Module rosetta
Classes
CD
EnergyMethod
PyJobDistributor
PyRosettaException
PythonPyExitCallback
Functions
MPIJobDistributor
Set
Vector1
add_extra_options
defineEnergyMethodCreator
etable_atom_pair_energies
generate_nonstandard_residue_set
get_rosetta_database_path
init
mpi_init
new_vector1_init
output_scorefile
pose_from_sequence
replace_init
rosetta_database_from_env
standard_packer_task
standard_task_factory
version
Variables
ACETYLAMINO_SUGAR
ACETYLATED_NTERMINUS
ACETYLATED_NTERMINUS_VARIANT
ACETYLATION
ACETYL_SUGAR
ADDUCT
ADDUCT_VARIANT
ALDONIC_ACID
ALDONIC_ACID_VARIANT
ALDOSE
ALL_STAGES
ALPHA_AA
ALPHA_SUGAR
ALREADY_SYMMETRIZED
ALTERNATIVE_PROTONATION
AMINO_SUGAR
AROMATIC
AUTOMATIC
AromaticBond
BB
BETA_AA
BETA_SUGAR
BRANCH_LOWER_TERMINUS
BRANCH_LOWER_TERMINUS_VARIANT
BRANCH_POINT
BULGE
BondInRing
BondNotInRing
C1_ACETYLAMINO_SUGAR
C1_AMINO_SUGAR
C1_BRANCH_POINT
C1_DEOXY_SUGAR
C1_MODIFIED
C1_PHOSPHATE
C2_ACETYLAMINO_SUGAR
C2_AMINO_SUGAR
C2_BRANCH_POINT
C2_DEOXY_SUGAR
C2_KETOALDONIC_ACID
C2_MODIFIED
C2_PHOSPHATE
C3_ACETYLAMINO_SUGAR
C3_AMINO_SUGAR
C3_BRANCH_POINT
C3_DEOXY_SUGAR
C3_KETOALDONIC_ACID
C3_MODIFIED
C3_PHOSPHATE
C4_ACETYLAMINO_SUGAR
C4_AMINO_SUGAR
C4_BRANCH_POINT
C4_DEOXY_SUGAR
C4_KETOALDONIC_ACID
C4_MODIFIED
C4_PHOSPHATE
C5_ACETYLAMINO_SUGAR
C5_AMINO_SUGAR
C5_BRANCH_POINT
C5_DEOXY_SUGAR
C5_KETOALDONIC_ACID
C5_MODIFIED
C5_PHOSPHATE
C6_ACETYLAMINO_SUGAR
C6_AMINO_SUGAR
C6_BRANCH_POINT
C6_DEOXY_SUGAR
C6_KETOALDONIC_ACID
C6_MODIFIED
C6_PHOSPHATE
C7_ACETYLAMINO_SUGAR
C7_AMINO_SUGAR
C7_BRANCH_POINT
C7_DEOXY_SUGAR
C7_KETOALDONIC_ACID
C7_MODIFIED
C7_PHOSPHATE
C8_ACETYLAMINO_SUGAR
C8_AMINO_SUGAR
C8_BRANCH_POINT
C8_DEOXY_SUGAR
C8_KETOALDONIC_ACID
C8_MODIFIED
C8_PHOSPHATE
C9_ACETYLAMINO_SUGAR
C9_AMINO_SUGAR
C9_BRANCH_POINT
C9_DEOXY_SUGAR
C9_MODIFIED
C9_PHOSPHATE
CARBOHYDRATE
CARBOXYLATION
CENTROID_HA
CHARGED
CHI
CHI1
CHI2
CHI3
CHI4
CIS_XP
CIS_XX
COARSE
CTERM_CONNECT
CUTPOINT_LOWER
CUTPOINT_UPPER
CYCLIC
C_METHYLAMIDATION
ConjugableBond
D
DCV_ALREADY_CYCLIZED
DCV_CYCLIZABLE
DCV_NOT_CYCLIZABLE
DEOXY_SUGAR
DEPROTONATED
DFIRE
DIIODINATION
DIMETHYLATION
DISULFIDE
DISULFIDE_BONDED
DNA
D_AA
D_SUGAR
DoubleBond
DoubleBondOrder
EIsometry
END_ABINITIO
EX_FOUR_HALF_STEP_STDDEVS
EX_ONE_HALF_STEP_STDDEV
EX_ONE_STDDEV
EX_SIX_QUARTER_STEP_STDDEVS
EX_THREE_THIRD_STEP_STDDEVS
EX_TWO_FULL_STEP_STDDEVS
EX_TWO_HALF_STEP_STDDEVS
ExtraRotSampleCardinality
FAIL_BAD_INPUT
FAIL_DO_NOT_RETRY
