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Suite 2012 Schrodinger Python API
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Identifier Index
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]
A
a
(in
schrodinger.application.desmond.mdkey
)
addRestraint()
(in
_FFIO
)
app
(in
schrodinger.application.bioluminate.sliderchart
)
AA_1_LETTER_MAP
(in
schrodinger.application.bioluminate.protein
)
addRestraints()
(in
_FFIO
)
App
(in
schrodinger.application.lid.ligand_interaction_diagram_gui
)
AA_3_LETTER_MAP
(in
schrodinger.application.bioluminate.protein
)
addRow()
(in
ActiveDatabaseTable
)
app
(in
schrodinger.application.lid.ligand_interaction_diagram_gui
)
AA_MAP
(in
_ProMut
)
addRow()
(in
PathModel
)
app
(in
schrodinger.job
)
AA_NAME
(in
_ProMut
)
addRow()
(in
ResiduesModel
)
App
(in
schrodinger.job.app
)
AA_NAME_KNOWN
(in
_ProMut
)
addRow()
(in
StrucListModel
)
APPDATA
(in
schrodinger.utils.fileutils
)
ABCMeta
addRow()
(in
WidgetTable
)
APPDATA_DIR
(in
schrodinger.application.desmond.mdkey
)
absolute
(in
schrodinger.protein.assignment
)
addSalt()
(in
SystemBuilderInput
)
appdata_dir
(in
schrodinger.utils.ligfilter
)
accept()
(in
ColumnSelectDialog
)
addScriptArgs()
(in
Launcher
)
appdata_file
(in
schrodinger.utils.ligfilter
)
accept()
(in
ActiveDatabaseDialog
)
addSearchDB()
(in
DBManagePanel
)
append()
(in
FFIOStructure
)
accept()
(in
PropFilterDialog
)
addSearchDirectory()
(in
DBManagePanel
)
append()
(in
XpDesWriter
)
accept()
(in
ValueSelectionDialog
)
addSearchFiles()
(in
DBManagePanel
)
append()
(in
QMRegion
)
accept()
(in
ChooseLigandDialog
)
addSearchWS()
(in
DBManagePanel
)
append()
(in
MMIMArgList
)
accept()
(in
ChooseLigandDialog
)
addSeries()
(in
Plotter
)
append()
(in
MaestroWriter
)
accept()
(in
PhaseDatabaseOpenDialog
)
addSettings()
(in
WriteInputs
)
append()
(in
Mol2Writer
)
accept()
(in
ProjectOpenDialog
)
addSite()
(in
_FFIO
)
append()
(in
PDBWriter
)
AcceptMode
addSites()
(in
_FFIO
)
append()
(in
SDWriter
)
ACCEPTOR_POS
(in
StructuralInteractionFingerprintGenerator
)
addStage()
(in
LinearWriter
)
append()
(in
SmilesCsvWriter
)
AcceptorConstraint
(in
schrodinger.application.glide.glide
)
addStage()
(in
Writer
)
append()
(in
SmilesStructure
)
ACCEPTORS
(in
schrodinger.structutils.interactions
)
addStretchfbhw()
(in
_FFIO
)
append()
(in
SmilesWriter
)
ACIDIC_RESIDUES
(in
schrodinger.application.bioluminate.protein
)
addStretchfbhws()
(in
_FFIO
)
append()
(in
Structure
)
ACIDIC_RESIDUES
(in
schrodinger.structutils
)
addString()
(in
sketcher
)
append()
(in
StructureWriter
)
ack()
(in
DebugEventSocketProxy
)
addStructure()
(in
sketcher
)
append()
(in
TextualStructure
)
actinide_series
(in
schrodinger.application.prime.primefix
)
addSubMenu()
(in
Factory
)
append()
(in
MultiFileWriter
)
actinide_series
(in
schrodinger.structutils.assignbondorders
)
addTempInputFile()
(in
Launcher
)
append()
(in
List
)
ACTION_NAME
(in
schrodinger.application.bioluminate.actions.factory
)
addTextToSet()
(in
AsetFrame
)
append_comment()
(in
schrodinger.application.desmond.util
)
ActionEvent
addToAuxListbox()
