schrodinger.application.desmond.system_builder_inp module

A script to create a system builder input file.

class schrodinger.application.desmond.system_builder_inp.SystemBuilderInput

Bases: object

__init__()

Initialize self. See help(type(self)) for accurate signature.

reset()
setVdwScalingFactor(value=0)
setOplsaaVersion(value='')
setSoluteAlignment(name='', value=1)
setMMFepioMapModeOption(value=1)
setMMFepioRetainAngleOption(value=1)
setSolute(name)
fixSolute()
setPositiveIon(name='Na.mae')
setNegativeIon(name='Cl.mae')
setSaltPositiveIon(name='Na.mae')
setSaltNegativeIon(name='Cl.mae')
setMembrane(name='DPPC.mae.gz')
setSolvent(name='spc.box.mae')
setMembranize(value=1)
setMembranePatch(x_mem=10.0, y_mem=10.0)
setNeutralize(value=1)
setAddAlchemicalIons(value=1)
setUseAlchemicalWater(value=1)
setRemoveOverlappedCrystalWater(value=1)
addIons(ion_type='positive', nion=0)
addSalt(c=0.0)
setExcludeLocation(value, distance)
setIonLocation(value)
setSolvate(value=1)
setBoundaryCondition(**kwargs)
setWriteOneMaeFile(name='-1')
setWriteMaeFile(name='-1')
setWriteMaeffFile(name='-1')
setWriteXyzFile(name='-1')
setWritePdbFile(name='-1')
setWriteTopFile(name='-1')
setWriteG96File(name='-1')
write(name)
read(name)
read_text(l)
extractSolventFromSt(st, asl='')
deleteSolventFromSt(st, asl='')
treatSolventFromSolute(op='separate', asl='')
run(name='desmond_setup', options=[])