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]
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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]