(in
PropertySelector
)
append_project_command()
(in
schrodinger.maestro.maestro
)
actionEvent()
(in
sketcher
)
addToolBars()
(in
ViewerWindow
)
append_stage()
(in
schrodinger.application.desmond.cmj
)
actionEvent()
(in
sketcherGUIMultiColumnToolBar
)
addTorsionRestraint()
(in
Minimizer
)
appendLigand()
(in
Complex
)
actionEvent()
(in
sketcherView
)
addUndoRedoToolBar()
(in
ViewerWindow
)
appendReceptor()
(in
Complex
)
ActionMenu
(in
schrodinger.application.bioluminate.pml_menus
)
addVar()
(in
LinearWriter
)
appframework
(in
schrodinger.ui
)
actions
(in
schrodinger.application.bioluminate
)
addVar()
(in
Writer
)
AppFramework
(in
schrodinger.ui.appframework
)
activate()
(in
StartDialogBase
)
addVdwtype()
(in
_FFIO
)
appframework
(in
schrodinger.ui.qt
)
activate()
(in
WriteDialog
)
addVdwtypes()
(in
_FFIO
)
AppFramework
(in
schrodinger.ui.qt.appframework
)
activate()
(in
StartDialog
)
addVdwtypescombined()
(in
_FFIO
)
AppJobInputFrame
(in
schrodinger.ui.appframework
)
activate()
(in
WriteDialog
)
addVdwtypescombineds()
(in
_FFIO
)
application
(in
schrodinger
)
ACTIVE
(in
schrodinger.job.queue
)
addVirtual()
(in
_FFIO
)
APPLICATION_NAME
(in
Startup
)
active_jobs
(in
JobDJ
)
addVirtuals()
(in
_FFIO
)
apply()
(in
GaussianFilter
)
ActiveDatabaseDialog
(in
schrodinger.application.bioluminate.antibody.management
)
adf()
(in
ComUtil
)
apply()
(in
schrodinger.application.desmond.periodicfix
)
ActiveDatabaseTable
(in
schrodinger.application.bioluminate.antibody.management
)
adjust()
(in
Structure
)
apply()
(in
_Rotamer
)
ActiveDecoyFingerprintAnalyzer
(in
schrodinger.analysis.enrichment
)
adjust_phi()
(in
Rama
)
apply()
(in
ColorScheme
)
adapt_dummy_types()
(in
Zmat
)
adjust_props()
(in
ReorgFitting
)
apply()
(in
Superimposer
)
adaptor
(in
mexpParser
)
adjust_props_offset2()
(in
ReorgFitting
)
apply()
(in
List
)
adaptor
(in
schrodinger.application.lid.lid2d.render
)
adjust_psi()
(in
Rama
)
apply()
(in
Map
)
ADD
(in
schrodinger.application.bioluminate.actions.icons
)
adjust_symbol_size()
(in
Rama
)
apply()
(in
Sea
)
ADD
(in
schrodinger.project
)
adjustDum()
(in
schrodinger.application.mcpro.perturbations
)
apply_color_scheme()
(in
schrodinger.structutils.color
)
add
(in
schrodinger.protein.assignment
)
adv_callback()
(in
_BaseGroup
)
apply_dihedral()
(in
Rama
)
add()
(in
RewriteRuleElementStream
)
AdvancedOptionsPanel
(in
schrodinger.antibody_db_manage_gui
)
apply_pkas()
(in
ProtAssign
)
add()
(in
JobOutput
)
AdvLabel
(in
schrodinger.application.desmond.cwidget
)
apply_style_sheet()
(in
schrodinger.ui.qt.style
)
add()
(in
_MdcBase
)
AdvLabel
(in
schrodinger.application.desmond.fep_gui
)
applySettings()
(in
AdvOptionsFrame
)
add()
(in
EntryGroup
)
AdvOptionsFrame
(in
schrodinger.application.desmond.gui
)
applyStyle()
(in
Structure
)
add()
(in
FirstSecondaryStructure
)
AGGREGATE_CALCULATIONS
(in
PropertyCalculator
)
applyStyle()
(in
_Chain
)
add()
(in
SecondSecondaryStructure
)
ahomo_prop
(in
MopacResults
)
applyStyle()
(in
_Molecule
)
add()
(in
Group
)
ai
(in
_FEPIOAngleMap
)
applyStyle()
(in
_Residue
)
add()
(in
LinkedList
