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[source]
Bases: object
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__init__()[source]
Initialize self. See help(type(self)) for accurate signature.
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reset()[source]
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setVdwScalingFactor(value=0)[source]
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setOplsaaVersion(value='')[source]
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setSoluteAlignment(name='', value=1)[source]
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setMMFepioMapModeOption(value=1)[source]
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setMMFepioRetainAngleOption(value=1)[source]
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setSolute(name)[source]
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fixSolute()[source]
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setPositiveIon(name='Na.mae')[source]
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setNegativeIon(name='Cl.mae')[source]
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setSaltPositiveIon(name='Na.mae')[source]
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setSaltNegativeIon(name='Cl.mae')[source]
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setMembrane(name='DPPC.mae.gz')[source]
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setSolvent(name='spc.box.mae')[source]
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setMembranize(value=1)[source]
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setMembranePatch(x_mem=10.0, y_mem=10.0)[source]
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setNeutralize(value=1)[source]
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setAddAlchemicalIons(value=1)[source]
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setUseAlchemicalWater(value=1)[source]
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setRemoveOverlappedCrystalWater(value=1)[source]
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addIons(ion_type='positive', nion=0)[source]
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addSalt(c=0.0)[source]
Add salt at a target concentration.
NOTE: In case of FEP inputs for membrane systems, the receptor may
already contain salt ions. In this case we will adjust the target
concentration to account for these ions. If the intput system
concentration is above the target concentration, salt concentration
will be set to 0.0
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setExcludeLocation(value, distance)[source]
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setIonLocation(value)[source]
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setSolvate(value=1)[source]
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setBoundaryCondition(**kwargs)[source]
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setWriteOneMaeFile(name='-1')[source]
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setWriteMaeFile(name='-1')[source]
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setWriteMaeffFile(name='-1')[source]
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setWriteXyzFile(name='-1')[source]
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setWritePdbFile(name='-1')[source]
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setWriteTopFile(name='-1')[source]
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setWriteG96File(name='-1')[source]
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write(name)[source]
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read(name)[source]
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read_text(l)[source]
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static
identifySolventAtoms(st, asl=None)[source]
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deleteSolventFromSt(st, asl='')[source]
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treatSolventFromSolute(op='separate', asl='')[source]
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run(name='desmond_setup', options=[])[source]