rdkit-to-params
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RDKit-to-Params overview
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Database entries
rdkit_to_params package
rdkit-to-params
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Index
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_
__init__() (rdkit_to_params.constraint.Constraints method)
(rdkit_to_params.entries.AAEntry method)
(rdkit_to_params.entries.ACT_COORD_ATOMSEntry method)
(rdkit_to_params.entries.ADD_RINGEntry method)
(rdkit_to_params.entries.ATOM_ALIASEntry method)
(rdkit_to_params.entries.ATOMEntry method)
(rdkit_to_params.entries.BACKBONE_AAEntry method)
(rdkit_to_params.entries.BONDEntry method)
(rdkit_to_params.entries.CHARGEEntry method)
(rdkit_to_params.entries.CHIEntry method)
(rdkit_to_params.entries.CommentEntry method)
(rdkit_to_params.entries.CONNECTEntry method)
(rdkit_to_params.entries.CUT_BONDEntry method)
(rdkit_to_params.entries.Entries method)
(rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry method)
(rdkit_to_params.entries.GenericEntry method)
(rdkit_to_params.entries.GenericListEntry method)
(rdkit_to_params.entries.ICOOR_INTERNALEntry method)
(rdkit_to_params.entries.IO_STRINGEntry method)
(rdkit_to_params.entries.MAINCHAIN_ATOMS method)
(rdkit_to_params.entries.METAL_BINDING_ATOMSEntry method)
(rdkit_to_params.entries.NBR_ATOMEntry method)
(rdkit_to_params.entries.NBR_RADIUSEntry method)
(rdkit_to_params.entries.PDB_ROTAMERSEntry method)
(rdkit_to_params.entries.PROPERTIESEntry method)
(rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry method)
(rdkit_to_params.entries.ROTAMER_AAEntry method)
(rdkit_to_params.entries.TYPEEntry method)
(rdkit_to_params.entries.UNKNOWNEntry method)
(rdkit_to_params.entries.VARIANTEntry method)
(rdkit_to_params.Params method)
(rdkit_to_params.rdkitside.utilities.DummyMasker method)
_abc_impl (rdkit_to_params.entries.Entries attribute)
_add_genrtypes() (rdkit_to_params.Params method)
_add_icoor() (rdkit_to_params.Params method)
_add_partial_charges() (rdkit_to_params.Params method)
_add_partial_charges_OLD() (rdkit_to_params.Params method)
_add_rtypes() (rdkit_to_params.Params method)
_aminoacid_override() (rdkit_to_params.Params method)
_assign_value() (rdkit_to_params.entries.Entries method)
_change_conn_for_terminal() (rdkit_to_params.Params method)
_find_centroid() (rdkit_to_params.Params method)
_fix_atom_names() (rdkit_to_params.Params method)
_from_smiles_w_pdb() (rdkit_to_params.Params class method)
_get_atom_descriptors() (rdkit_to_params.Params method)
_get_conformer() (rdkit_to_params.constraint.Constraints method)
_get_measurements() (rdkit_to_params.Params method)
_get_new_index() (rdkit_to_params.constraint.Constraints class method)
_get_nondummy_neighbors() (rdkit_to_params.Params method)
_get_PDBInfo_atomname() (rdkit_to_params.Params method)
_get_resn_from_PDBInfo() (rdkit_to_params.Params method)
_get_unseen_neighbors() (rdkit_to_params.Params method)
_Measure (rdkit_to_params.Params attribute)
_parse_atom() (rdkit_to_params.Params method)
_parse_atoms() (rdkit_to_params.Params method)
_parse_bond() (rdkit_to_params.Params method)
_parse_bonds() (rdkit_to_params.Params method)
_parse_icoors() (rdkit_to_params.Params method)
_parse_line() (rdkit_to_params.Params method)
_parse_rotatables() (rdkit_to_params.Params method)
_parse_w_virtuals() (rdkit_to_params.Params method)
_prep_dump_pdb() (rdkit_to_params.Params method)
_prep_for_terminal() (rdkit_to_params.Params method)
_prevent_overcycling() (rdkit_to_params.Params method)
_relax() (rdkit_to_params.Params method)
_rename_atom_in_entries() (rdkit_to_params.Params method)
_repr_html_() (rdkit_to_params.constraint.Constraints method)
(rdkit_to_params.entries.AAEntry method)
(rdkit_to_params.entries.ACT_COORD_ATOMSEntry method)
(rdkit_to_params.entries.ADD_RINGEntry method)
(rdkit_to_params.entries.ATOM_ALIASEntry method)
(rdkit_to_params.entries.ATOMEntry method)