)
ai
(in
_FEPIOAtomMap
)
applyStyle()
(in
_Ring
)
add()
(in
RunningJobs
)
ai
(in
_FEPIOBondMap
)
apps
(in
schrodinger.application.macromodel
)
add()
(in
_Callback
)
ai
(in
_FEPIODihedMap
)
arccosh
(in
schrodinger.protein.assignment
)
add()
(in
ColorScheme
)
ai
(in
_FEPIOExclMap
)
archive_wm()
(in
schrodinger.application.watermap.utils
)
add()
(in
ButtonBox
)
ai
(in
_FEPIOPairMap
)
arcsinh
(in
schrodinger.protein.assignment
)
add()
(in
NoteBook
)
ai
(in
_FFIOAngle
)
arctan
(in
schrodinger.protein.assignment
)
add()
(in
PanedWidget
)
ai
(in
_FFIOAngleFBHW
)
arctan2
(in
schrodinger.protein.assignment
)
add()
(in
RadioSelect
)
ai
(in
_FFIOBond
)
areBound()
(in
Structure
)
add_atom()
(in
PertReorder
)
ai
(in
_FFIOConstraint
)
areCOsPara()
(in
AssignBondOrders
)
add_attribute_aliases()
(in
schrodinger.application.jaguar.output
)
ai
(in
_FFIODihedral
)
areIntersecting2Dpts()
(in
schrodinger.application.lid.lid2d.utils
)
add_bounding_rect_offset()
(in
schrodinger.application.lid.lid2d.utils
)
ai
(in
_FFIOExclusion
)
areIntersecting2DptsAdjacent()
(in
schrodinger.application.lid.lid2d.utils
)
add_bounding_rect_offset_xy()
(in
schrodinger.application.lid.lid2d.utils
)
ai
(in
_FFIOImproperFBHW
)
ARG
(in
schrodinger.application.desmond.antlr3.treewizard
)
add_bounding_rect_offset_xywh()
(in
schrodinger.application.lid.lid2d.utils
)
ai
(in
_FFIOPair
)
argc
(in
schrodinger.application.desmond.gchart
)
add_code()
(in
ReturnCode
)
ai
(in
_FFIOPosFBHW
)
ark
(in
schrodinger.infra
)
add_col()
(in
Table
)
ai
(in
_FFIORestraint
)
AROMATIC_FLUORINES
(in
schrodinger.structutils.interactions
)
add_common_context_items()
(in
schrodinger.application.bioluminate.pml_menus
)
ai
(in
_FFIOVirtual
)
AROMATIC_POS
(in
StructuralInteractionFingerprintGenerator
)
add_complex()
(in
FitNewxpReorgEnergy
)
ai
(in
_FFAngle
)
AROMATIC_RESIDUE
(in
StructuralInteractionFingerprintGenerator
)
add_current_to_states()
(in
changeable
)
ai
(in
_FFBond
)
AROMATIC_RESIDUES
(in
schrodinger.application.bioluminate.protein
)
add_current_to_states()
(in
rotatable_changeable
)
ai
(in
_FFConstraint
)
AROMATIC_RESIDUES
(in
schrodinger.structutils
)
add_current_to_states()
(in
water_changeable
)
ai
(in
_FFDihedral
)
AROMATIC_RESIDUES
(in
StructuralInteractionFingerprintGenerator
)
add_host_lists()
(in
schrodinger.pipeline.pipeline
)
ai
(in
_FFExclusion
)
AROMATICS
(in
schrodinger.structutils.interactions
)
add_hydrogens()
(in
schrodinger.structutils.build
)
ai
(in
_FFPair
)
Around
(in
schrodinger.application.bioluminate.pml_menus
)
add_job_launch_log()
(in
schrodinger.maestro.maestro
)
ai
(in
_FFRestraint
)
AroundExpandSubMenu
(in
schrodinger.application.bioluminate.pml_menus
)
add_lig_solvent_cap()
(in
Zmat
)
ai
(in
_FFVirtual
)
Array_Prop
(in
schrodinger.application.desmond.simulation_block_data
)
add_ligand_fitting_data()
(in
ReorgFitting
)
aj
(in
_FEPIOAngleMap
)
ArraySyntax
(in
schrodinger.application.desmond.enhanced_sampling.FcnTypes
)
add_moldescriptors_options()
(in
schrodinger.application.moldescriptors
)
aj
(in
_FEPIOAtomMap
)
arrow
(in
schrodinger.graphics3d
