Index

A

align_principal_axis() (MDAnalysis.core.topologyattrs.Masses method) AltLocs (class in MDAnalysis.core.topologyattrs) Angles (class in MDAnalysis.core.topologyattrs) Aromaticities (class in MDAnalysis.core.topologyattrs) asphericity() (MDAnalysis.core.topologyattrs.Masses method)

AtomAttr (class in MDAnalysis.core.topologyattrs) Atomids (class in MDAnalysis.core.topologyattrs) Atomindices (class in MDAnalysis.core.topologyattrs) Atomnames (class in MDAnalysis.core.topologyattrs) AtomStringAttr (class in MDAnalysis.core.topologyattrs) Atomtypes (class in MDAnalysis.core.topologyattrs)

B

bar() bfactor() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactor_setter() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactors() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactors_setter() (MDAnalysis.core.topologyattrs.Tempfactors method)

bonded_atoms() (MDAnalysis.core.topologyattrs.Bonds method) Bonds (class in MDAnalysis.core.topologyattrs) built-in function format_exception() send_message()

C

center_of_charge() (MDAnalysis.core.topologyattrs.Charges method) center_of_mass() (MDAnalysis.core.topologyattrs.Masses method) ChainIDs (class in MDAnalysis.core.topologyattrs) Charges (class in MDAnalysis.core.topologyattrs) chi1_selection() (MDAnalysis.core.topologyattrs.Atomnames method) chi1_selections() (MDAnalysis.core.topologyattrs.Atomnames method) CMaps (class in MDAnalysis.core.topologyattrs) copy() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method)

D

Dihedrals (class in MDAnalysis.core.topologyattrs) dipole_moment() (MDAnalysis.core.topologyattrs.Charges method) dipole_vector() (MDAnalysis.core.topologyattrs.Charges method) dtype (MDAnalysis.core.topologyattrs.AltLocs attribute) (MDAnalysis.core.topologyattrs.Aromaticities attribute) (MDAnalysis.core.topologyattrs.Atomids attribute) (MDAnalysis.core.topologyattrs.Atomindices attribute) (MDAnalysis.core.topologyattrs.Atomnames attribute) (MDAnalysis.core.topologyattrs.Atomtypes attribute) (MDAnalysis.core.topologyattrs.ChainIDs attribute) (MDAnalysis.core.topologyattrs.Charges attribute) (MDAnalysis.core.topologyattrs.Elements attribute) (MDAnalysis.core.topologyattrs.Epsilon14s attribute) (MDAnalysis.core.topologyattrs.Epsilons attribute) (MDAnalysis.core.topologyattrs.FormalCharges attribute) (MDAnalysis.core.topologyattrs.GBScreens attribute) (MDAnalysis.core.topologyattrs.ICodes attribute) (MDAnalysis.core.topologyattrs.Masses attribute) (MDAnalysis.core.topologyattrs.Molnums attribute) (MDAnalysis.core.topologyattrs.Moltypes attribute) (MDAnalysis.core.topologyattrs.NonbondedIndices attribute) (MDAnalysis.core.topologyattrs.Occupancies attribute) (MDAnalysis.core.topologyattrs.Radii attribute) (MDAnalysis.core.topologyattrs.RecordTypes attribute) (MDAnalysis.core.topologyattrs.Resids attribute) (MDAnalysis.core.topologyattrs.Resindices attribute) (MDAnalysis.core.topologyattrs.Resnames attribute) (MDAnalysis.core.topologyattrs.Resnums attribute) (MDAnalysis.core.topologyattrs.RMin14s attribute) (MDAnalysis.core.topologyattrs.RMins attribute) (MDAnalysis.core.topologyattrs.Segids attribute) (MDAnalysis.core.topologyattrs.Segindices attribute) (MDAnalysis.core.topologyattrs.SolventRadii attribute) (MDAnalysis.core.topologyattrs.Tempfactors attribute)