FAIL_RETRY
FIRST_PROPERTY
FIRST_VARIANT
FIVE_PRIME_END_OH
FIVE_PRIME_END_PHOSPHATE
FIVE_PRIME_PACKABLE_PHOSPHATE
FIVE_PRIME_PHOSPHATE
FORMS_DISULFIDE_BOND
FURANOSE
FaMPEnv
FaMPEnvSmooth
FaMPSolv
GAMMA_AA
GLYCOSIDE
HBS_POST
HBS_PRE
HYBRID_MAX
HYDROXYLATION
HYDROXYLATION1
HYDROXYLATION2
Hpol_bond_geometry
IsAromaticBond
JUMP
KETOSE
LAST_STAGE
LIGAND
LIPID
LOOP_CLOSURE
LOWERTERM_TRUNC
LOWERTERM_TRUNC_VARIANT
LOWER_TERMINUS
LOWER_TERMINUS_VARIANT
L_AA
L_SUGAR
MCA_accepted_score_beat_last
MCA_accepted_score_beat_low
MCA_accepted_thermally
MCA_rejected
MEMBRANE
METAL
METALBINDING
METHYLATED_CTERMINUS
METHYLATED_CTERMINUS_VARIANT
METHYLATED_NTERM_VARIANT
METHYLATION
METHYL_GLYCOSIDE
MPCbeta
MPEnv
MPLipo
MPNonHelix
MPPair
MPTMProj
MPTermini
MS_SUCCESS
Mcbeta
Menv
Menv_non_helix
Menv_smooth
Menv_termini
Menv_tm_proj
Mlipo
Mpair
NAIVE
NE2_CONNECT
NO_EXTRA_CHI_SAMPLES
NO_SYMMETRIZATION_REQUEST
NRAMATABLES
NTERM_CONNECT
NU
N_ACETYLATION
N_PROPERTIES
N_VARIANTS
NoBondIsometry
NonaromaticBond
NotConjugableBond
OCTREE
OMEGA
OOP_POST
OOP_PRE
OXETOSE
OXIROSE
OrbitalBond
OrbitalBondOrder
PB_elec
PEPTOID
PHI
PHOSPHATE
PHOSPHONATE
PHOSPHONATE_UPPER
PHOSPHONATE_UPPER_VARIANT
PHOSPHORYLATION
POLYMER
PROTEIN
PROTONATED
PROTONATED_H1_ADENOSINE
PSI
PYRANOSE
ProQ
ProQM
PseudoBondOrder
PyRosettaEnergy_first
PyRosettaEnergy_last
PyRosettaTwoBodyContextDependentEnergy_first
PyRosettaTwoBodyContextDependentEnergy_last
PyRosettaTwoBodyContextIndepenedentEnergy_first
PyRosettaTwoBodyContextIndepenedentEnergy_last
RB1
RB2
RB3
RB4
RB5
RB6
RELAX
REPLONLY
REQUEST_SYMMETRIZE_BY_INTERSECTION
REQUEST_SYMMETRIZE_BY_UNION
RING_HYBRID
RNA
SC_BRANCH_POINT
SC_FRAGMENT
SC_ORBITALS
SEPTANOSE
SG_CONNECT
SHOVE_BB
SIALIC_ACID
SIDECHAIN_CONJUGATION
SP2_HYBRID
SP3_HYBRID
SPECIAL_ROT
SRI
STAGE_1
STAGE_2
STAGE_3
STAGE_3a
STAGE_3b
STAGE_4
STRIPEHASH
SULFATION
SURFACE
SWITCH_TO_FULLATOM
ScoreTypesRegistry
SingleBond
SingleBondOrder
TAUTOMER
THETA
THREEDGRID
THREE_PRIME_END_OH
THREE_PRIME_PACKABLE_PHOSPHATE
THREE_PRIME_PHOSPHATE
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
TRIAZOLEMER
TRIMETHYLATION
TripleBond
TripleBondOrder
UNKNOWN_HYBRID
UPPERTERM_TRUNC
UPPERTERM_TRUNC_VARIANT
UPPER_TERMINUS
UPPER_TERMINUS_VARIANT
URONIC_ACID
URONIC_ACID_VARIANT
UnknownAromaticity
UnknownBond
UnknownBondOrder
UnknownConjugability
UnknownIsometry
UnknownRingness
VIRTUAL_BACKBONE_EXCEPT_C1PRIME
VIRTUAL_BASE
VIRTUAL_BASE_HEAVY_ATOM