)
add_multi_job_finalizer()
(in
schrodinger.job.queue
)
aj
(in
_FEPIOBondMap
)
Arrow
(in
schrodinger.graphics3d.arrow
)
add_output()
(in
Env
)
aj
(in
_FEPIODihedMap
)
ARROW_GROUP
(in
schrodinger.application.desmond.maestro
)
add_para_job_options()
(in
schrodinger.application.macromodel.paraUtils
)
aj
(in
_FEPIOExclMap
)
ARROW_GROUP_refcount
(in
schrodinger.application.desmond.maestro
)
add_plugin()
(in
schrodinger.application.desmond.config
)
aj
(in
_FEPIOPairMap
)
ArrowCore
(in
schrodinger.graphics3d.arrow
)
add_plugin()
(in
schrodinger.application.desmond.mdkey
)
aj
(in
_FFIOAngle
)
ASCENDING
(in
schrodinger.structutils.sort
)
add_point()
(in
data_set
)
aj
(in
_FFIOAngleFBHW
)
asDock()
(in
SimplifiedSequenceViewer
)
add_point_to_bbx()
(in
schrodinger.application.lid.lid2d.utils
)
aj
(in
_FFIOBond
)
asea_copy()
(in
schrodinger.utils.sea
)
add_prot_solvent_cap()
(in
Zmat
)
aj
(in
_FFIOConstraint
)
aset()
(in
ComUtil
)
add_row()
(in
Table
)
aj
(in
_FFIODihedral
)
AsetFrame
(in
schrodinger.ui.macromodel
)
add_smiles()
(in
schrodinger.structutils.smilesfilter
)
aj
(in
_FFIOExclusion
)
asFrame()
(in
SimplifiedSequenceViewer
)
add_static()
(in
Env
)
aj
(in
_FFIOImproperFBHW
)
asGrid()
(in
ImportWidget
)
add_step()
(in
Guide
)
aj
(in
_FFIOPair
)
askdirectory()
(in
schrodinger.ui.widget.tkinterwidget
)
add_step()
(in
Guide
)
aj
(in
_FFIOVirtual
)
askopenfilename()
(in
schrodinger.ui.widget.tkinterwidget
)
add_subjob_files()
(in
schrodinger.application.jaguar.utils
)
aj
(in
_FFAngle
)
askopenfilenames()
(in
schrodinger.ui.widget.tkinterwidget
)
add_tag()
(in
Sea
)
aj
(in
_FFBond
)
askOverwrite()
(in
AppFramework
)
add_to_dict_if_no_key()
(in
schrodinger.application.lid.lid2d.utils
)
aj
(in
_FFConstraint
)
askOverwrite()
(in
AppFramework
)
add_var()
(in
binding
)
aj
(in
_FFDihedral
)
askOverwriteIfNecessary()
(in
AppFramework
)
addActionItem()
(in
RowActionItem
)
aj
(in
_FFExclusion
)
askOverwriteIfNecessary()
(in
AppFramework
)
addActions()
(in
Factory
)
aj
(in
_FFPair
)
askOverwriteJobname()
(in
GuiApp
)
addAlignToolBar()
(in
ViewerWindow
)
aj
(in
_FFVirtual
)
asksaveasfilename()
(in
schrodinger.ui.widget.tkinterwidget
)
addAngle()
(in
_FFIO
)
ak
(in
_FEPIOAngleMap
)
askUsernamePassword()
(in
ProxyPasswordManager
)
addAnglefbhw()
(in
_FFIO
)
ak
(in
_FEPIODihedMap
)
askUsernamePassword()
(in
ProxyPasswordManagerQt
)
addAnglefbhws()
(in
_FFIO
)
ak
(in
_FFIOAngle
)
asl
(in
schrodinger.application.desmond.fepana
)
addAnglemap()
(in
_FEPIO
)
ak
(in
_FFIOAngleFBHW
)
asl
(in
amide_changeable
)
addAnglemaps()
(in
_FEPIO
)
ak
(in
_FFIOConstraint
)
asl
(in
amine_changeable
)
addAngleRestraint()
(in
Minimizer
)
ak
(in
_FFIODihedral
)
asl
(in
carboxyl_changeable
)
addAngles()
(in
_FFIO
)
ak
(in
_FFIOImproperFBHW
)
asl
(in
changeable
)
addAnnotationAction()
(in
SimplifiedSequenceViewer
)
ak
(in
_FFIOVirtual
)
asl
(in
histidine_changeable
)
addAntibodyNumberingToolBar()
(in
ViewerWindow
)
ak
(in
_FFAngle
)
asl
(in
rotatable_changeable
)
addAtom()
(in
Structure
)
ak
(in
_FFConstraint
)
asl
(in
water_changeable
)
addAtomGroupRow()
