Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
_
__call__() (vermouth.molecule.LinkParameterEffector method)
_apply() (vermouth.molecule.LinkParameterEffector method)
A
active_molecule (vermouth.pdb.pdb.PDBParser attribute)
add_atom() (vermouth.molecule.Block method)
add_block_from() (vermouth.map_parser.MappingBuilder method)
add_block_to() (vermouth.map_parser.MappingBuilder method)
add_edge_from() (vermouth.map_parser.MappingBuilder method)
add_edge_to() (vermouth.map_parser.MappingBuilder method)
add_edges_at_distance() (in module vermouth.edge_tuning)
add_edges_threshold() (in module vermouth.edge_tuning)
add_element_attr() (in module vermouth.graph_utils)
add_inter_molecule_edges() (in module vermouth.edge_tuning)
add_interaction() (vermouth.molecule.Molecule method)
add_mapping() (vermouth.map_parser.MappingBuilder method)
add_molecule() (vermouth.system.System method)
add_name() (vermouth.map_parser.MappingBuilder method)
add_node() (vermouth.molecule.Molecule method)
add_node_from() (vermouth.map_parser.MappingBuilder method)
add_node_to() (vermouth.map_parser.MappingBuilder method)
add_or_replace_interaction() (vermouth.molecule.Molecule method)
add_reference() (vermouth.map_parser.MappingBuilder method)
add_virtual_sites() (in module vermouth.processors.go_vs_includes)
AddCysteinBridgesThreshold (class in vermouth.processors.tune_cystein_bridges)
addHandler() (vermouth.log_helpers.PassingLoggerAdapter method)
AddMoleculeEdgesAtDistance (class in vermouth.processors.add_molecule_edges)
align (vermouth.truncating_formatter.FormatSpec attribute)
allow_dist (vermouth.processors.make_bonds.MakeBonds attribute)
allow_names (vermouth.processors.make_bonds.MakeBonds attribute)
allowed_ptms() (in module vermouth.processors.canonicalize_modifications)
alt (vermouth.truncating_formatter.FormatSpec attribute)
always_true() (in module vermouth.processors.apply_rubber_band)
analyze_symmetry() (vermouth.ismags.ISMAGS method)
angle() (in module vermouth.geometry)
anisou() (vermouth.pdb.pdb.PDBParser static method)
annotate_dssp() (in module vermouth.dssp.dssp)
annotate_modifications() (in module vermouth.processors.annotate_mut_mod)
annotate_residues_from_sequence() (in module vermouth.dssp.dssp)
AnnotateDSSP (class in vermouth.dssp.dssp)
AnnotateMartiniSecondaryStructures (class in vermouth.dssp.dssp)
AnnotateMutMod (class in vermouth.processors.annotate_mut_mod)
AnnotateResidues (class in vermouth.dssp.dssp)
apply_block_mapping() (in module vermouth.processors.do_mapping)
apply_mod_mapping() (in module vermouth.processors.do_mapping)
apply_posres() (in module vermouth.processors.apply_posres)
apply_rubber_band() (in module vermouth.processors.apply_rubber_band)
ApplyPosres (class in vermouth.processors.apply_posres)
ApplyRubberBand (class in vermouth.processors.apply_rubber_band)
are_all_equal() (in module vermouth.utils)
are_connected() (in module vermouth.processors.apply_rubber_band)
are_different() (in module vermouth.utils)
atom() (vermouth.pdb.pdb.PDBParser method)
atom_attrs (vermouth.molecule.DeleteInteraction attribute)
atom_idxs (vermouth.gmx.itp_read.ITPDirector attribute)
atoms (vermouth.molecule.Block attribute)
(vermouth.molecule.DeleteInteraction attribute)
(vermouth.molecule.Interaction attribute)
(vermouth.molecule.Molecule attribute)
attach_mass() (in module vermouth.processors.attach_mass)
AttachMass (class in vermouth.processors.attach_mass)
attribute_keep (vermouth.processors.do_mapping.DoMapping attribute)
attribute_must (vermouth.processors.do_mapping.DoMapping attribute)
attribute_stash (vermouth.processors.do_mapping.DoMapping attribute)
attributes_match() (in module vermouth.molecule)