E

Elements (class in MDAnalysis.core.topologyattrs) environment

Epsilon14s (class in MDAnalysis.core.topologyattrs) Epsilons (class in MDAnalysis.core.topologyattrs)

F

foo() (in module numpydoc_example) Foo.Client (built-in class) FormalCharges (class in MDAnalysis.core.topologyattrs) format_exception() built-in function fragindex() (MDAnalysis.core.topologyattrs.Bonds method) fragindices() (MDAnalysis.core.topologyattrs.Bonds method) fragment() (MDAnalysis.core.topologyattrs.Bonds method) fragments() (MDAnalysis.core.topologyattrs.Bonds method) from_blank() (MDAnalysis.core.topologyattrs.AltLocs class method) (MDAnalysis.core.topologyattrs.Angles class method) (MDAnalysis.core.topologyattrs.Aromaticities class method) (MDAnalysis.core.topologyattrs.AtomAttr class method) (MDAnalysis.core.topologyattrs.Atomids class method) (MDAnalysis.core.topologyattrs.Atomindices class method) (MDAnalysis.core.topologyattrs.Atomnames class method) (MDAnalysis.core.topologyattrs.AtomStringAttr class method) (MDAnalysis.core.topologyattrs.Atomtypes class method) (MDAnalysis.core.topologyattrs.Bonds class method) (MDAnalysis.core.topologyattrs.ChainIDs class method) (MDAnalysis.core.topologyattrs.Charges class method) (MDAnalysis.core.topologyattrs.CMaps class method) (MDAnalysis.core.topologyattrs.Dihedrals class method) (MDAnalysis.core.topologyattrs.Elements class method) (MDAnalysis.core.topologyattrs.Epsilon14s class method) (MDAnalysis.core.topologyattrs.Epsilons class method) (MDAnalysis.core.topologyattrs.FormalCharges class method) (MDAnalysis.core.topologyattrs.GBScreens class method) (MDAnalysis.core.topologyattrs.ICodes class method) (MDAnalysis.core.topologyattrs.Impropers class method) (MDAnalysis.core.topologyattrs.Masses class method) (MDAnalysis.core.topologyattrs.Molnums class method) (MDAnalysis.core.topologyattrs.Moltypes class method) (MDAnalysis.core.topologyattrs.NonbondedIndices class method) (MDAnalysis.core.topologyattrs.Occupancies class method) (MDAnalysis.core.topologyattrs.Radii class method) (MDAnalysis.core.topologyattrs.RecordTypes class method) (MDAnalysis.core.topologyattrs.Resids class method) (MDAnalysis.core.topologyattrs.ResidueAttr class method) (MDAnalysis.core.topologyattrs.ResidueStringAttr class method) (MDAnalysis.core.topologyattrs.Resindices class method) (MDAnalysis.core.topologyattrs.Resnames class method) (MDAnalysis.core.topologyattrs.Resnums class method) (MDAnalysis.core.topologyattrs.RMin14s class method) (MDAnalysis.core.topologyattrs.RMins class method) (MDAnalysis.core.topologyattrs.RSChirality class method) (MDAnalysis.core.topologyattrs.Segids class method) (MDAnalysis.core.topologyattrs.Segindices class method) (MDAnalysis.core.topologyattrs.SegmentAttr class method) (MDAnalysis.core.topologyattrs.SegmentStringAttr class method) (MDAnalysis.core.topologyattrs.SolventRadii class method) (MDAnalysis.core.topologyattrs.Tempfactors class method) (MDAnalysis.core.topologyattrs.TopologyAttr class method) (MDAnalysis.core.topologyattrs.UreyBradleys class method)

G

GBScreens (class in MDAnalysis.core.topologyattrs) get_atoms() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method) get_residues() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method)

get_segments() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method) global substitutions group (MDAnalysis.core.topologyattrs.Tempfactors attribute) gyration_moments() (MDAnalysis.core.topologyattrs.Masses method)