(in
AtomGroupFrame
)
ak
(in
_FFDihedral
)
ASL
(in
schrodinger.utils.ligfilter
)
addAtommap()
(in
_FEPIO
)
ak
(in
_FFVirtual
)
asl_expr
(in
_AtomSelection
)
addAtommaps()
(in
_FEPIO
)
al
(in
_FEPIODihedMap
)
ASL_IONS
(in
Consensus
)
addAtoms()
(in
Structure
)
al
(in
_FFIOConstraint
)
ASL_IONS
(in
ConsensusToolBar
)
addAtomsToSet()
(in
AsetFrame
)
al
(in
_FFIODihedral
)
ASL_LIGAND
(in
Consensus
)
addBond()
(in
_FFIO
)
al
(in
_FFIOImproperFBHW
)
ASL_LIGAND
(in
ConsensusToolBar
)
addBond()
(in
Structure
)
al
(in
_FFIOVirtual
)
ASL_WATER
(in
Consensus
)
addBond()
(in
_StructureAtom
)
al
(in
_FFConstraint
)
ASL_WATER
(in
ConsensusToolBar
)
addBondmap()
(in
_FEPIO
)
al
(in
_FFDihedral
)
AslCriterion
(in
schrodinger.utils.ligfilter
)
addBondmaps()
(in
_FEPIO
)
al
(in
_FFVirtual
)
AslLigandSearcher
addBonds()
(in
_FFIO
)
alie_analysis()
(in
schrodinger.application.jaguar.output
)
ASLObject
(in
schrodinger.application.desmond.enhsamp
)
addBonds()
(in
Structure
)
alie_analysis_precision
(in
JaguarResults
)
aslselect_atom()
(in
schrodinger.application.desmond.cms
)
addc()
(in
ComUtil
)
alie_precision
(in
JaguarAtomicResults
)
AslValidator
(in
schrodinger.application.desmond.cmj
)
addcascademenu()
(in
MainMenuBar
)
align()
(in
StructAlign
)
AsMenu
(in
schrodinger.application.bioluminate.pml_menus
)
addCellForEachRow()
(in
_Column
)
ALIGN_TOOLBAR
(in
ViewerWindow
)
asp_prop
(in
MopacResults
)
addCentralWidget()
(in
AppFramework
)
ALIGNED_COLOR
(in
schrodinger.structutils.sitealign
)
asp_tot_prop
(in
MopacResults
)
addChild()
(in
DebugEventListener
)
ALIGNED_STYLE
(in
schrodinger.structutils.sitealign
)
assemble_energy_results()
(in
schrodinger.trajectory.analyze_trajectories
)
addChild()
(in
DebugEventSocketProxy
)
ALIGNMENT_ACTIONS
(in
schrodinger.application.bioluminate.actions.configs
)
assign()
(in
AssignBondOrders
)
addChild()
(in
DebugTreeAdaptor
)
alignSites()
(in
BindingSiteAligner
)
assign_best_combinations()
(in
ProtAssign
)
addChild()
(in
TraceDebugEventListener
)
alignStructure()
(in
StructAlign
)
assign_cluster_combination()
(in
ProtAssign
)
addChild()
(in
BaseTree
)
ALIPHATIC_FLUORINES
(in
schrodinger.structutils.interactions
)
assign_combination()
(in
hbond_cluster
)
addChild()
(in
BaseTreeAdaptor
)
ALIPHATIC_RESIDUES
(in
schrodinger.structutils
)
assign_st()
(in
schrodinger.structutils.assignbondorders
)
addChild()
(in
Tree
)
alkali_metals
(in
schrodinger.application.prime.primefix
)
assign_state()
(in
amide_changeable
)
addChild()
(in
TreeAdaptor
)
alkali_metals
(in
schrodinger.structutils.assignbondorders
)
assign_state()
(in
amine_changeable
)
addChildren()
(in
BaseTree
)
alkaline_earth_metals
(in
schrodinger.application.prime.primefix
)
assign_state()
(in
carboxyl_changeable
)
addColumn()
(in
WidgetTable
)
alkaline_earth_metals
(in
schrodinger.structutils.assignbondorders
)
assign_state()
(in
changeable
)
addCommandLineOptions()
(in
App
)
ALL
(in
schrodinger.application.glide.glide
)
assign_state()
(in
histidine_changeable
)
addConsensusToolBar()
(in
ViewerWindow
)
ALL
(in
schrodinger.project
)
