Module _core_chemical_
Classes
AA
APolarHydrogenFilter
APolarHydrogenFilterAP
APolarHydrogenFilterCAP
AcceptorAtomFilter
AcceptorAtomFilterAP
AcceptorAtomFilterCAP
AddAtom
AddAtomAP
AddAtomAlias
AddAtomAliasAP
AddAtomAliasCAP
AddAtomCAP
AddBond
AddBondAP
AddBondCAP
AddBondType
AddBondTypeAP
AddBondTypeCAP
AddChi
AddChiAP
AddChiCAP
AddChiRotamer
AddChiRotamerAP
AddChiRotamerCAP
AddConnect
AddConnectAP
AddConnectCAP
AddProperty
AddPropertyAP
AddPropertyCAP
AddProtonChi
AddProtonChiAP
AddProtonChiCAP
Adduct
AdductAP
AdductCAP
AppendInterchangeabilityGroup_String
AppendInterchangeabilityGroup_StringAP
AppendInterchangeabilityGroup_StringCAP
AppendMainchainAtom
AppendMainchainAtomAP
AppendMainchainAtomCAP
AromaticAtomFilter
AromaticAtomFilterAP
AromaticAtomFilterCAP
Atom
AtomAP
AtomCAP
AtomICoor
AtomICoorAP
AtomICoorCAP
AtomType
AtomTypeAP
AtomTypeCAP
AtomTypeDatabaseIO
AtomTypeDatabaseIOAP
AtomTypeDatabaseIOCAP
AtomTypeSet
AtomTypeSetAP
AtomTypeSetCAP
AutomorphismIterator
AutomorphismIteratorAP
AutomorphismIteratorCAP
Bond
BondAP
BondAromaticity
BondCAP
BondConjugability
BondIsometry
BondName
BondOrder
BondRingness
CPParameter
ChemicalManager
ChemicalManagerAP
ChemicalManagerCAP
DeleteAtom
DeleteAtomAP
DeleteAtomCAP
DeleteMetalbindingAtom
DeleteMetalbindingAtomAP
DeleteMetalbindingAtomCAP
DeleteProperty
DeletePropertyAP
DeletePropertyCAP
DeleteTerminalChi
DeleteTerminalChiAP
DeleteTerminalChiCAP
ElectronConfiguration
ElectronConfigurationAP
ElectronConfigurationCAP
Element
ElementAP
ElementCAP
ElementSet
ElementSetAP
ElementSetCAP
HeavyAtomFilter
HeavyAtomFilterAP
HeavyAtomFilterCAP
HeavyAtomWithHydrogensFilter
HeavyAtomWithHydrogensFilterAP
HeavyAtomWithHydrogensFilterCAP
HeavyAtomWithPolarHydrogensFilter
HeavyAtomWithPolarHydrogensFilterAP
HeavyAtomWithPolarHydrogensFilterCAP
Hybridization
HydrogenAtomFilter
HydrogenAtomFilterAP
HydrogenAtomFilterCAP
ICoorAtomID
ICoorAtomIDAP
ICoorAtomIDCAP
IdealBondLengthSet
IdealBondLengthSetAP
IdealBondLengthSetCAP
MMAtomType
MMAtomTypeAP
MMAtomTypeCAP
MMAtomTypeSet
MMAtomTypeSetAP
MMAtomTypeSetCAP
NCAARotLibPath
NCAARotLibPathAP
NCAARotLibPathCAP
Orbital
OrbitalAP
OrbitalCAP
Patch
PatchAP
PatchCAP
PatchCase
PatchCaseAP
PatchCaseCAP
PatchOperation
PatchOperationAP
PatchOperationCAP
PolarHydrogenFilter
PolarHydrogenFilterAP
PolarHydrogenFilterCAP
PrependMainchainAtom
PrependMainchainAtomAP
PrependMainchainAtomCAP
RealFilter
RealFilterAP
RealFilterCAP
RedefineChi
RedefineChiAP
RedefineChiCAP
ResConnID
ResConnIDAP
ResConnIDCAP
ResidueConnection
ResidueConnectionAP
ResidueConnectionCAP
ResidueDatabaseIO
ResidueDatabaseIOAP
ResidueDatabaseIOCAP
ResidueLoader
ResidueLoaderAP
ResidueLoaderCAP
ResidueLoaderCreator
ResidueLoaderCreatorAP
ResidueLoaderCreatorCAP
ResidueLoaderOptions
ResidueLoaderOptionsAP
ResidueLoaderOptionsCAP
ResidueLoaderOptionsCreator
ResidueLoaderOptionsCreatorAP
ResidueLoaderOptionsCreatorCAP
ResidueProperties
ResiduePropertiesAP
ResiduePropertiesCAP
ResidueProperty
ResidueSelector
ResidueSelectorAP
ResidueSelectorCAP
ResidueSelectorSingle
ResidueSelectorSingleAP
ResidueSelectorSingleCAP
ResidueType
