pose
store_RDC_ROHL_in_pose
store_RDC_in_pose
superimpose_pose
xyz_gdtmm
xyz_gdttm
xyz_maxsub
Variables
CHI1
CHI2
CHI3
CHI4
CIS_XP
CIS_XX
DFIRE
FaMPEnv
FaMPEnvSmooth
FaMPSolv
Hpol_bond_geometry
MPCbeta
MPEnv
MPLipo
MPNonHelix
MPPair
MPTMProj
MPTermini
Mcbeta
Menv
Menv_non_helix
Menv_smooth
Menv_termini
Menv_tm_proj
Mlipo
Mpair
NRAMATABLES
OMEGA
PB_elec
PHI
PSI
ProQ
ProQM
PyRosettaEnergy_first
PyRosettaEnergy_last
PyRosettaTwoBodyContextDependentEnergy_first
PyRosettaTwoBodyContextDependentEnergy_last
PyRosettaTwoBodyContextIndepenedentEnergy_first
PyRosettaTwoBodyContextIndepenedentEnergy_last
TRANS_GG
TRANS_GP
TRANS_GV
TRANS_GX
TRANS_PG
TRANS_PP
TRANS_PV
TRANS_PX
TRANS_VG
TRANS_VP
TRANS_VV
TRANS_VX
TRANS_XG
TRANS_XP
TRANS_XV
TRANS_XX
__package__
aa_cmp
abego
angle_constraint
atom_pair_constraint
backbone_stub_constraint
backbone_stub_linear_constraint
big_bin_constraint
bond_geometry
burial
cart_bonded
cart_bonded_angle
cart_bonded_length
cart_bonded_torsion
cbeta
cbeta_smooth
cen_env_smooth
cen_hb
cen_pair_smooth
cen_rot_cbeta
cen_rot_dun
cen_rot_env
cen_rot_pair
cen_rot_pair_ang
cen_rot_pair_dih
cenpack
cenpack_smooth
centroid_neighbor_graph
ch_bond
ch_bond_bb_bb
ch_bond_bb_sc
ch_bond_sc_sc
chainbreak
co
coarse_beadlj
coarse_fa_atr
coarse_fa_rep
coarse_fa_sol
constant_constraint
coordinate_constraint
csa
cst_res_data
cst_respair_data
custom_atom_pair
d2h_sa
dab_sasa
dab_sev
dc
dihedral_constraint
distance_chainbreak
dna_base_distance
dna_bb_torsion
dna_bp
dna_bs
dna_chi
dna_dr
dna_sugar_close
dock_ens_conf
dof_constraint
dslf_ca_dih
dslf_cbs_ds
dslf_cs_ang
dslf_fa13
dslf_ss_dih
dslf_ss_dst
dslfc_RT
dslfc_ang
dslfc_bb_dih
dslfc_cb_dih
dslfc_cb_dst
dslfc_cen_dst
dslfc_rot
dslfc_trans
dummy_score_type
dunbrack_constraint
e_pH
elec_dens_atomwise
elec_dens_fast
elec_dens_whole_structure_allatom
elec_dens_whole_structure_ca
elec_dens_window
elec_pair_nblist
end_of_score_type_enumeration
env
envsmooth
etab_classic_intrares_pair_nblist
etab_classic_intrares_single_nblist
etab_pair_nblist
etab_single_nblist
fa_atr
fa_atr_dummy
fa_cust_pair_dist
fa_custom_pair_dist_data
fa_dslf_respair_data
fa_dun
fa_dun_dev
fa_dun_rot
fa_dun_semi
fa_elec
fa_elec_aro_all
fa_elec_aro_aro
fa_elec_bb_bb
fa_elec_bb_sc
fa_elec_rna_base_base
fa_elec_rna_base_base_fast
fa_elec_rna_phos_base
fa_elec_rna_phos_base_fast
fa_elec_rna_phos_phos
fa_elec_rna_phos_phos_fast
fa_elec_rna_phos_sugr
fa_elec_rna_phos_sugr_fast
fa_elec_rna_sugr_base
fa_elec_rna_sugr_base_fast
fa_elec_rna_sugr_sugr
fa_elec_rna_sugr_sugr_fast
fa_elec_sc_sc
fa_grpelec
fa_intra_RNA_base_phos_atr
fa_intra_RNA_base_phos_rep
fa_intra_RNA_base_phos_sol
fa_intra_atr
fa_intra_atr_xover4
fa_intra_rep
fa_intra_rep_xover4
fa_intra_sol
fa_intra_sol_xover4
