schrodinger.application.desmond.system_builder_inp module¶
A script to create a system builder input file.
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class
schrodinger.application.desmond.system_builder_inp.
SystemBuilderInput
¶ Bases:
object
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__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
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reset
()¶
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setVdwScalingFactor
(value=0)¶
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setOplsaaVersion
(value='')¶
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setSoluteAlignment
(name='', value=1)¶
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setMMFepioMapModeOption
(value=1)¶
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setMMFepioRetainAngleOption
(value=1)¶
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setSolute
(name)¶
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fixSolute
()¶
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setPositiveIon
(name='Na.mae')¶
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setNegativeIon
(name='Cl.mae')¶
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setSaltPositiveIon
(name='Na.mae')¶
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setSaltNegativeIon
(name='Cl.mae')¶
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setMembrane
(name='DPPC.mae.gz')¶
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setSolvent
(name='spc.box.mae')¶
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setMembranize
(value=1)¶
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setMembranePatch
(x_mem=10.0, y_mem=10.0)¶
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setNeutralize
(value=1)¶
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setAddAlchemicalIons
(value=1)¶
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setUseAlchemicalWater
(value=1)¶
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setRemoveOverlappedCrystalWater
(value=1)¶
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addIons
(ion_type='positive', nion=0)¶
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addSalt
(c=0.0)¶
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setExcludeLocation
(value, distance)¶
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setIonLocation
(value)¶
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setSolvate
(value=1)¶
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setBoundaryCondition
(**kwargs)¶
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setWriteOneMaeFile
(name='-1')¶
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setWriteMaeFile
(name='-1')¶
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setWriteMaeffFile
(name='-1')¶
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setWriteXyzFile
(name='-1')¶
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setWritePdbFile
(name='-1')¶
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setWriteTopFile
(name='-1')¶
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setWriteG96File
(name='-1')¶
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write
(name)¶
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read
(name)¶
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read_text
(l)¶
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extractSolventFromSt
(st, asl='')¶
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deleteSolventFromSt
(st, asl='')¶
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treatSolventFromSolute
(op='separate', asl='')¶
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run
(name='desmond_setup', options=[])¶
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