VIRTUAL_BB
VIRTUAL_DNA_PHOSPHATE
VIRTUAL_NTERM
VIRTUAL_O2PRIME_HYDROGEN
VIRTUAL_PHOSPHATE
VIRTUAL_RESIDUE
VIRTUAL_RESIDUE_VARIANT
VIRTUAL_RIBOSE
VIRTUAL_RNA_RESIDUE
VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE
VIRTUAL_SIDE_CHAIN
WATER
X11_COLORS
XC_AliceBlue
XC_AntiqueWhite
XC_BlanchedAlmond
XC_BlueViolet
XC_CadetBlue
XC_CornflowerBlue
XC_DarkBlue
XC_DarkCyan
XC_DarkGoldenrod
XC_DarkGray
XC_DarkGreen
XC_DarkGrey
XC_DarkKhaki
XC_DarkMagenta
XC_DarkOliveGreen
XC_DarkOrange
XC_DarkOrchid
XC_DarkRed
XC_DarkSalmon
XC_DarkSeaGreen
XC_DarkSlateBlue
XC_DarkSlateGray
XC_DarkSlateGrey
XC_DarkTurquoise
XC_DarkViolet
XC_DebianRed
XC_DeepPink
XC_DeepSkyBlue
XC_DimGray
XC_DimGrey
XC_DodgerBlue
XC_FloralWhite
XC_ForestGreen
XC_GhostWhite
XC_GreenYellow
XC_HotPink
XC_IndianRed
XC_LavenderBlush
XC_LawnGreen
XC_LemonChiffon
XC_LightBlue
XC_LightCoral
XC_LightCyan
XC_LightGoldenrod
XC_LightGoldenrodYellow
XC_LightGray
XC_LightGreen
XC_LightGrey
XC_LightPink
XC_LightSalmon
XC_LightSeaGreen
XC_LightSkyBlue
XC_LightSlateBlue
XC_LightSlateGray
XC_LightSlateGrey
XC_LightSteelBlue
XC_LightYellow
XC_LimeGreen
XC_MediumAquamarine
XC_MediumBlue
XC_MediumOrchid
XC_MediumPurple
XC_MediumSeaGreen
XC_MediumSlateBlue
XC_MediumSpringGreen
XC_MediumTurquoise
XC_MediumVioletRed
XC_MidnightBlue
XC_MintCream
XC_MistyRose
XC_NavajoWhite
XC_NavyBlue
XC_OldLace
XC_OliveDrab
XC_OrangeRed
XC_PaleGoldenrod
XC_PaleGreen
XC_PaleTurquoise
XC_PaleVioletRed
XC_PapayaWhip
XC_PeachPuff
XC_PowderBlue
XC_RosyBrown
XC_RoyalBlue
XC_SaddleBrown
XC_SandyBrown
XC_SeaGreen
XC_SkyBlue
XC_SlateBlue
XC_SlateGray
XC_SlateGrey
XC_SpringGreen
XC_SteelBlue
XC_VioletRed
XC_WhiteSmoke
XC_YellowGreen
XC_aquamarine
XC_azure
XC_beige
XC_bisque
XC_black
XC_blue
XC_blue1
XC_blue2
XC_blue3
XC_blue4
XC_brown
XC_burlywood
XC_chartreuse
XC_chocolate
XC_coral
XC_cornsilk
XC_cyan
XC_firebrick
XC_first_color
XC_gainsboro
XC_gold
XC_goldenrod
XC_gray
XC_gray0
XC_gray10
XC_gray100
XC_gray20
XC_gray30
XC_gray40
XC_gray50
XC_gray60
XC_gray70
XC_gray80
XC_gray90
XC_green
XC_green1
XC_green2
XC_green3
XC_green4
XC_honeydew
XC_ivory
XC_khaki
XC_last_color
XC_lavender
XC_linen
XC_magenta
XC_maroon
XC_moccasin
XC_navy
XC_orange
XC_orchid
XC_peru
XC_pink
XC_plum
XC_purple
XC_red
XC_red1
XC_red2
XC_red3
XC_red4
XC_salmon
XC_seashell
XC_sienna
XC_snow
XC_snow1
XC_snow2
XC_snow3
XC_snow4
XC_tan
XC_thistle
XC_tomato
XC_turquoise
XC_violet