attrs_from_node() (in module vermouth.processors.do_mapping)
author() (vermouth.pdb.pdb.PDBParser static method)
B
base_constant (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
BibTexDirector (class in vermouth.citation_parser)
BipolarFormatter (class in vermouth.log_helpers)
Block (class in vermouth.molecule)
block_from (vermouth.map_parser.Mapping attribute)
block_to (vermouth.map_parser.Mapping attribute)
blocks (vermouth.forcefield.ForceField attribute)
blocks_from (vermouth.map_parser.MappingBuilder attribute)
blocks_to (vermouth.map_parser.MappingBuilder attribute)
bond_type (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
bond_type_variable (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
build_connectivity_matrix() (in module vermouth.processors.apply_rubber_band)
build_graph_mapping_collection() (in module vermouth.processors.do_mapping)
build_pair_matrix() (in module vermouth.processors.apply_rubber_band)
builder (vermouth.map_parser.MappingDirector attribute)
C
CanonicalizeModifications (class in vermouth.processors.canonicalize_modifications)
categorical_cartesian_product() (in module vermouth.graph_utils)
categorical_maximum_common_subgraph() (in module vermouth.graph_utils)
categorical_modular_product() (in module vermouth.graph_utils)
caveat() (vermouth.pdb.pdb.PDBParser static method)
Choice (class in vermouth.molecule)
cispep() (vermouth.pdb.pdb.PDBParser static method)
citation_formatter() (in module vermouth.citation_parser)
citations (vermouth.molecule.Molecule attribute)
close() (vermouth.file_writer.DeferredFileWriter method)
colinear_pair() (in module vermouth.processors.locate_charge_dummies)
collect_residues() (in module vermouth.graph_utils)
combine_mappings() (in module vermouth.map_input)
comma (vermouth.truncating_formatter.FormatSpec attribute)
COMMENT_CHAR (vermouth.ffinput.FFDirector attribute)
(vermouth.gmx.itp_read.ITPDirector attribute)
(vermouth.map_parser.MappingDirector attribute)
(vermouth.parser_utils.LineParser attribute)
compnd() (vermouth.pdb.pdb.PDBParser static method)
compute_decay() (in module vermouth.processors.apply_rubber_band)
compute_force_constants() (in module vermouth.processors.apply_rubber_band)
conect() (vermouth.pdb.pdb.PDBParser method)
convert_dssp_annotation_to_martini() (in module vermouth.dssp.dssp)
convert_dssp_to_martini() (in module vermouth.dssp.dssp)
copy() (vermouth.molecule.Molecule method)
(vermouth.system.System method)
CountingHandler (class in vermouth.log_helpers)
cover() (in module vermouth.processors.do_mapping)
cryst1() (vermouth.pdb.pdb.PDBParser static method)
D
dbref() (vermouth.pdb.pdb.PDBParser static method)
dbref1() (vermouth.pdb.pdb.PDBParser static method)
dbref2() (vermouth.pdb.pdb.PDBParser static method)
decay_factor (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
decay_power (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
decimal (vermouth.truncating_formatter.FormatSpec attribute)
DeferredFileWriter (class in vermouth.file_writer)
delete_unknown (vermouth.processors.do_mapping.DoMapping attribute)
(vermouth.processors.repair_graph.RepairGraph attribute)
DeleteInteraction (class in vermouth.molecule)
dihedral() (in module vermouth.geometry)
dihedral_phase() (in module vermouth.geometry)
dispatch() (vermouth.gmx.itp_read.ITPDirector method)
(vermouth.parser_utils.LineParser method)
(vermouth.parser_utils.SectionLineParser method)
(vermouth.pdb.pdb.PDBParser method)
distance_matrix() (in module vermouth.geometry)
do_average_bead() (in module vermouth.processors.average_beads)
do_conect() (vermouth.pdb.pdb.PDBParser method)
