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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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_
__contains__() (msys.Atom method)
(msys.Bond method)
__delitem__() (msys.Ct method)
__eq__() (msys.ParamTable method)
(msys.System method)
(msys.TermTable method)
__getinitargs__() (msys.System method)
__getitem__() (msys.Atom method)
(msys.Bond method)
(msys.Ct method)
(msys.IndexedFileLoader method)
(msys.Param method)
(msys.Term method)
__hash__() (msys.ParamTable method)
(msys.System method)
(msys.TermTable method)
__init__() (msys.AnnotatedSystem method)
(msys.atomsel.Atomsel method)
(msys.Graph method)
(msys.HydrogenBondFinder method)
(msys.InChI method)
(msys.IndexedFileLoader method)
(msys.ParamTable method)
(msys.SmartsPattern method)
(msys.SpatialHash method)
(msys.System method)
(msys.SystemImporter method)
(msys.TermTable method)
__len__() (msys.atomsel.Atomsel method)
(msys.IndexedFileLoader method)
__lt__() (msys.Atom method)
(msys.Bond method)
__ne__() (msys.ParamTable method)
(msys.System method)
(msys.TermTable method)
__repr__() (msys.AnnotatedSystem method)
(msys.Atom method)
(msys.atomsel.Atomsel method)
(msys.Bond method)
(msys.Chain method)
(msys.Param method)
(msys.Residue method)
(msys.SmartsPattern method)
(msys.System method)
(msys.Term method)
(msys.TermTable method)
__setitem__() (msys.Atom method)
(msys.Bond method)
(msys.Ct method)
(msys.Param method)
(msys.Term method)
__str__() (msys.atomsel.Atomsel method)
(msys.InChI method)
__weakref__ (msys.AnnotatedSystem attribute)
(msys.BrokenBondsError attribute)
(msys.Graph attribute)
(msys.HydrogenBondFinder attribute)
(msys.InChI attribute)
(msys.IndexedFileLoader attribute)
(msys.SmartsPattern attribute)
(msys.SpatialHash attribute)
(msys.SystemImporter attribute)
A
addAtom() (msys.Residue method)
(msys.System method)
(msys.SystemImporter method)
addAtomProp() (msys.System method)
addAuxTable() (msys.System method)
addBond() (msys.Atom method)
addbond() (msys.molfile.Atom method)
addBondProp() (msys.System method)
addChain() (msys.Ct method)
(msys.System method)
addCt() (msys.System method)
addNonbondedFromSchema() (msys.System method)
addParam() (msys.ParamTable method)
addProp() (msys.ParamTable method)
addResidue() (msys.Chain method)
(msys.System method)
addTable() (msys.System method)
addTableFromSchema() (msys.System method)
addTerm() (msys.TermTable method)
,
[1]
addTermProp() (msys.TermTable method)
,
[1]
alignCoordinates() (msys.atomsel.Atomsel method)
aligned_rmsd() (in module msys.pfx)
alignedRMSD() (msys.atomsel.Atomsel method)
altloc (msys.molfile.Atom attribute)
analyze() (msys.System method)
AnnotatedSystem (class in msys)
,
[1]
anum (msys.molfile.Atom attribute)
append() (msys.Ct method)
(msys.System method)
apply() (in module msys.posre)
(in module msys.thermalize)
ApplyDihedralGeometry() (in module msys)
aromatic() (msys.AnnotatedSystem method)
,
[1]
(msys.Atom property)
asCapsule() (msys.System method)
AssignBondOrderAndFormalCharge() (in module msys)
at_time_ge() (msys.molfile.Reader method)
at_time_gt() (msys.molfile.Reader method)
at_time_le() (msys.molfile.Reader method)
at_time_lt() (msys.molfile.Reader method)
at_time_near() (msys.molfile.Reader method)
(msys.molfile.SeqFile.Reader method)
Atom (class in msys)
(class in msys.molfile)
atom() (msys.System method)
atom_props() (msys.System property)
atomic_number() (msys.Atom property)
atomPropType() (msys.System method)
atoms() (msys.Bond property)
(msys.Ct property)
(msys.Graph method)
(msys.molfile.Reader property)
(msys.Residue property)
(msys.System property)
(msys.Term property)
Atomsel (class in msys.atomsel)
atomsel() (msys.System method)
atomsGroupedBy() (msys.System method)
auxinfo() (msys.InChI property)
auxtable() (msys.System method)
auxtable_names() (msys.System property)
auxtables() (msys.System property)
axis() (msys.molfile.Grid property)
B
bfactor (msys.molfile.Atom attribute)
Bond (class in msys)
bond() (msys.System method)
bond_props() (msys.System property)
bonded_atoms() (msys.Atom property)
bondorders() (msys.molfile.Reader property)