(rdkit_to_params.entries.BACKBONE_AAEntry method)
(rdkit_to_params.entries.BONDEntry method)
(rdkit_to_params.entries.CHARGEEntry method)
(rdkit_to_params.entries.CHIEntry method)
(rdkit_to_params.entries.CommentEntry method)
(rdkit_to_params.entries.CONNECTEntry method)
(rdkit_to_params.entries.CUT_BONDEntry method)
(rdkit_to_params.entries.Entries method)
(rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry method)
(rdkit_to_params.entries.GenericEntry method)
(rdkit_to_params.entries.GenericListEntry method)
(rdkit_to_params.entries.ICOOR_INTERNALEntry method)
(rdkit_to_params.entries.IO_STRINGEntry method)
(rdkit_to_params.entries.MAINCHAIN_ATOMS method)
(rdkit_to_params.entries.METAL_BINDING_ATOMSEntry method)
(rdkit_to_params.entries.NBR_ATOMEntry method)
(rdkit_to_params.entries.NBR_RADIUSEntry method)
(rdkit_to_params.entries.PDB_ROTAMERSEntry method)
(rdkit_to_params.entries.PROPERTIESEntry method)
(rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry method)
(rdkit_to_params.entries.ROTAMER_AAEntry method)
(rdkit_to_params.entries.TYPEEntry method)
(rdkit_to_params.entries.UNKNOWNEntry method)
(rdkit_to_params.entries.VARIANTEntry method)
(rdkit_to_params.Params method)
_set_PDBInfo_atomname() (rdkit_to_params.Params method)
A
AAEntry (class in rdkit_to_params.entries)
ACT_COORD_ATOMSEntry (class in rdkit_to_params.entries)
add_conformer() (rdkit_to_params.Params method)
add_Hs() (rdkit_to_params.Params method)
add_names() (rdkit_to_params.Params class method)
add_residuetype() (rdkit_to_params.Params method)
ADD_RINGEntry (class in rdkit_to_params.entries)
angle_covalent (rdkit_to_params.constraint.Constraints property)
angle_target (rdkit_to_params.constraint.Constraints property)
append() (rdkit_to_params.entries.Entries method)
assign_names() (rdkit_to_params.constraint.Constraints class method)
atom (rdkit_to_params.entries.CHARGEEntry attribute)
ATOM_ALIASEntry (class in rdkit_to_params.entries)
atom_name (rdkit_to_params.entries.CONNECTEntry attribute)
ATOMEntry (class in rdkit_to_params.entries)
B
BACKBONE_AAEntry (class in rdkit_to_params.entries)
BONDEntry (class in rdkit_to_params.entries)
C
charge (rdkit_to_params.entries.CHARGEEntry attribute)
CHARGEEntry (class in rdkit_to_params.entries)
CHIEntry (class in rdkit_to_params.entries)
child (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
choices (rdkit_to_params.entries.Entries attribute)
clear() (rdkit_to_params.entries.Entries method)
CommentEntry (class in rdkit_to_params.entries)
conformer (rdkit_to_params.constraint.Constraints property)
connect_name (rdkit_to_params.entries.CONNECTEntry attribute)
connect_type (rdkit_to_params.entries.CONNECTEntry attribute)
CONNECTEntry (class in rdkit_to_params.entries)
Constraints (class in rdkit_to_params.constraint)
convert_mol() (rdkit_to_params.Params method)
count() (rdkit_to_params.entries.Entries method)
CUT_BONDEntry (class in rdkit_to_params.entries)
D
dihedral (rdkit_to_params.constraint.Constraints property)
distance (rdkit_to_params.constraint.Constraints property)
(rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
dummyless (rdkit_to_params.Params property)
DummyMasker (class in rdkit_to_params.rdkitside.utilities)
dump() (rdkit_to_params.constraint.Constraints method)
(rdkit_to_params.Params method)
dump_pdb() (rdkit_to_params.Params method)
dump_pdb_conf() (rdkit_to_params.Params method)
dumps() (rdkit_to_params.constraint.Constraints method)
(rdkit_to_params.Params method)
dumps_pdb() (rdkit_to_params.Params method)
E
Entries (class in rdkit_to_params.entries)
extend() (rdkit_to_params.entries.Entries method)
F
fields (rdkit_to_params.Params property)
first (rdkit_to_params.entries.BONDEntry attribute)
(rdkit_to_params.entries.CHIEntry attribute)
(rdkit_to_params.entries.CUT_BONDEntry attribute)
FIRST_SIDECHAIN_ATOMEntry (class in rdkit_to_params.entries)
fix_mol() (rdkit_to_params.Params method)