do_mapping() (in module vermouth.processors.do_mapping)
DoAverageBead (class in vermouth.processors.average_beads)
DoLinks (class in vermouth.processors.do_links)
domain_criterion (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
DoMapping (class in vermouth.processors.do_mapping)
DSSPError
E
edge_equality (vermouth.ismags.ISMAGS attribute)
edge_matcher() (in module vermouth.processors.do_mapping)
edges_between() (vermouth.molecule.Molecule method)
end() (vermouth.pdb.pdb.PDBParser method)
endmdl() (vermouth.pdb.pdb.PDBParser method)
exclude (vermouth.processors.pdb_reader.PDBInput attribute)
expdta() (vermouth.pdb.pdb.PDBParser static method)
extract_fields() (vermouth.citation_parser.BibTexDirector static method)
F
features (vermouth.forcefield.ForceField attribute)
ff_from (vermouth.map_parser.Mapping attribute)
(vermouth.map_parser.MappingBuilder attribute)
ff_to (vermouth.map_parser.Mapping attribute)
(vermouth.map_parser.MappingBuilder attribute)
FFDirector (class in vermouth.ffinput)
fibonacci_sphere() (in module vermouth.processors.locate_charge_dummies)
filename (vermouth.processors.pdb_reader.PDBInput attribute)
fill (vermouth.truncating_formatter.FormatSpec attribute)
filter_minimal() (in module vermouth.selectors)
finalize() (vermouth.gmx.itp_read.ITPDirector method)
(vermouth.parser_utils.LineParser method)
(vermouth.parser_utils.SectionLineParser method)
(vermouth.pdb.pdb.PDBParser method)
finalize_section() (vermouth.ffinput.FFDirector method)
(vermouth.gmx.itp_read.ITPDirector method)
(vermouth.map_parser.MappingDirector method)
(vermouth.parser_utils.SectionLineParser method)
find_anchor() (in module vermouth.processors.locate_charge_dummies)
find_atoms() (vermouth.molecule.Molecule method)
find_entries() (vermouth.citation_parser.BibTexDirector static method)
find_force_fields() (in module vermouth.forcefield)
find_isomorphisms() (vermouth.ismags.ISMAGS method)
find_ptm_atoms() (in module vermouth.processors.canonicalize_modifications)
first_alpha() (in module vermouth.utils)
fix_ptm() (in module vermouth.processors.canonicalize_modifications)
force_field (vermouth.molecule.Molecule attribute)
(vermouth.system.System attribute)
ForceField (class in vermouth.forcefield)
format_atom_string() (in module vermouth.utils)
format_field() (vermouth.truncating_formatter.TruncFormatter method)
format_spec_re (vermouth.truncating_formatter.TruncFormatter attribute)
FormatSpec (class in vermouth.truncating_formatter)
formul() (vermouth.pdb.pdb.PDBParser static method)
from_ff (vermouth.map_parser.MappingDirector attribute)
from_ff() (vermouth.map_parser.MappingBuilder method)
fudge (vermouth.processors.make_bonds.MakeBonds attribute)
G
generate_all_self_mappings() (in module vermouth.map_input)
generate_self_mappings() (in module vermouth.map_input)
get_attrs() (in module vermouth.graph_utils)
get_context() (vermouth.ffinput.FFDirector method)
get_default() (in module vermouth.processors.repair_graph)
get_interaction() (vermouth.molecule.Molecule method)
get_logger() (in module vermouth.log_helpers)
get_mapping() (vermouth.map_parser.MappingBuilder method)
get_mod_mappings() (in module vermouth.processors.do_mapping)
get_native_force_field() (in module vermouth.forcefield)
get_not_none() (in module vermouth.pdb.pdb)
GoVirtIncludes (class in vermouth.processors.go_vs_includes)
graph (vermouth.ismags.ISMAGS attribute)
GROInput (class in vermouth.processors.gro_reader)
guess_angles() (vermouth.molecule.Block method)
guess_dihedrals() (vermouth.molecule.Block method)
H
handle() (vermouth.log_helpers.CountingHandler method)
has_context() (vermouth.ffinput.FFDirector method)
has_dihedral_around() (vermouth.molecule.Block method)