assign_state()
(in
rotatable_changeable
)
addConstraint()
(in
_FFIO
)
ALL
(in
schrodinger.utils.cmdline
)
assign_state()
(in
water_changeable
)
addConstraint()
(in
ConstraintGroup
)
all_jobs
(in
JobDJ
)
assign_state_of_changeable()
(in
ProtAssign
)
addConstraintGroup()
(in
Dock
)
all_metal_atomic_numbers
(in
schrodinger.application.lid.lid2d.compute
)
assignAromaticBonders()
(in
AssignBondOrders
)
addConstraints()
(in
_FFIO
)
all_metals
(in
schrodinger.application.prime.primefix
)
assignAromaticRing()
(in
AssignBondOrders
)
addContext()
(in
Factory
)
all_metals
(in
schrodinger.structutils.assignbondorders
)
assignAromaticRingGroup()
(in
AssignBondOrders
)
addCriterion()
(in
PropFilterDialog
)
all_multicomb()
(in
schrodinger.application.desmond.autopartition
)
assignAromaticRingOrders()
(in
AssignBondOrders
)
addCV()
(in
Meta
)
ALL_PROTEINS
(in
schrodinger.application.bioluminate.actions.icons
)
assignbondorders
(in
schrodinger.structutils
)
addData()
(in
Grid
)
ALL_RESIDUES
(in
PrimeConfig
)
AssignBondOrders
(in
schrodinger.structutils.assignbondorders
)
addData()
(in
PhaseDB
)
all_rows
(in
EntryGroup
)
assignChainOrders()
(in
AssignBondOrders
)
addData()
(in
Structures
)
all_rows
(in
Project
)
ASSIGNED_AROMATIC
(in
schrodinger.structutils.assignbondorders
)
addData()
(in
Text
)
ALL_TAR
(in
_RingMut
)
AssignForcefield
addDatabase()
(in
ActiveDatabaseDialog
)
ALL_TYPES
(in
schrodinger.utils.preferences
)
assignGroupDoubleBonds()
(in
AssignBondOrders
)
AddDefinitionDialog
(in
schrodinger.ui.ligfilter
)
allocate()
(in
Queue
)
assignGroupTripleBonds()
(in
AssignBondOrders
)
addDihedmap()
(in
_FEPIO
)
ALLOW_THREADS
(in
schrodinger.protein.assignment
)
assignment
(in
schrodinger.protein
)
addDihedmaps()
(in
_FEPIO
)
ALLOWED_COLOR
(in
Rama
)
assignTemplatedSubstructures()
(in
AssignBondOrders
)
addDihedral()
(in
_FFIO
)
allowed_function_modules
(in
schrodinger.infra.propedit
)
at_values
(in
Scan
)
addDihedrals()
(in
_FFIO
)
allowed_function_names
(in
schrodinger.infra.propedit
)
atid2atomsel()
(in
CmsModel
)
addDistanceRestraint()
(in
Minimizer
)
allowed_functions
(in
schrodinger.infra.propedit
)
atom
(in
Sequence
)
addElement()
(in
_OtherBlock
)
allowed_operators
(in
schrodinger.infra.propedit
)
atom
(in
TextualStructure
)
addElements()
(in
_OtherBlock
)
ALOGP_INTERVAL
(in
schrodinger.application.moldescriptors
)
atom
(in
_Chain
)
addEnv()
(in
Launcher
)
ALPHA
(in
schrodinger.application.desmond.enhanced_sampling.mexpLexer
)
atom
(in
_Molecule
)
addExclmap()
(in
_FEPIO
)
ALPHA
(in
schrodinger.application.desmond.enhanced_sampling.mexpParser
)
atom
(in
_Residue
)
addExclmaps()
(in
_FEPIO
)
alpha_polar()
(in
schrodinger.application.jaguar.output
)
atom
(in
_Ring
)
addExclusion()
(in
_FFIO
)
alpha_polar_precision
(in
JaguarResults
)
Atom
(in
schrodinger.utils.sea
)
addExclusions()
(in
_FFIO
)
alphabetizeNames()
(in
PropertySelector
)
atom()
(in
mexpParser
)
addExpectedInput()
(in
Stage
)
alreadyParsedRule()
(in
BaseRecognizer
)
atom()
(in
AcceptorConstraint
)
addExpectedKeyword()
(in
QSiteStage
)
alt_xyz
(in
_StructureAtom
)