XC_wheat
XC_white
XC_yellow
ZIsometry
ZN_CONNECT
_ROSETTA_DATABASE_PATH_
_ScoreTypesRegistryByType_
__package__
_mem_EnergyCreators_
_mem_EnergyMethods_
aa_ala
aa_arg
aa_asn
aa_asp
aa_b3a
aa_b3c
aa_b3cisACHC
aa_b3cisACPC
aa_b3cisACPrC
aa_b3d
aa_b3e
aa_b3f
aa_b3g
aa_b3h
aa_b3i
aa_b3k
aa_b3l
aa_b3m
aa_b3n
aa_b3p
aa_b3q
aa_b3r
aa_b3s
aa_b3t
aa_b3v
aa_b3w
aa_b3y
aa_cmp
aa_cys
aa_dal
aa_dan
aa_dar
aa_das
aa_dcs
aa_dgn
aa_dgu
aa_dhi
aa_dil
aa_dle
aa_dly
aa_dme
aa_dph
aa_dpr
aa_dse
aa_dth
aa_dtr
aa_dty
aa_dva
aa_gln
aa_glu
aa_gly
aa_h2o
aa_his
aa_ile
aa_leu
aa_lys
aa_met
aa_phe
aa_pro
aa_ser
aa_thr
aa_trp
aa_tyr
aa_unk
aa_unp
aa_val
aa_vrt
abego
accept_reject
all_stats
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
chainID
chainbreak
co
coarse_beadlj
coarse_fa_atr
coarse_fa_rep
coarse_fa_sol
config
config_file_name
constant_constraint
coordinate_constraint
csa
cst_res_data
cst_respair_data
custom_atom_pair
cut_point
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
extend
extras
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
first_DNA_aa
first_D_aa
first_beta3_aa
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
iCode
interchain_contact
interchain_env
interchain_pair
interchain_vdw
interface_dd_pair
intermol
k
last_DNA_aa
last_D_aa
last_beta3_aa
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
logger
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_ppo_torsion_bins
n_score_types
n_shortranged_2b_score_types
na_ade
na_cyt
na_gua
na_rad
na_rcy
na_rgu
na_thy
na_ura
natbias_hh
natbias_hs
natbias_ss
natbias_stwist
neigh_count
neigh_vect
neigh_vect_raw
nmer_pssm
nmer_ref
nmer_svm
no_stats
num_aa_types
num_canonical_aas
num_context_graph_types
number_of_configuration_keywords
number_of_residue_identifiers
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
ppo_torbin_A
ppo_torbin_B
ppo_torbin_E
ppo_torbin_G
ppo_torbin_U
ppo_torbin_X
ppo_torbin_a
ppo_torbin_b
ppo_torbin_e
ppo_torbin_g
pro_close
protein_torsion_end
python
q
rama
rama2b
rama2b_offset
rdc
rdc_rohl
rdc_segments
ref
ref_nc
resSeq
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
skip_rate
special_rot
ss_pair
stack_elec
stack_elec_base_base
stack_elec_base_bb
start
stop
suck
sugar_bb
suiteness_bonus
surface
symE_bonus
sym_lig
ten_A_neighbor_graph
total_score
twelve_A_neighbor_graph
unfolded
use_pose_numbering
vall_lb
vdw
xtal_ml
xtal_rfree
xtal_rwork
yhh_planarity
[hide private]