I

ICodes (class in MDAnalysis.core.topologyattrs) Impropers (class in MDAnalysis.core.topologyattrs) is_guessed (MDAnalysis.core.topologyattrs.AltLocs property) (MDAnalysis.core.topologyattrs.Angles property) (MDAnalysis.core.topologyattrs.Aromaticities property) (MDAnalysis.core.topologyattrs.AtomAttr property) (MDAnalysis.core.topologyattrs.Atomids property) (MDAnalysis.core.topologyattrs.Atomindices property) (MDAnalysis.core.topologyattrs.Atomnames property) (MDAnalysis.core.topologyattrs.AtomStringAttr property) (MDAnalysis.core.topologyattrs.Atomtypes property) (MDAnalysis.core.topologyattrs.Bonds property) (MDAnalysis.core.topologyattrs.ChainIDs property) (MDAnalysis.core.topologyattrs.Charges property) (MDAnalysis.core.topologyattrs.CMaps property) (MDAnalysis.core.topologyattrs.Dihedrals property) (MDAnalysis.core.topologyattrs.Elements property) (MDAnalysis.core.topologyattrs.Epsilon14s property) (MDAnalysis.core.topologyattrs.Epsilons property) (MDAnalysis.core.topologyattrs.FormalCharges property) (MDAnalysis.core.topologyattrs.GBScreens property) (MDAnalysis.core.topologyattrs.ICodes property) (MDAnalysis.core.topologyattrs.Impropers property) (MDAnalysis.core.topologyattrs.Masses property) (MDAnalysis.core.topologyattrs.Molnums property) (MDAnalysis.core.topologyattrs.Moltypes property) (MDAnalysis.core.topologyattrs.NonbondedIndices property) (MDAnalysis.core.topologyattrs.Occupancies property) (MDAnalysis.core.topologyattrs.Radii property) (MDAnalysis.core.topologyattrs.RecordTypes property) (MDAnalysis.core.topologyattrs.Resids property) (MDAnalysis.core.topologyattrs.ResidueAttr property) (MDAnalysis.core.topologyattrs.ResidueStringAttr property) (MDAnalysis.core.topologyattrs.Resindices property) (MDAnalysis.core.topologyattrs.Resnames property) (MDAnalysis.core.topologyattrs.Resnums property) (MDAnalysis.core.topologyattrs.RMin14s property) (MDAnalysis.core.topologyattrs.RMins property) (MDAnalysis.core.topologyattrs.RSChirality property) (MDAnalysis.core.topologyattrs.Segids property) (MDAnalysis.core.topologyattrs.Segindices property) (MDAnalysis.core.topologyattrs.SegmentAttr property) (MDAnalysis.core.topologyattrs.SegmentStringAttr property) (MDAnalysis.core.topologyattrs.SolventRadii property) (MDAnalysis.core.topologyattrs.Tempfactors property) (MDAnalysis.core.topologyattrs.TopologyAttr property) (MDAnalysis.core.topologyattrs.UreyBradleys property)

M

Masses (class in MDAnalysis.core.topologyattrs) MDAnalysis.core.topologyattrs module module MDAnalysis.core.topologyattrs numpydoc_example

Molnums (class in MDAnalysis.core.topologyattrs) Moltypes (class in MDAnalysis.core.topologyattrs) moment_of_inertia() (MDAnalysis.core.topologyattrs.Masses method) MyAnimal() (class)

N

n_fragments() (MDAnalysis.core.topologyattrs.Bonds method) NonbondedIndices (class in MDAnalysis.core.topologyattrs)

numpydoc_example module

O

Occupancies (class in MDAnalysis.core.topologyattrs)

omega_selection() (MDAnalysis.core.topologyattrs.Atomnames method) omega_selections() (MDAnalysis.core.topologyattrs.Atomnames method)