atom()
(in
DonorConstraint
)
addExpectedOutput()
(in
Stage
)
alumo_prop
(in
MopacResults
)
atom()
(in
MetalConstraint
)
addFinalizer()
(in
BaseJob
)
alwaysLocal()
(in
App
)
atom()
(in
Structure
)
addFindToolBar()
(in
ViewerWindow
)
am
(in
_FFIOConstraint
)
atom_b_factor()
(in
schrodinger.application.bioluminate.pml_menus
)
addForceInputFile()
(in
Launcher
)
am
(in
_FFIOVirtual
)
ATOM_BALLNSTICK
(in
schrodinger.application.bioluminate.pml_menus
)
addGroupPrereq()
(in
BaseJob
)
am
(in
_FFConstraint
)
ATOM_BALLNSTICK
(in
schrodinger.structure
)
addHydrogenCap()
(in
QSiteInput
)
am
(in
_FFVirtual
)
ATOM_CIRCLE
(in
schrodinger.structure
)
AddHydrogens
(in
schrodinger.application.bioluminate.pml_menus
)
AM1
(in
schrodinger.application.mopac
)
ATOM_CPK
(in
schrodinger.structure
)
addImportToolBar()
(in
ViewerWindow
)
amide_changeable
(in
ProtAssign
)
atom_exch
(in
schrodinger.protein.remediate
)
addImproperfbhw()
(in
_FFIO
)
AMIDINE
(in
schrodinger.structutils.interactions
)
atom_indexes
(in
Ligand
)
addImproperfbhws()
(in
_FFIO
)
amine_changeable
(in
ProtAssign
)
atom_indices
(in
Consensus
)
addInputFile()
(in
App
)
an
(in
_FFIOVirtual
)
atom_indices
(in
_Group
)
addInputFile()
(in
Launcher
)
an
(in
_FFVirtual
)
atom_is_nonpolar()
(in
schrodinger.application.bioluminate.protein
)
addIons()
(in
SystemBuilderInput
)
ana
(in
schrodinger.application.desmond
)
ATOM_MARKER
(in
_LigMut
)
addJob()
(in
JobDJ
)
analysis
(in
schrodinger
)
ATOM_MARKER
(in
_ProMut
)
addKey()
(in
Key
)
Analysis
ATOM_MARKER
(in
_RingMut
)
addKey()
(in
Definition
)
analysis
(in
schrodinger.protein
)
atom_name
(in
_StructureAtom
)
addLicense()
(in
Launcher
)
analysis
(in
schrodinger.trajectory
)
ATOM_NONE
(in
schrodinger.application.bioluminate.pml_menus
)
addLigand()
(in
sketcher
)
AnalysisJob
ATOM_NOSTYLE
(in
schrodinger.structure
)
addLine()
(in
CriteriaListModel
)
analysistool
(in
schrodinger.trajectory
)
atom_prop_link
(in
schrodinger.structure
)
addLine()
(in
CriteriaListModel
)
AnalysisTool
(in
schrodinger.trajectory.analysistool
)
ATOM_RAINBOW_COLORS
(in
schrodinger.application.bioluminate.pml_menus
)
addLogFile()
(in
App
)
analyze
(in
schrodinger.structutils
)
atom_return
(in
mexpParser
)
addLogFile()
(in
_Backend
)
analyze()
(in
Bfactor_data_set
)
atom_selection_dialog()
(in
schrodinger.maestro.maestro
)
addLogFile()
(in
Launcher
)
analyze()
(in
Gfactor_summary_data_set
)
atom_style
(in
_StructureAtom
)
addmenu()
(in
MainMenuBar
)
analyze()
(in
backbone_dihedral_data_set
)
atom_total
(in
JaguarResults
)
addmenuitem()
(in
MainMenuBar
)
analyze()
(in
bond_angle_data_set
)
atom_total
(in
Structure
)
addMessageName()
(in
_Backend
)
analyze()
(in
bond_length_data_set
)
atom_total
(in
_DesmondFrame
)
addMolsToSet()
(in
AsetFrame
)
analyze()
(in
chirality_data_set
)
atom_total
(in
FFStructure
)
addMonitorFile()
(in
_Backend
)
analyze()
(in
data_set
)
atom_type
(in
_StructureAtom
)
addNavigationNode()
(in
CommonTreeNodeStream
)
analyze()
(in
gamma_Bfactor_data_set
)
atom_type_name
(in
_StructureAtom
)
AddNeighborGroups
(in
schrodinger.protein.findhets