has_feature() (vermouth.forcefield.ForceField method)
has_improper_around() (vermouth.molecule.Block method)
header() (vermouth.pdb.pdb.PDBParser static method)
helix() (vermouth.pdb.pdb.PDBParser static method)
het() (vermouth.pdb.pdb.PDBParser static method)
hetatm() (vermouth.pdb.pdb.PDBParser method)
hetnam() (vermouth.pdb.pdb.PDBParser static method)
hetsyn() (vermouth.pdb.pdb.PDBParser static method)
I
identifiers (vermouth.map_parser.MappingDirector attribute)
identify_ptms() (in module vermouth.processors.canonicalize_modifications)
ignh (vermouth.processors.pdb_reader.PDBInput attribute)
ignore_warnings_and_count() (in module vermouth.log_helpers)
include_graph (vermouth.processors.repair_graph.RepairGraph attribute)
Interaction (class in vermouth.molecule)
interaction_match() (in module vermouth.molecule)
interactions (vermouth.molecule.Molecule attribute)
interactions_natoms (vermouth.ffinput.FFDirector attribute)
intersect() (in module vermouth.ismags)
is_isomorphic() (vermouth.ismags.ISMAGS method)
is_pragma() (vermouth.gmx.itp_read.ITPDirector static method)
is_protein() (in module vermouth.selectors)
is_section_header() (vermouth.parser_utils.SectionLineParser static method)
ISMAGS (class in vermouth.ismags)
isomorphisms_iter() (vermouth.ismags.ISMAGS method)
iter_force_field_files() (in module vermouth.forcefield)
iter_residues() (vermouth.molecule.Molecule method)
ITPDirector (class in vermouth.gmx.itp_read)
J
jrnl() (vermouth.pdb.pdb.PDBParser static method)
K
keywds() (vermouth.pdb.pdb.PDBParser static method)
L
largest_common_subgraph() (vermouth.ismags.ISMAGS method)
LineParser (class in vermouth.parser_utils)
Link (class in vermouth.molecule)
link() (vermouth.pdb.pdb.PDBParser static method)
LinkParameterEffector (class in vermouth.molecule)
LinkPredicate (class in vermouth.molecule)
links (vermouth.forcefield.ForceField attribute)
locate_all_dummies() (in module vermouth.processors.locate_charge_dummies)
locate_dummy() (in module vermouth.processors.locate_charge_dummies)
LocateChargeDummies (class in vermouth.processors.locate_charge_dummies)
log() (vermouth.log_helpers.PassingLoggerAdapter method)
(vermouth.log_helpers.StyleAdapter method)
lower_bound (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
M
macros (vermouth.map_parser.MappingDirector attribute)
(vermouth.parser_utils.SectionLineParser attribute)
make_bonds() (in module vermouth.processors.make_bonds)
make_edges_from_interaction_type() (vermouth.molecule.Molecule method)
make_edges_from_interactions() (vermouth.molecule.Molecule method)
make_mapping_object() (in module vermouth.map_input)
make_partitions() (in module vermouth.ismags)
make_reference() (in module vermouth.processors.repair_graph)
make_residue_graph() (in module vermouth.graph_utils)
make_same_region_criterion() (in module vermouth.processors.apply_rubber_band)
MakeBonds (class in vermouth.processors.make_bonds)
manager (logging.PassingLoggerAdapter.Logger attribute)
(vermouth.log_helpers.PassingLoggerAdapter attribute)
map() (vermouth.map_parser.Mapping method)
Mapping (class in vermouth.map_parser)
mapping (vermouth.map_parser.Mapping attribute)
(vermouth.map_parser.MappingBuilder attribute)
MappingBuilder (class in vermouth.map_parser)
MappingDirector (class in vermouth.map_parser)
MappingGraphMatcher (class in vermouth.graph_utils)
mappings (vermouth.processors.do_mapping.DoMapping attribute)
master() (vermouth.pdb.pdb.PDBParser static method)
match() (vermouth.molecule.Choice method)
(vermouth.molecule.LinkPredicate method)
(vermouth.molecule.NotDefinedOrNot method)
match_link() (in module vermouth.processors.do_links)