P

phi_selection() (MDAnalysis.core.topologyattrs.Atomnames method) phi_selections() (MDAnalysis.core.topologyattrs.Atomnames method)

principal_axes() (MDAnalysis.core.topologyattrs.Masses method) psi_selection() (MDAnalysis.core.topologyattrs.Atomnames method) psi_selections() (MDAnalysis.core.topologyattrs.Atomnames method)

Q

quadrupole_moment() (MDAnalysis.core.topologyattrs.Charges method)

quadrupole_tensor() (MDAnalysis.core.topologyattrs.Charges method)

R

Radii (class in MDAnalysis.core.topologyattrs) radius_of_gyration() (MDAnalysis.core.topologyattrs.Masses method) RecordTypes (class in MDAnalysis.core.topologyattrs) Resids (class in MDAnalysis.core.topologyattrs) ResidueAttr (class in MDAnalysis.core.topologyattrs) ResidueStringAttr (class in MDAnalysis.core.topologyattrs)

Resindices (class in MDAnalysis.core.topologyattrs) Resnames (class in MDAnalysis.core.topologyattrs) Resnums (class in MDAnalysis.core.topologyattrs) RMin14s (class in MDAnalysis.core.topologyattrs) RMins (class in MDAnalysis.core.topologyattrs) RSChirality (class in MDAnalysis.core.topologyattrs)

S

Segids (class in MDAnalysis.core.topologyattrs) Segindices (class in MDAnalysis.core.topologyattrs) SegmentAttr (class in MDAnalysis.core.topologyattrs) SegmentStringAttr (class in MDAnalysis.core.topologyattrs) send_message() built-in function sequence() (MDAnalysis.core.topologyattrs.Resnames method) set_atoms() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method) set_residues() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method)

set_segments() (MDAnalysis.core.topologyattrs.AltLocs method) (MDAnalysis.core.topologyattrs.Angles method) (MDAnalysis.core.topologyattrs.Aromaticities method) (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomids method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Atomnames method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.Atomtypes method) (MDAnalysis.core.topologyattrs.Bonds method) (MDAnalysis.core.topologyattrs.ChainIDs method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.CMaps method) (MDAnalysis.core.topologyattrs.Dihedrals method) (MDAnalysis.core.topologyattrs.Elements method) (MDAnalysis.core.topologyattrs.Epsilon14s method) (MDAnalysis.core.topologyattrs.Epsilons method) (MDAnalysis.core.topologyattrs.FormalCharges method) (MDAnalysis.core.topologyattrs.GBScreens method) (MDAnalysis.core.topologyattrs.ICodes method) (MDAnalysis.core.topologyattrs.Impropers method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.Molnums method) (MDAnalysis.core.topologyattrs.Moltypes method) (MDAnalysis.core.topologyattrs.NonbondedIndices method) (MDAnalysis.core.topologyattrs.Occupancies method) (MDAnalysis.core.topologyattrs.Radii method) (MDAnalysis.core.topologyattrs.RecordTypes method) (MDAnalysis.core.topologyattrs.Resids method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Resnames method) (MDAnalysis.core.topologyattrs.Resnums method) (MDAnalysis.core.topologyattrs.RMin14s method) (MDAnalysis.core.topologyattrs.RMins method) (MDAnalysis.core.topologyattrs.RSChirality method) (MDAnalysis.core.topologyattrs.Segids method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.SolventRadii method) (MDAnalysis.core.topologyattrs.Tempfactors method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.topologyattrs.UreyBradleys method) shape_parameter() (MDAnalysis.core.topologyattrs.Masses method) SolventRadii (class in MDAnalysis.core.topologyattrs) source directory substitutions global

T

Tempfactors (class in MDAnalysis.core.topologyattrs) TopologyAttr (class in MDAnalysis.core.topologyattrs)

total_charge() (MDAnalysis.core.topologyattrs.Charges method) total_mass() (MDAnalysis.core.topologyattrs.Masses method)

U

UreyBradleys (class in MDAnalysis.core.topologyattrs)