bondPropType() (msys.System method)
bonds (msys.molfile.Atom attribute)
bonds() (msys.Atom property)
(msys.Ct property)
(msys.System property)
box() (msys.molfile.Frame property)
BrokenBondsError
C
CalcAngle() (in module msys)
CalcDihedral() (in module msys)
CalcDistance() (in module msys)
CalcPlanarity() (in module msys)
can_read() (msys.molfile.Plugin property)
can_write() (msys.molfile.Plugin property)
category() (msys.TermTable property)
,
[1]
cell() (msys.System property)
center() (msys.Residue property)
(msys.System property)
Chain (class in msys)
chain (msys.molfile.Atom attribute)
chain() (msys.Residue property)
(msys.System method)
chains() (msys.Ct property)
(msys.System property)
charge (msys.molfile.Atom attribute)
charge() (msys.Atom property)
clone() (msys.System method)
CloneSystem() (in module msys)
close() (msys.molfile.Writer method)
,
[1]
coalesce() (msys.TermTable method)
,
[1]
coalesceTables() (msys.System method)
ComputeTopologicalIds() (in module msys)
ConvertFromOEChem() (in module msys)
ConvertFromRdkit() (in module msys)
ConvertToOEChem() (in module msys)
ConvertToRdkit() (in module msys)
count_overrides() (msys.TermTable method)
,
[1]
CreateParamTable() (in module msys)
CreateSystem() (in module msys)
Ct (class in msys)
ct() (msys.Chain property)
(msys.System method)
cts() (msys.System property)
currentRMSD() (msys.atomsel.Atomsel method)
D
data() (msys.molfile.Grid property)
degree() (msys.AnnotatedSystem method)
,
[1]
delAtomProp() (msys.System method)
delAtoms() (msys.System method)
delAuxTable() (msys.System method)
delbond() (msys.molfile.Atom method)
delBondProp() (msys.System method)
delBonds() (msys.System method)
delChains() (msys.System method)
delProp() (msys.ParamTable method)
delResidues() (msys.System method)
delTermProp() (msys.TermTable method)
,
[1]
delTermsWithAtom() (msys.TermTable method)
,
[1]
dpos() (msys.molfile.Frame property)
DtrReader (class in msys.molfile)
duplicate() (msys.Param method)
dvel() (msys.molfile.Frame property)
E
errors() (msys.AnnotatedSystem property)
,
[1]
es_funct() (msys.NonbondedInfo property)
extended_energy() (msys.molfile.Frame property)
F
fileinfo() (msys.molfile.DtrReader method)
filename_extensions (msys.molfile.SeqFile attribute)
filename_extensions() (msys.molfile.Plugin property)
find() (msys.HydrogenBondFinder method)
(msys.ParamTable method)
findBond() (msys.Atom method)
(msys.System method)
findContactIds() (msys.System method)
findContacts() (msys.SpatialHash method)
FindDistinctFragments() (in module msys)
findExact() (msys.TermTable method)
,
[1]
findMatches() (msys.SmartsPattern method)
,
[1]
findNearest() (msys.SpatialHash method)
findWithAll() (msys.TermTable method)
,
[1]
findWithAny() (msys.TermTable method)
,
[1]
findWithin() (msys.SpatialHash method)
findWithOnly() (msys.TermTable method)
,
[1]
first() (msys.Bond property)
formal_charge() (msys.Atom property)
FormatDMS() (in module msys)
FormatJson() (in module msys)
FormatSDF() (in module msys)
fpos() (msys.molfile.Frame property)
fragid() (msys.Atom property)
Frame (class in msys.molfile)
frame() (msys.molfile.DtrReader method)
(msys.molfile.Reader method)
,
[1]
(msys.molfile.SeqFile.Reader method)
(msys.molfile.Writer method)
,
[1]
frames() (msys.molfile.Reader method)
(msys.molfile.SeqFile.Reader method)
frameset_is_compact() (msys.molfile.DtrReader method)
frameset_path() (msys.molfile.DtrReader method)
frameset_size() (msys.molfile.DtrReader method)
fromCapsule() (msys.System class method)
FromSmilesString() (in module msys)
fromTimekeys() (msys.molfile.DtrReader static method)
fvel() (msys.molfile.Frame property)
G
get() (msys.Ct method)
get_prop() (msys.molfile.SeqFile.Reader method)
getbondorder() (msys.molfile.Atom method)
GetBondsAnglesDihedrals() (in module msys)
getCell() (msys.System method)
getOverride() (msys.TermTable method)
,
[1]
getPositions() (msys.System method)
GetRingSystems() (in module msys)
GetSSSR() (in module msys)
getTable() (msys.System method)
getVelocities() (msys.System method)
Graph (class in msys)
Grease() (in module msys.grease)
Grid (class in msys.molfile)