match_order() (in module vermouth.processors.do_links)
maxes() (in module vermouth.utils)
mdltyp() (vermouth.pdb.pdb.PDBParser static method)
merge_chains() (in module vermouth.processors.merge_chains)
merge_molecule() (vermouth.molecule.Molecule method)
MergeAllMolecules (class in vermouth.processors.merge_all_molecules)
MergeChains (class in vermouth.processors.merge_chains)
MergeNucleicStrands (class in vermouth.processors.add_molecule_edges)
Message (class in vermouth.log_helpers)
meta (vermouth.molecule.DeleteInteraction attribute)
(vermouth.molecule.Interaction attribute)
(vermouth.molecule.Molecule attribute)
METH_DICT (vermouth.ffinput.FFDirector attribute)
(vermouth.gmx.itp_read.ITPDirector attribute)
(vermouth.map_parser.MappingDirector attribute)
(vermouth.parser_utils.SectionLineParser attribute)
minimum_force (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
model() (vermouth.pdb.pdb.PDBParser method)
modelidx (vermouth.pdb.pdb.PDBParser attribute)
(vermouth.processors.pdb_reader.PDBInput attribute)
Modification (class in vermouth.molecule)
modification_matches() (in module vermouth.processors.do_mapping)
modifications (vermouth.forcefield.ForceField attribute)
(vermouth.processors.annotate_mut_mod.AnnotateMutMod attribute)
modres() (vermouth.pdb.pdb.PDBParser static method)
Molecule (class in vermouth.molecule)
molecules (vermouth.pdb.pdb.PDBParser attribute)
(vermouth.system.System attribute)
mtrix1() (vermouth.pdb.pdb.PDBParser static method)
mtrix2() (vermouth.pdb.pdb.PDBParser static method)
mtrix3() (vermouth.pdb.pdb.PDBParser static method)
mutations (vermouth.processors.annotate_mut_mod.AnnotateMutMod attribute)
N
n_keys_asked (vermouth.molecule.LinkParameterEffector attribute)
(vermouth.molecule.ParamAngle attribute)
(vermouth.molecule.ParamDihedral attribute)
(vermouth.molecule.ParamDihedralPhase attribute)
(vermouth.molecule.ParamDistance attribute)
name (vermouth.dssp.dssp.AnnotateDSSP attribute)
(vermouth.dssp.dssp.AnnotateMartiniSecondaryStructures attribute)
(vermouth.dssp.dssp.AnnotateResidues attribute)
(vermouth.forcefield.ForceField attribute)
(vermouth.molecule.Block attribute)
(vermouth.processors.merge_chains.MergeChains attribute)
NameMolType (class in vermouth.processors.name_moltype)
names (vermouth.map_parser.Mapping attribute)
(vermouth.map_parser.MappingBuilder attribute)
NO_FETCH_BLOCK (vermouth.map_parser.MappingDirector attribute)
node_dict_factory (vermouth.molecule.Block attribute)
(vermouth.molecule.Link attribute)
(vermouth.molecule.Molecule attribute)
node_equality (vermouth.ismags.ISMAGS attribute)
node_matcher() (in module vermouth.processors.do_mapping)
node_should_exist() (in module vermouth.processors.do_mapping)
NotDefinedOrNot (class in vermouth.molecule)
nrexcl (vermouth.molecule.Molecule attribute)
num_particles (vermouth.system.System attribute)
number_of_counts_by() (vermouth.log_helpers.CountingHandler method)
nummdl() (vermouth.pdb.pdb.PDBParser static method)
O
obslte() (vermouth.pdb.pdb.PDBParser static method)
open() (vermouth.file_writer.DeferredFileWriter method)
origx1() (vermouth.pdb.pdb.PDBParser static method)
origx2() (vermouth.pdb.pdb.PDBParser static method)
origx3() (vermouth.pdb.pdb.PDBParser static method)
P
pairs_under_threshold() (in module vermouth.edge_tuning)
ParamAngle (class in vermouth.molecule)
ParamDihedral (class in vermouth.molecule)
ParamDihedralPhase (class in vermouth.molecule)
ParamDistance (class in vermouth.molecule)
parameters (vermouth.molecule.DeleteInteraction attribute)
(vermouth.molecule.Interaction attribute)
parse() (vermouth.citation_parser.BibTexDirector method)
(vermouth.parser_utils.LineParser method)