ResidueTypeAP
ResidueTypeCAP
ResidueTypeKinWriter
ResidueTypeKinWriterAP
ResidueTypeKinWriterCAP
ResidueTypeSet
ResidueTypeSetAP
ResidueTypeSetCAP
RingConformer
RingConformerAP
RingConformerCAP
RingConformerManager
RingConformerManagerAP
RingConformerManagerCAP
RingConformerSet
RingConformerSetAP
RingConformerSetCAP
Selector_AA
Selector_AAAP
Selector_AACAP
Selector_CMDFLAG
Selector_CMDFLAGAP
Selector_CMDFLAGCAP
Selector_MATCH_VARIANTS
Selector_MATCH_VARIANTSAP
Selector_MATCH_VARIANTSCAP
Selector_NAME1
Selector_NAME1AP
Selector_NAME1CAP
Selector_NAME3
Selector_NAME3AP
Selector_NAME3CAP
Selector_NO_VARIANTS
Selector_NO_VARIANTSAP
Selector_NO_VARIANTSCAP
Selector_PROPERTY
Selector_PROPERTYAP
Selector_PROPERTYCAP
Selector_UPPER_POSITION
Selector_UPPER_POSITIONAP
Selector_UPPER_POSITIONCAP
Selector_VARIANT_TYPE
Selector_VARIANT_TYPEAP
Selector_VARIANT_TYPECAP
SetAtomType
SetAtomTypeAP
SetAtomTypeCAP
SetAtomicCharge
SetAtomicChargeAP
SetAtomicChargeCAP
SetBackboneHeavyatom
SetBackboneHeavyatomAP
SetBackboneHeavyatomCAP
SetFormalCharge
SetFormalChargeAP
SetFormalChargeCAP
SetICoor
SetICoorAP
SetICoorCAP
SetIO_String
SetIO_StringAP
SetIO_StringCAP
SetInterchangeabilityGroup_String
SetInterchangeabilityGroup_StringAP
SetInterchangeabilityGroup_StringCAP
SetMMAtomType
SetMMAtomTypeAP
SetMMAtomTypeCAP
SetNbrAtom
SetNbrAtomAP
SetNbrAtomCAP
SetNbrRadius
SetNbrRadiusAP
SetNbrRadiusCAP
SetOrientAtom
SetOrientAtomAP
SetOrientAtomCAP
SetPolymerConnectAtom
SetPolymerConnectAtomAP
SetPolymerConnectAtomCAP
SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase_T_core_chemical_ChemicalManager_TAP
SingletonBase_T_core_chemical_ChemicalManager_TCAP
SingletonBase_T_core_chemical_RingConformerManager_T
SingletonBase_T_core_chemical_RingConformerManager_TAP
SingletonBase_T_core_chemical_RingConformerManager_TCAP
VariantType
__CPP_AddAtomAlias__
__CPP_AddAtom__
__CPP_AddBondType__
__CPP_AddBond__
__CPP_AddChiRotamer__
__CPP_AddChi__
__CPP_AddConnect__
__CPP_AddProperty__
__CPP_AddProtonChi__
__CPP_AppendInterchangeabilityGroup_String__
__CPP_AppendMainchainAtom__
__CPP_DeleteAtom__
__CPP_DeleteMetalbindingAtom__
__CPP_DeleteProperty__
__CPP_DeleteTerminalChi__
__CPP_NCAARotLibPath__
__CPP_PatchCase__
__CPP_PatchOperation__
__CPP_Patch__
__CPP_PrependMainchainAtom__
__CPP_RedefineChi__
__CPP_ResidueLoaderCreator__
__CPP_ResidueLoaderOptionsCreator__
__CPP_ResidueLoaderOptions__
__CPP_ResidueLoader__
__CPP_ResidueProperties__
__CPP_ResidueSelectorSingle__
__CPP_RingConformerSet__
__CPP_Selector_AA__
__CPP_Selector_CMDFLAG__
__CPP_Selector_MATCH_VARIANTS__
__CPP_Selector_NAME1__
__CPP_Selector_NAME3__
__CPP_Selector_NO_VARIANTS__
__CPP_Selector_PROPERTY__
__CPP_Selector_UPPER_POSITION__
__CPP_Selector_VARIANT_TYPE__
__CPP_SetAtomType__
__CPP_SetAtomicCharge__
__CPP_SetBackboneHeavyatom__
__CPP_SetFormalCharge__
__CPP_SetICoor__
__CPP_SetIO_String__
__CPP_SetInterchangeabilityGroup_String__
__CPP_SetMMAtomType__
__CPP_SetNbrAtom__
__CPP_SetNbrRadius__
__CPP_SetOrientAtom__
__CPP_SetPolymerConnectAtom__
Functions
aa_from_name
aa_from_oneletter_code
add_atom_type_set_parameters_from_command_line
