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AutoMapper
finds the best mapping from reactant side atoms
to product side atoms of a reaction.Sgroup.XSTATE_C
.
MolImportIface.createMol()
must be used.
Sgroup.XSTATE_X
or Sgroup.XSTATE_XC
.
double[][]
2xN
table
to a 2-column tab-separated string representation of the table.
geom3D=true
, see PolarizabilityPlugin.setGeom3D(boolean)
).
Double.NaN
for no value.
-1
for no value.
ChargePlugin.run()
returned false (calculation error): hydrogen valence error.
HBDAPlugin.run()
returned false (calculation error): hydrogen valence error.
IonChargePlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
MajorMicrospeciesPlugin.run()
returned false (calculation error): hydrogen valence error.
PolarizabilityPlugin.run()
returned false (calculation error): hydrogen valence error.
RefractivityPlugin.run()
returned false (calculation error): hydrogen valence error.
TPSAPlugin.run()
returned false (calculation error): hydrogen valence error.
logDPlugin.run()
returned false (calculation error): hydrogen valence error.
logPPlugin.run()
returned false (calculation error): hydrogen valence error.
pKaPlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
CalculatorPlugin.run()
returned false (calculation error).
MajorMicrospeciesPlugin.setpH(double)
.
Double.NaN
for no value.
-1
for no value.
Double.NaN
for no value.
a(xx), a(yy), a(zz)
of polarizability tensor
(for geom3D=true
, see PolarizabilityPlugin.setGeom3D(boolean)
).
Double.NaN
, otherwise returns the input molecule itself.
1
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or CalculatorPlugin.MOLECULE
.
CalculatorPlugin.ATOM
or CalculatorPlugin.MOLECULE
.
A
for acceptor, D
for donor.
pKaPlugin.setpH(double)
.
Double.NaN
for no value.
String[]
).
String[]
).
logDPlugin.setpH(double)
.
true
if the plugin handles multifragment molecules,
false
otherwise.
true
if the plugin handles multifragment molecules,
false
otherwise.
true
if the plugin handles multifragment molecules,
false
otherwise.
true
if plugin has chart.
true
if aromatic atom.
true
if atom is selected.
true
if atom is selected.
true
if chain atom.
true
sketcher canvas is empty.
true
if molecule cell is empty.
true
sketcher canvas is empty.
true
if molecule cell is empty.
true
if major microspecies required,
ie, if pH is different from Double.NaN
.
true
if major microspecies required,
false
otherwise.
true
if majority microspecies calculation takes place,
ie, if pH is different formDouble.NaN
.
true
if microspecies calculation.
true
if microspecies calculation.
true
if microspecies calculation.
true
if molecule with R-groups.
true
if ring atom.
setReaction()
and
setMap()
in one method.
setReaction()
and
setMap()
in one method.
Double.NaN
.
mark
method was last called on this input stream.
20
).
-10
).
Cl-
concentration (default: 0.1
).
Cl-
concentration (default: 0.1
).
RxnMolecule
passed in
setReaction( final
RxnMolecule rm )
according to the mapId
map.
Na+, K+
concentration (default: 0.1
).
Na+, K+
concentration (default: 0.1
).
298
Kelvin).
Double.NaN
then the input molecule is taken as it is.
0.0
).
1.0
).
14.0
).
[O-]-[N+] >> O=N
sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
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