(vermouth.pdb.pdb.PDBParser method)
parse_entry() (vermouth.citation_parser.BibTexDirector method)
parse_header() (vermouth.ffinput.FFDirector method)
(vermouth.gmx.itp_read.ITPDirector method)
(vermouth.parser_utils.SectionLineParser method)
parse_line() (vermouth.parser_utils.LineParser method)
parse_mapping_file() (in module vermouth.map_parser)
parse_pragma() (vermouth.gmx.itp_read.ITPDirector method)
parse_residue_spec() (in module vermouth.processors.annotate_mut_mod)
parse_section() (vermouth.parser_utils.SectionLineParser method)
partition_graph() (in module vermouth.graph_utils)
partition_to_color() (in module vermouth.ismags)
PassingLoggerAdapter (class in vermouth.log_helpers)
PDBInput (class in vermouth.processors.pdb_reader)
PDBParser (class in vermouth.pdb.pdb)
pop_entry_type() (vermouth.citation_parser.BibTexDirector method)
pop_key() (vermouth.citation_parser.BibTexDirector static method)
precision (vermouth.truncating_formatter.FormatSpec attribute)
prepare_file() (vermouth.citation_parser.BibTexDirector static method)
process() (vermouth.log_helpers.PassingLoggerAdapter method)
(vermouth.log_helpers.TypeAdapter method)
Processor (class in vermouth.processors.processor)
proto_multi_templates() (in module vermouth.selectors)
proto_select_attribute_in() (in module vermouth.selectors)
prune_edges_between_selections() (in module vermouth.edge_tuning)
prune_edges_with_selectors() (in module vermouth.edge_tuning)
ptm_node_matcher() (in module vermouth.processors.canonicalize_modifications)
ptm_resname_match() (in module vermouth.processors.do_mapping)
Q
Quoter (class in vermouth.processors.quote)
R
rate_match() (in module vermouth.graph_utils)
read_backmapping_file() (in module vermouth.map_input)
read_bib() (in module vermouth.citation_parser)
read_dssp2() (in module vermouth.dssp.dssp)
read_ff() (in module vermouth.ffinput)
read_from() (vermouth.forcefield.ForceField method)
read_gro() (in module vermouth.gmx.gro)
read_itp() (in module vermouth.gmx.itp_read)
read_mapping_directory() (in module vermouth.map_input)
read_mapping_file() (in module vermouth.map_input)
read_pdb() (in module vermouth.pdb.pdb)
read_quote_file() (in module vermouth.processors.quote)
read_rtp() (in module vermouth.gmx.rtp)
reference_graphs (vermouth.forcefield.ForceField attribute)
references (vermouth.map_parser.Mapping attribute)
(vermouth.map_parser.MappingBuilder attribute)
remark() (vermouth.pdb.pdb.PDBParser static method)
remove_cystein_bridge_edges() (in module vermouth.processors.tune_cystein_bridges)
remove_interaction() (vermouth.molecule.Molecule method)
remove_matching_interaction() (vermouth.molecule.Molecule method)
remove_node() (vermouth.molecule.Molecule method)
remove_nodes_from() (vermouth.molecule.Molecule method)
RemoveCysteinBridgeEdges (class in vermouth.processors.tune_cystein_bridges)
rename_modified_residues() (in module vermouth.processors.rename_modified_residues)
renamed_residues (vermouth.forcefield.ForceField attribute)
RenameModifiedResidues (class in vermouth.processors.rename_modified_residues)
repair_graph() (in module vermouth.processors.repair_graph)
repair_residue() (in module vermouth.processors.repair_graph)
RepairGraph (class in vermouth.processors.repair_graph)
res_min_dist (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
res_min_dist_variable (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
reset() (vermouth.map_parser.MappingBuilder method)
RESIDUE_ATOM_SEP (vermouth.map_parser.MappingDirector attribute)
residue_matches() (in module vermouth.processors.annotate_mut_mod)
RESNAME_NUM_SEP (vermouth.map_parser.MappingDirector attribute)
