schrodinger.application.desmond.system_builder_inp module

A script to create a system builder input file.

class schrodinger.application.desmond.system_builder_inp.SystemBuilderInput

addIons(ion_type='positive', nion=0)

addSalt(c=0.0)

deleteSolventFromSt(st, asl='')

extractSolventFromSt(st, asl='')

fixSolute()

read(name)

read_text(l)

reset()

run(name='desmond_setup', options=[])

setAddAlchemicalIons(value=1)

setBoundaryCondition(**kwargs)

setExcludeLocation(value, distance)

setIonLocation(value)

setMMFepioMapModeOption(value=1)

setMMFepioRetainAngleOption(value=1)

setMembrane(name='DPPC.mae.gz')

setMembranePatch(x_mem=10.0, y_mem=10.0)

setMembranize(value=1)

setNegativeIon(name='Cl.mae')

setNeutralize(value=1)

setOplsaaVersion(value='')

setPositiveIon(name='Na.mae')

setSaltNegativeIon(name='Cl.mae')

setSaltPositiveIon(name='Na.mae')

setSolute(name)

setSoluteAlignment(name='', value=1)

setSolvate(value=1)

setSolvent(name='spc.box.mae')

setVdwScalingFactor(value=0)

setWriteG96File(name='-1')

setWriteMaeFile(name='-1')

setWriteMaeffFile(name='-1')

setWriteOneMaeFile(name='-1')

setWritePdbFile(name='-1')

setWriteTopFile(name='-1')

setWriteXyzFile(name='-1')

treatSolventFromSolute(op='separate', asl='')

write(name)