grid() (msys.molfile.Reader method)
(msys.molfile.Writer method)
grid_data() (msys.molfile.Reader method)
grid_meta() (msys.molfile.Reader method)
guessBonds() (msys.System method)
GuessHydrogenPositions() (in module msys)
H
has_velocities() (msys.molfile.Reader property)
hash() (msys.Graph method)
(msys.System method)
hash_atoms() (msys.Graph static method)
hasTerm() (msys.TermTable method)
,
[1]
hcount() (msys.AnnotatedSystem method)
,
[1]
hybridization() (msys.AnnotatedSystem method)
,
[1]
HydrogenBondFinder (class in msys)
I
id() (msys.Param property)
(msys.Term property)
ids() (msys.atomsel.Atomsel property)
InChI (class in msys)
index_ge() (msys.molfile.DtrReader method)
index_gt() (msys.molfile.DtrReader method)
index_le() (msys.molfile.DtrReader method)
index_lt() (msys.molfile.DtrReader method)
index_near() (msys.molfile.DtrReader method)
IndexedFileLoader (class in msys)
initialize() (msys.SystemImporter method)
insertion (msys.molfile.Atom attribute)
insertion() (msys.Residue property)
inverse_3x3() (in module msys.pfx)
K
key() (msys.InChI property)
keys() (msys.Ct method)
(msys.Param method)
(msys.Term method)
keyvals() (msys.molfile.DtrReader method)
kinetic_energy() (msys.molfile.Frame property)
L
LineIntersectsTriangle() (in module msys)
Load() (in module msys)
LoadDMS() (in module msys)
LoadMAE() (in module msys)
LoadMany() (in module msys)
LoadMol2() (in module msys)
LoadPDB() (in module msys)
LoadPrmTop() (in module msys)
LoadXYZ() (in module msys)
loneelectrons() (msys.AnnotatedSystem method)
,
[1]
M
mass (msys.molfile.Atom attribute)
mass() (msys.Atom property)
match() (msys.Graph method)
(msys.SmartsPattern method)
,
[1]
matchAll() (msys.Graph method)
MatchFragments() (in module msys)
message() (msys.InChI property)
metadata() (msys.molfile.DtrReader property)
module
msys
msys.atomsel
msys.grease
msys.knot
msys.molfile
msys.pfx
msys.posre
msys.sequence
msys.thermalize
msys.update
moveby() (msys.molfile.Frame method)
msys
module
msys.atomsel
module
msys.grease
module
msys.knot
module
msys.molfile
module
msys.pfx
module
msys.posre
module
msys.sequence
module
msys.thermalize
module
msys.update
module
N
name (msys.molfile.Atom attribute)
(msys.molfile.SeqFile attribute)
name() (msys.Atom property)
(msys.Chain property)
(msys.Ct property)
(msys.molfile.Grid property)
(msys.molfile.Plugin property)
(msys.Residue property)
(msys.System property)
(msys.TermTable property)
,
[1]
natoms() (msys.Ct property)
(msys.molfile.DtrReader property)
(msys.molfile.Reader property)
(msys.molfile.SeqFile.Reader property)
(msys.Residue property)
(msys.SmartsPattern property)
,
[1]
(msys.System property)
(msys.TermTable property)
,
[1]
nbonds() (msys.Atom property)
(msys.System property)
nchains() (msys.Ct property)
(msys.System property)
ncts() (msys.System property)
next() (msys.molfile.Reader method)
nframes() (msys.molfile.DtrReader property)
(msys.molfile.Reader property)
(msys.molfile.SeqFile.Reader property)
nframesets() (msys.molfile.DtrReader property)
ngrids() (msys.molfile.Reader property)
nhydrogens() (msys.Atom property)
nonbonded_info() (msys.System property)
NonbondedInfo (class in msys)
NonbondedSchemas() (in module msys)
noverrides() (msys.TermTable property)
,
[1]
nparams() (msys.ParamTable property)
nprops() (msys.ParamTable property)
nresidues() (msys.Chain property)
(msys.System property)
nterms() (msys.TermTable property)
,
[1]
O
occupancy (msys.molfile.Atom attribute)
ok() (msys.InChI property)
order() (msys.Bond property)
origin() (msys.molfile.Grid property)
other() (msys.Bond method)
override_params() (msys.TermTable property)
,
[1]
overrides() (msys.TermTable method)
,
[1]
P
Param (class in msys)
param() (msys.ParamTable method)
(msys.Term property)
params() (msys.ParamTable property)
(msys.TermTable property)
,
[1]
ParamTable (class in msys)
ParseSDF() (in module msys)
path() (msys.IndexedFileLoader property)
(msys.molfile.DtrReader property)
pattern() (msys.SmartsPattern property)
,
[1]
Plugin (class in msys.molfile)
pos() (msys.Atom property)
(msys.molfile.Frame property)
position() (msys.molfile.Frame property)