revdat() (vermouth.pdb.pdb.PDBParser static method)
reverse_mapping (vermouth.map_parser.Mapping attribute)
run_dssp() (in module vermouth.dssp.dssp)
run_molecule() (vermouth.dssp.dssp.AnnotateDSSP method)
(vermouth.dssp.dssp.AnnotateMartiniSecondaryStructures static method)
(vermouth.dssp.dssp.AnnotateResidues method)
(vermouth.processors.annotate_mut_mod.AnnotateMutMod method)
(vermouth.processors.apply_posres.ApplyPosres method)
(vermouth.processors.apply_rubber_band.ApplyRubberBand method)
(vermouth.processors.attach_mass.AttachMass method)
(vermouth.processors.average_beads.DoAverageBead method)
(vermouth.processors.canonicalize_modifications.CanonicalizeModifications method)
(vermouth.processors.do_links.DoLinks method)
(vermouth.processors.do_mapping.DoMapping method)
(vermouth.processors.go_vs_includes.GoVirtIncludes method)
(vermouth.processors.locate_charge_dummies.LocateChargeDummies method)
(vermouth.processors.merge_all_molecules.MergeAllMolecules static method)
(vermouth.processors.processor.Processor method)
(vermouth.processors.rename_modified_residues.RenameModifiedResidues method)
(vermouth.processors.repair_graph.RepairGraph method)
(vermouth.processors.set_molecule_meta.SetMoleculeMeta method)
(vermouth.processors.sort_molecule_atoms.SortMoleculeAtoms method)
(vermouth.processors.tune_cystein_bridges.RemoveCysteinBridgeEdges method)
run_system() (vermouth.dssp.dssp.AnnotateResidues method)
(vermouth.processors.add_molecule_edges.AddMoleculeEdgesAtDistance method)
(vermouth.processors.do_mapping.DoMapping method)
(vermouth.processors.gro_reader.GROInput method)
(vermouth.processors.make_bonds.MakeBonds method)
(vermouth.processors.merge_all_molecules.MergeAllMolecules method)
(vermouth.processors.merge_chains.MergeChains method)
(vermouth.processors.name_moltype.NameMolType method)
(vermouth.processors.pdb_reader.PDBInput method)
(vermouth.processors.processor.Processor method)
(vermouth.processors.quote.Quoter method)
(vermouth.processors.repair_graph.RepairGraph method)
S
same_chain() (in module vermouth.processors.apply_rubber_band)
same_edges() (vermouth.molecule.Molecule method)
same_interactions() (vermouth.molecule.Molecule method)
same_nodes() (vermouth.molecule.Molecule method)
same_non_edges() (vermouth.molecule.Link method)
scale1() (vermouth.pdb.pdb.PDBParser static method)
scale2() (vermouth.pdb.pdb.PDBParser static method)
scale3() (vermouth.pdb.pdb.PDBParser static method)
section (vermouth.map_parser.MappingDirector attribute)
(vermouth.parser_utils.SectionLineParser attribute)
SECTION_ENDS (vermouth.map_parser.MappingDirector attribute)
section_parser() (vermouth.parser_utils.SectionParser static method)
SectionLineParser (class in vermouth.parser_utils)
SectionParser (class in vermouth.parser_utils)
select_all() (in module vermouth.selectors)
select_backbone() (in module vermouth.selectors)
select_nodes_multi() (in module vermouth.edge_tuning)
selector (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
selector_has_position() (in module vermouth.selectors)
self_distance_matrix() (in module vermouth.processors.apply_rubber_band)
semantic_feasibility() (vermouth.graph_utils.MappingGraphMatcher method)
seqadv() (vermouth.pdb.pdb.PDBParser static method)
seqres() (vermouth.pdb.pdb.PDBParser static method)
sequence_from_residues() (in module vermouth.dssp.dssp)
SetMoleculeMeta (class in vermouth.processors.set_molecule_meta)
share_moltype_with() (vermouth.molecule.Molecule method)
sheet() (vermouth.pdb.pdb.PDBParser static method)
sign (vermouth.truncating_formatter.FormatSpec attribute)
Singleton (class in vermouth.file_writer)
site() (vermouth.pdb.pdb.PDBParser static method)