fa_mbenv
fa_mbsolv
fa_pair
fa_pair_aro_aro
fa_pair_aro_pol
fa_pair_pol_pol
fa_plane
fa_rep
fa_rep_dummy
fa_sol
fa_sol_dummy
fa_stack
fa_stack_aro
fa_stack_lower
fa_stack_upper
facts_elec
facts_sasa
facts_solv
fastsaxs
fiberdiffraction
fiberdiffractiondens
free_2HOprime
free_base
free_dof
free_res
free_side_chain
free_suite
gauss
gb_elec
geom_sol
geom_sol_fast
geom_sol_fast_intra_RNA
geom_sol_intra_RNA
geom_solv_pair_nblist
goap
goap_angle
goap_dist
h2o_hbond
h2o_intra
hack_aro
hbond
hbond_bb_sc
hbond_intra
hbond_lr_bb
hbond_lr_bb_sc
hbond_res_data
hbond_respair_data
hbond_sc
hbond_sr_bb
hbond_sr_bb_sc
holes
holes_decoy
holes_min
holes_min_mean
holes_resl
hpatch
hs_pair
hybrid_vdw
interchain_contact
interchain_env
interchain_pair
interchain_vdw
interface_dd_pair
intermol
linear_chainbreak
lk_PolarNonPolar_pair_nblist
lk_ball
lk_ball_iso
lk_ball_wtd
lk_costheta
lk_hack
lk_nonpolar
lk_nonpolar_intra_RNA
lk_polar
lk_polar_intra_RNA
lkb_res_data
lkb_respair_data
loop_close
metalhash_constraint
mg_ref
missing_res
mm_bend
mm_lj_inter_atr
mm_lj_inter_rep
mm_lj_intra_atr
mm_lj_intra_rep
mm_stretch
mm_twist
n_ci_2b_score_types
n_min_pair_data
n_min_single_data
n_score_types
n_shortranged_2b_score_types
natbias_hh
natbias_hs
natbias_ss
natbias_stwist
neigh_count
neigh_vect
neigh_vect_raw
nmer_pssm
nmer_ref
nmer_svm
num_context_graph_types
occ_sol_exact
occ_sol_fitted
occ_sol_fitted_onebody
omega
omega2b_offset
orbitals_hpol_bb
other_pose
overlap_chainbreak
p_aa
p_aa_pp
p_aa_pp_offset
pack_stat
pair
patterson_cc
pci_cation_pi
pci_hbond
pci_pi_pi
pci_salt_bridge
pcs
pcs2
pcsTs1
pcsTs2
pcsTs3
pcsTs4
pddf_score
peptide_bond
pocket_constraint
pro_close
protein_torsion_end
python
rama
rama2b
rama2b_offset
rdc
rdc_rohl
rdc_segments
ref
ref_nc
res_type_constraint
res_type_linking_constraint
rg
rg_local
rms
rna_backbone_backbone
rna_base_axis
rna_base_axis_pairwise
rna_base_backbone
rna_base_pair
rna_base_pair_pairwise
rna_base_stack
rna_base_stack_axis
rna_base_stack_axis_pairwise
rna_base_stack_pairwise
rna_base_stagger
rna_base_stagger_pairwise
rna_bond_geometry
rna_bulge
rna_chem_map
rna_chem_map_lores
rna_chem_shift
rna_data_backbone
rna_data_base
rna_fa_atr_base
rna_fa_rep_base
rna_jr_suite
rna_mg
rna_mg_indirect
rna_mg_rep
rna_repulsive
rna_rg
rna_sugar_close
rna_suite
rna_torsion
rna_torsion_sc
rna_vdw
rsigma
sa
saxs_cen_score
saxs_fa_score
saxs_score
seqdep_ref
sheet
site_constraint
special_rot
ss_pair
stack_elec
stack_elec_base_base
stack_elec_base_bb
suck
sugar_bb
suiteness_bonus
surface
symE_bonus
sym_lig
ten_A_neighbor_graph
total_score
twelve_A_neighbor_graph
unfolded
vall_lb
vdw
xtal_ml
xtal_rfree
xtal_rwork
yhh_planarity
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