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| setVdwScalingFactor(self,
value=0) |
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setOplsaaVersion(self,
value='') |
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setSoluteAlignment(self,
name='',
value=1) |
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| setMMFepioMapModeOption(self,
value=1) |
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| setMMFepioRetainAngleOption(self,
value=1) |
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setPositiveIon(self,
name='Na.mae') |
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setNegativeIon(self,
name='Cl.mae') |
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setSaltPositiveIon(self,
name='Na.mae') |
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setSaltNegativeIon(self,
name='Cl.mae') |
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setMembrane(self,
name='DPPC.mae.gz') |
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setSolvent(self,
name='spc.box.mae') |
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| setMembranize(self,
value=1) |
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| setMembranePatch(self,
x_mem=10.0,
y_mem=10.0) |
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| setNeutralize(self,
value=1) |
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addIons(self,
ion_type='positive',
nion=0) |
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| setExcludeLocation(self,
value,
distance) |
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| setIonLocation(self,
value) |
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| setSolvate(self,
value=1) |
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| setBoundaryCondition(self,
**kwargs) |
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setWriteOneMaeFile(self,
name='-1') |
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setWriteMaeFile(self,
name='-1') |
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setWriteMaeffFile(self,
name='-1') |
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setWriteXyzFile(self,
name='-1') |
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setWritePdbFile(self,
name='-1') |
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setWriteTopFile(self,
name='-1') |
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setWriteG96File(self,
name='-1') |
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extractSolventFromSt(self,
st,
asl='') |
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deleteSolventFromSt(self,
st,
asl='') |
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treatSolventFromSolute(self,
op='separate',
asl='') |
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run(self,
name='desmond_setup',
options=[]) |
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