sort_interactions() (vermouth.molecule.Molecule static method)
SortMoleculeAtoms (class in vermouth.processors.sort_molecule_atoms)
source() (vermouth.pdb.pdb.PDBParser static method)
split_comments() (in module vermouth.parser_utils)
splt() (vermouth.pdb.pdb.PDBParser static method)
sprsde() (vermouth.pdb.pdb.PDBParser static method)
ssbond() (vermouth.pdb.pdb.PDBParser static method)
StyleAdapter (class in vermouth.log_helpers)
subgraph (vermouth.ismags.ISMAGS attribute)
subgraph() (vermouth.molecule.Molecule method)
subgraph_is_isomorphic() (vermouth.ismags.ISMAGS method)
subgraph_isomorphisms_iter() (vermouth.ismags.ISMAGS method)
System (class in vermouth.system)
T
ter() (vermouth.pdb.pdb.PDBParser method)
title() (vermouth.pdb.pdb.PDBParser static method)
to_ff (vermouth.map_parser.MappingDirector attribute)
(vermouth.processors.do_mapping.DoMapping attribute)
to_ff() (vermouth.map_parser.MappingBuilder method)
to_molecule() (vermouth.molecule.Block method)
TruncFormatter (class in vermouth.truncating_formatter)
type (vermouth.truncating_formatter.FormatSpec attribute)
TypeAdapter (class in vermouth.log_helpers)
U
upper_bound (vermouth.processors.apply_rubber_band.ApplyRubberBand attribute)
V
variables (vermouth.forcefield.ForceField attribute)
vermouth (module)
vermouth.citation_parser (module)
vermouth.dssp (module)
vermouth.dssp.dssp (module)
vermouth.edge_tuning (module)
vermouth.ffinput (module)
vermouth.file_writer (module)
vermouth.forcefield (module)
vermouth.geometry (module)
vermouth.gmx (module)
vermouth.gmx.gro (module)
vermouth.gmx.itp (module)
vermouth.gmx.itp_read (module)
vermouth.gmx.rtp (module)
vermouth.graph_utils (module)
vermouth.ismags (module)
vermouth.log_helpers (module)
vermouth.map_input (module)
vermouth.map_parser (module)
vermouth.molecule (module)
vermouth.parser_utils (module)
vermouth.pdb (module)
vermouth.pdb.pdb (module)
vermouth.processors (module)
vermouth.processors.add_molecule_edges (module)
vermouth.processors.annotate_mut_mod (module)
vermouth.processors.apply_posres (module)
vermouth.processors.apply_rubber_band (module)
vermouth.processors.attach_mass (module)
vermouth.processors.average_beads (module)
vermouth.processors.canonicalize_modifications (module)
vermouth.processors.do_links (module)
vermouth.processors.do_mapping (module)
vermouth.processors.go_vs_includes (module)
vermouth.processors.gro_reader (module)
vermouth.processors.locate_charge_dummies (module)
vermouth.processors.make_bonds (module)
vermouth.processors.merge_all_molecules (module)
vermouth.processors.merge_chains (module)
vermouth.processors.name_moltype (module)
vermouth.processors.pdb_reader (module)
vermouth.processors.processor (module)
vermouth.processors.quote (module)
vermouth.processors.rename_modified_residues (module)
vermouth.processors.repair_graph (module)
vermouth.processors.set_molecule_meta (module)
vermouth.processors.sort_molecule_atoms (module)
vermouth.processors.tune_cystein_bridges (module)
vermouth.selectors (module)
vermouth.system (module)
vermouth.truncating_formatter (module)
vermouth.utils (module)
W
width (vermouth.truncating_formatter.FormatSpec attribute)
write() (vermouth.file_writer.DeferredFileWriter method)
write_gro() (in module vermouth.gmx.gro)
write_molecule_itp() (in module vermouth.gmx.itp)
write_pdb() (in module vermouth.pdb.pdb)
write_pdb_string() (in module vermouth.pdb.pdb)
Z
zero_padding (vermouth.truncating_formatter.FormatSpec attribute)
VerMoUTH
Navigation
Contents:
General Overview
Martinize 2 workflow
Technical background
File formats
Tutorials
vermouth
Related Topics
Documentation overview
Quick search