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

CHECK_SOLVENT_OVERLAP = 'check_solvent_overlap'

CHECK_CRYSTAL_WATER_OVERLAP = 'check_crystal_water_overlap'

YES = 'Yes'

NO = 'No'

__init__()

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: int)

setRemoveOverlappedSolvent(value: int)

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

addSalt(c=0.0)

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

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(text)

static identifySolventAtoms(st, asl=None)

extractSolventFromSt(st, asl='')

deleteSolventFromSt(st, asl='')

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

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