fourth (rdkit_to_params.entries.CHIEntry attribute)
from_mol() (rdkit_to_params.Params class method)
from_name() (rdkit_to_params.entries.Entries class method)
from_smiles() (rdkit_to_params.Params class method)
from_smiles_w_pdbblock() (rdkit_to_params.Params class method)
from_smiles_w_pdbfile() (rdkit_to_params.Params class method)
from_str() (rdkit_to_params.entries.AAEntry class method)
(rdkit_to_params.entries.ACT_COORD_ATOMSEntry class method)
(rdkit_to_params.entries.ADD_RINGEntry class method)
(rdkit_to_params.entries.ATOM_ALIASEntry class method)
(rdkit_to_params.entries.ATOMEntry class method)
(rdkit_to_params.entries.BACKBONE_AAEntry class method)
(rdkit_to_params.entries.BONDEntry class method)
(rdkit_to_params.entries.CHARGEEntry class method)
(rdkit_to_params.entries.CHIEntry class method)
(rdkit_to_params.entries.CommentEntry class method)
(rdkit_to_params.entries.CONNECTEntry class method)
(rdkit_to_params.entries.CUT_BONDEntry class method)
(rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry class method)
(rdkit_to_params.entries.GenericEntry class method)
(rdkit_to_params.entries.GenericListEntry class method)
(rdkit_to_params.entries.ICOOR_INTERNALEntry class method)
(rdkit_to_params.entries.IO_STRINGEntry class method)
(rdkit_to_params.entries.MAINCHAIN_ATOMS class method)
(rdkit_to_params.entries.METAL_BINDING_ATOMSEntry class method)
(rdkit_to_params.entries.NBR_ATOMEntry class method)
(rdkit_to_params.entries.NBR_RADIUSEntry class method)
(rdkit_to_params.entries.PDB_ROTAMERSEntry class method)
(rdkit_to_params.entries.PROPERTIESEntry class method)
(rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry class method)
(rdkit_to_params.entries.ROTAMER_AAEntry class method)
(rdkit_to_params.entries.TYPEEntry class method)
(rdkit_to_params.entries.UNKNOWNEntry class method)
(rdkit_to_params.entries.VARIANTEntry class method)
G
GenericEntry (class in rdkit_to_params.entries)
GenericListEntry (class in rdkit_to_params.entries)
get_atom() (rdkit_to_params.constraint.Constraints method)
get_atom_by_name() (rdkit_to_params.Params method)
get_conn() (rdkit_to_params.constraint.Constraints class method)
get_correct_atomname() (rdkit_to_params.Params method)
greekification (rdkit_to_params.Params attribute)
greekify() (rdkit_to_params.Params method)
H
html_span() (in module rdkit_to_params.entries)
I
ICOOR_INTERNALEntry (class in rdkit_to_params.entries)
index (rdkit_to_params.entries.CHIEntry attribute)
(rdkit_to_params.entries.CONNECTEntry attribute)
index() (rdkit_to_params.entries.Entries method)
insert() (rdkit_to_params.entries.Entries method)
IO_STRINGEntry (class in rdkit_to_params.entries)
is_aminoacid() (rdkit_to_params.Params method)
J
join_by_dummy() (rdkit_to_params.constraint.Constraints class method)
L
list_singleton (rdkit_to_params.entries.Singletony attribute)
load() (rdkit_to_params.Params class method)
load_mol() (rdkit_to_params.Params class method)
load_smiles() (rdkit_to_params.Params class method)
loads() (rdkit_to_params.Params class method)
log (rdkit_to_params.entries.AAEntry attribute)
(rdkit_to_params.entries.ADD_RINGEntry attribute)
(rdkit_to_params.entries.ATOM_ALIASEntry attribute)
(rdkit_to_params.entries.BACKBONE_AAEntry attribute)
(rdkit_to_params.entries.CommentEntry attribute)
(rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry attribute)
(rdkit_to_params.entries.GenericEntry attribute)
(rdkit_to_params.entries.NBR_ATOMEntry attribute)
(rdkit_to_params.entries.NBR_RADIUSEntry attribute)
(rdkit_to_params.entries.PDB_ROTAMERSEntry attribute)
(rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry attribute)
(rdkit_to_params.entries.ROTAMER_AAEntry attribute)
(rdkit_to_params.entries.TYPEEntry attribute)
(rdkit_to_params.entries.UNKNOWNEntry attribute)
(rdkit_to_params.Params attribute)
M
MAINCHAIN_ATOMS (class in rdkit_to_params.entries)
make_C_terminal_cap() (rdkit_to_params.Params method)
make_coordinate_constraints() (rdkit_to_params.constraint.Constraints class method)