apply_adducts_to_residue
calculate_rigid_matrix
convert_residuetype_to_light_graph
convert_to_BondName
create_bond_length
define_mainchain_atoms
enlarge_h_lj_wdepth
error_check_requested_adducts
fill_ideal_xyz_from_icoor
find_bonds_in_rings
find_chi_bonds
find_nbr_dist
fixup_patches
formatted_icoord_tree
get_D_equivalent
get_L_equivalent
get_bond
get_connecting_atoms
get_residue_path_distances
get_rpp_charge
has
is_canonical_D_aa
is_sp2_proton_chi
modify_atom_properties_from_command_line
name_from_aa
nonadduct_variants_match
oneletter_code_from_aa
oneletter_code_specifies_aa
parse_adduct_string
patch_operation_from_patch_file_line
pretty_print_atomicoor
print_chis
read_conformers_from_database_file_for_ring_size
read_topology_file
rename_atoms
reroot_restype
residue_selector_single_from_line
residue_type_all_patches_name
residue_type_base_name
retype_is_aromatic
rosetta_recharge_fullatom
rosetta_retype_fullatom
rsd_set_from_cmd_line
setup_atom_type_reassignments_from_commandline
setup_icoor_reassignments_from_commandline
turn_off_hbonds_to_ester_oxygens
variants_match
variants_match_with_exceptions
write_topology_file
Variables
ACETYLAMINO_SUGAR
ACETYLATED_NTERMINUS
ACETYLATED_NTERMINUS_VARIANT
ACETYLATION
ACETYL_SUGAR
ADDUCT
ADDUCT_VARIANT
ALDONIC_ACID
ALDONIC_ACID_VARIANT
ALDOSE
ALPHA_AA
ALPHA_SUGAR
ALTERNATIVE_PROTONATION
AMINO_SUGAR
AROMATIC
AromaticBond
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
COARSE
CTERM_CONNECT
CUTPOINT_LOWER
CUTPOINT_UPPER
CYCLIC
C_METHYLAMIDATION
ConjugableBond
DEOXY_SUGAR
DEPROTONATED
DIIODINATION
DIMETHYLATION
DISULFIDE
DISULFIDE_BONDED
DNA
D_AA
D_SUGAR
DoubleBond
DoubleBondOrder
EIsometry
FIRST_PROPERTY
FIRST_VARIANT
FIVE_PRIME_END_OH
FIVE_PRIME_END_PHOSPHATE
FIVE_PRIME_PACKABLE_PHOSPHATE
FIVE_PRIME_PHOSPHATE
FORMS_DISULFIDE_BOND
FURANOSE
GAMMA_AA
GLYCOSIDE
HBS_POST
HBS_PRE
HYBRID_MAX
HYDROXYLATION
HYDROXYLATION1
HYDROXYLATION2
IsAromaticBond
KETOSE
LIGAND
LIPID
LOWERTERM_TRUNC
LOWERTERM_TRUNC_VARIANT
LOWER_TERMINUS
LOWER_TERMINUS_VARIANT
L_AA
L_SUGAR
MEMBRANE
METAL
METALBINDING
METHYLATED_CTERMINUS
METHYLATED_CTERMINUS_VARIANT
METHYLATED_NTERM_VARIANT
METHYLATION
METHYL_GLYCOSIDE
NE2_CONNECT
NTERM_CONNECT
N_ACETYLATION
N_PROPERTIES
N_VARIANTS
NoBondIsometry
NonaromaticBond
NotConjugableBond
OOP_POST
OOP_PRE
OXETOSE
OXIROSE
OrbitalBond
OrbitalBondOrder
PEPTOID
PHI
PHOSPHATE
PHOSPHONATE
PHOSPHONATE_UPPER
PHOSPHONATE_UPPER_VARIANT
PHOSPHORYLATION
POLAR
POLYMER
PROTEIN
PROTONATED
PROTONATED_H1_ADENOSINE
PYRANOSE
PseudoBondOrder
REPLONLY
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
SULFATION
SURFACE
SingleBond
SingleBondOrder
TAUTOMER
THETA
THREE_PRIME_END_OH
THREE_PRIME_PACKABLE_PHOSPHATE
THREE_PRIME_PHOSPHATE
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
ZIsometry
ZN_CONNECT
__package__
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_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
first_DNA_aa
first_D_aa
first_beta3_aa
last_DNA_aa
last_D_aa
last_beta3_aa
na_ade
na_cyt
na_gua
na_rad
na_rcy
na_rgu
na_thy
na_ura
num_aa_types
num_canonical_aas
q
[
hide private
]