positions() (msys.System property)
potential_energy() (msys.molfile.Frame property)
pressure() (msys.molfile.Frame property)
pressure_tensor() (msys.molfile.Frame property)
prettyname() (msys.molfile.Plugin property)
props() (msys.ParamTable property)
(msys.TermTable property)
,
[1]
propType() (msys.ParamTable method)
provenance() (msys.System property)
R
radius (msys.molfile.Atom attribute)
raw_alignment() (msys.atomsel.Atomsel method)
read() (msys.molfile.Plugin method)
(msys.molfile.SeqFile class method)
ReadCrdCoordinates() (in module msys)
Reader (class in msys.molfile)
ReadPDBCoordinates() (in module msys)
reload() (msys.molfile.DtrReader method)
remove() (msys.Atom method)
(msys.Bond method)
(msys.Chain method)
(msys.Ct method)
(msys.Residue method)
(msys.Term method)
(msys.TermTable method)
,
[1]
remove_drift() (in module msys.thermalize)
reopen() (msys.molfile.Reader method)
replaceWithSortedTerms() (msys.TermTable method)
,
[1]
resid (msys.molfile.Atom attribute)
resid() (msys.Residue property)
Residue (class in msys)
residue() (msys.System method)
residues() (msys.Chain property)
(msys.System property)
resname (msys.molfile.Atom attribute)
ringbondcount() (msys.AnnotatedSystem method)
,
[1]
S
Save() (in module msys)
save() (msys.System method)
SaveDMS() (in module msys)
SaveMAE() (in module msys)
SaveMol2() (in module msys)
SavePDB() (in module msys)
second() (msys.Bond property)
segid (msys.molfile.Atom attribute)
segid() (msys.Chain property)
select() (msys.molfile.Frame method)
(msys.System method)
selectArr() (msys.System method)
selectAtom() (msys.Residue method)
selectChain() (msys.System method)
selectCt() (msys.System method)
selectIds() (msys.System method)
selectResidue() (msys.Chain method)
SeqFile (class in msys.molfile)
SeqFile.Reader (class in msys.molfile)
Sequences() (in module msys.sequence)
SerializeMAE() (in module msys)
setbondorder() (msys.molfile.Atom method)
setCell() (msys.System method)
setOverride() (msys.TermTable method)
,
[1]
setPositions() (msys.System method)
setVelocities() (msys.System method)
size() (msys.Graph method)
skip() (msys.molfile.Reader method)
SmartsPattern (class in msys)
,
[1]
sorted() (msys.System method)
SpatialHash (class in msys)
string() (msys.InChI property)
svd_3x3() (in module msys.pfx)
sync() (msys.molfile.Writer method)
System (class in msys)
system() (msys.atomsel.Atomsel property)
(msys.Param property)
(msys.SystemImporter property)
(msys.Term property)
(msys.TermTable property)
,
[1]
SystemImporter (class in msys)
T
table() (msys.Param property)
(msys.System method)
(msys.Term property)
table_names() (msys.System property)
tables() (msys.System property)
TableSchemas() (in module msys)
temperature() (msys.molfile.Frame property)
Term (class in msys)
term() (msys.TermTable method)
,
[1]
term_props() (msys.TermTable property)
,
[1]
termPropType() (msys.TermTable method)
,
[1]
terms() (msys.TermTable property)
,
[1]
TermTable (class in msys)
,
[1]
time() (msys.molfile.Frame property)
times() (msys.molfile.DtrReader method)
(msys.molfile.Reader property)
topology() (msys.molfile.Reader property)
(msys.System property)
total_bytes() (msys.molfile.DtrReader method)
total_energy() (msys.molfile.Frame property)
translate() (msys.System method)
truncate() (msys.molfile.Writer method)
type (msys.molfile.Atom attribute)
U
Update() (in module msys.update)
updateFragids() (msys.System method)
V
valence() (msys.AnnotatedSystem method)
,
[1]
(msys.Atom property)
vdw_funct() (msys.NonbondedInfo property)
vdw_rule() (msys.NonbondedInfo property)
vel() (msys.Atom property)
(msys.molfile.Frame property)
velocity() (msys.molfile.Frame property)
version() (msys.molfile.Plugin property)
virial_tensor() (msys.molfile.Frame property)
voxelize() (msys.SpatialHash method)
vx() (msys.Atom property)
vy() (msys.Atom property)
vz() (msys.Atom property)
W
warnings() (msys.SmartsPattern property)
,
[1]
write() (msys.molfile.Plugin method)
Writer (class in msys.molfile)
X
x() (msys.Atom property)
Y
y() (msys.Atom property)
Z
z() (msys.Atom property)
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