make_inverse_coordinate_constraints_by_neighbours() (rdkit_to_params.constraint.Constraints class method)
make_N_terminal_cap() (rdkit_to_params.Params method)
mask() (rdkit_to_params.rdkitside.utilities.DummyMasker method)
METAL_BINDING_ATOMSEntry (class in rdkit_to_params.entries)
mock() (rdkit_to_params.constraint.Constraints class method)
module
rdkit_to_params
rdkit_to_params.cli
rdkit_to_params.constraint
rdkit_to_params.entries
rdkit_to_params.rdkitside
rdkit_to_params.rdkitside.utilities
move_aside() (rdkit_to_params.Params method)
move_back() (rdkit_to_params.Params method)
mtype (rdkit_to_params.entries.ATOMEntry attribute)
multiton (rdkit_to_params.entries.Singletony attribute)
N
name (rdkit_to_params.entries.ATOMEntry attribute)
NAME (rdkit_to_params.Params property)
name1 (rdkit_to_params.entries.IO_STRINGEntry attribute)
name3 (rdkit_to_params.entries.IO_STRINGEntry attribute)
nbr (rdkit_to_params.Params property)
NBR_ATOMEntry (class in rdkit_to_params.entries)
NBR_RADIUSEntry (class in rdkit_to_params.entries)
neutralise() (in module rdkit_to_params.rdkitside.utilities)
neutralize() (in module rdkit_to_params.rdkitside.utilities)
nominalise() (rdkit_to_params.constraint.Constraints class method)
nominalize() (rdkit_to_params.constraint.Constraints class method)
O
order (rdkit_to_params.entries.BONDEntry attribute)
ordering (rdkit_to_params.Params attribute)
P
pad_name() (rdkit_to_params.Params class method)
Params (class in rdkit_to_params)
params_to_pose() (rdkit_to_params.Params static method)
parent (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
partial (rdkit_to_params.entries.ATOMEntry attribute)
PDB_ROTAMERSEntry (class in rdkit_to_params.entries)
phi (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
polish_mol() (rdkit_to_params.Params method)
pop() (rdkit_to_params.entries.Entries method)
PROPERTIESEntry (class in rdkit_to_params.entries)
R
RAMA_PREPRO_FILENAMEEntry (class in rdkit_to_params.entries)
rdkit_to_params
module
rdkit_to_params.cli
module
rdkit_to_params.constraint
module
rdkit_to_params.entries
module
rdkit_to_params.rdkitside
module
rdkit_to_params.rdkitside.utilities
module
remove() (rdkit_to_params.entries.Entries method)
rename() (rdkit_to_params.Params method)
rename_atom() (rdkit_to_params.Params method)
rename_atom_by_name() (rdkit_to_params.Params method)
rename_by_substructure() (rdkit_to_params.Params method)
rename_from_dict() (rdkit_to_params.Params method)
rename_from_list() (rdkit_to_params.Params method)
rename_from_str() (rdkit_to_params.Params method)
rename_from_template() (rdkit_to_params.Params method)
rename_repeated_atoms() (rdkit_to_params.Params method)
retype_by_name() (rdkit_to_params.Params method)
reverse() (rdkit_to_params.entries.Entries method)
ROTAMER_AAEntry (class in rdkit_to_params.entries)
rtype (rdkit_to_params.entries.ATOMEntry attribute)
S
second (rdkit_to_params.entries.BONDEntry attribute)
(rdkit_to_params.entries.CHIEntry attribute)
(rdkit_to_params.entries.CUT_BONDEntry attribute)
second_parent (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
singleton (rdkit_to_params.entries.Singletony attribute)
Singletony (class in rdkit_to_params.entries)
smiles() (in module rdkit_to_params.cli)
split_stereoisomers() (rdkit_to_params.Params static method)
T
test() (rdkit_to_params.Params method)
theta (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
third (rdkit_to_params.entries.CHIEntry attribute)
third_parent (rdkit_to_params.entries.ICOOR_INTERNALEntry attribute)
to_polymeric_pose() (rdkit_to_params.Params method)
to_pose() (rdkit_to_params.Params method)
TYPEEntry (class in rdkit_to_params.entries)
U
UNKNOWNEntry (class in rdkit_to_params.entries)
unmask() (rdkit_to_params.rdkitside.utilities.DummyMasker method)
V
validate() (rdkit_to_params.Params method)
VARIANTEntry (class in rdkit_to_params.entries)
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