)
analyze()
(in
improper_torsion_data_set
)
ATOM_TYPING_SCHEMES
(in
CanvasFingerprintGenerator
)
addOneRow()
(in
AtomGroupModel
)
analyze()
(in
missing_atoms_data_set
)
ATOM_WIRE
(in
schrodinger.application.bioluminate.pml_menus
)
addOneRow()
(in
PosResModel
)
analyze()
(in
peptide_planarity_data_set
)
AtomContextMenu
(in
schrodinger.application.bioluminate.pml_menus
)
ADDOP
(in
schrodinger.application.desmond.enhanced_sampling.mexpLexer
)
analyze()
(in
sidechain_dihedral_data_set
)
AtomGroup
(in
schrodinger.application.desmond.cms
)
ADDOP
(in
schrodinger.application.desmond.enhanced_sampling.mexpParser
)
analyze()
(in
sidechain_planarity_data_set
)
AtomGroup
(in
schrodinger.application.desmond.mdkey
)
addOptions()
(in
SequenceFileDialog
)
analyze()
(in
steric_clash_data_set
)
ATOMGROUP_PREFIX
(in
Cms
)
addOptions()
(in
CanvasFingerprintClusterCLI
)
analyze()
(in
DesmondSimulation
)
ATOMGROUP_PREFIX_LEN
(in
schrodinger.application.desmond.mdkey
)
addOptions()
(in
CanvasFingerprintGeneratorCLI
)
analyze_paths()
(in
Perturbations
)
ATOMGROUP_PREFIX_NAME
(in
schrodinger.application.desmond.mdkey
)
addOptions()
(in
CanvasFingerprintSimilarityCLI
)
analyze_trajectories
(in
schrodinger.trajectory
)
AtomGroupDelegate
(in
schrodinger.application.desmond.gui
)
addOtherBlock()
(in
_FEPIO
)
analyzeBetweenGroups()
(in
TwoGroupFingerprintAnalyzer
)
AtomGroupFrame
(in
schrodinger.application.desmond.gui
)
addOtherBlock()
(in
_FFIO
)
analyzeFingerprints()
(in
ActiveDecoyFingerprintAnalyzer
)
AtomGroupModel
(in
schrodinger.application.desmond.gui
)
addOutputFile()
(in
_Backend
)
analyzeGroups()
(in
TwoGroupFingerprintAnalyzer
)
AtomGroupRow
(in
schrodinger.application.desmond.gui
)
addOutputFile()
(in
Launcher
)
analyzeWithinGroups()
(in
TwoGroupFingerprintAnalyzer
)
atomic_charge_prop
(in
MopacResults
)
addOutputFile()
(in
Stage
)
AND
(in
schrodinger.application.bioluminate.propfilter
)
atomic_number
(in
_StructureAtom
)
addOutputFileBE()
(in
App
)
ANG_TOL
(in
schrodinger.application.mcpro.modelsystemwizard
)
atomic_weight
(in
_StructureAtom
)
addOutputFileFE()
(in
App
)
angle
(in
schrodinger.application.desmond.fepana
)
atommap()
(in
_FEPIO
)
addPair()
(in
_FFIO
)
Angle
(in
schrodinger.trajectory.analysis
)
atoms
(in
Consensus
)
addPairmap()
(in
_FEPIO
)
angle()
(in
_FFIO
)
ATOMS
(in
schrodinger.structutils.rmsd
)
addPairmaps()
(in
_FEPIO
)
angle_bend_energy()
(in
schrodinger.application.qsite.output
)
atoms()
(in
AcceptorConstraint
)
addPairs()
(in
_FFIO
)
angle_builtin_prop
(in
schrodinger.trajectory.ffstructure
)
atoms()
(in
DonorConstraint
)
addPattern()
(in
LigfilterFrame
)
anglefbhw()
(in
_FFIO
)
atoms()
(in
MetalConstraint
)
addPatternCriterion()
(in
LigfilterFrame
)
anglemap()
(in
_FEPIO
)
atomsasl()
(in
schrodinger.application.prepwizard
)
addPiPiInteraction()
(in
sketcher
)
angstrom_per_bohr
(in
schrodinger.application.jaguar.constants
)
atomsel()
(in
ASLObject
)
addPoints()
(in
_RamachandranCallback
)
ANNIHILATION
(in
schrodinger.application.desmond.fep_gui
)
atomselection
(in
schrodinger.trajectory
)
addPosfbhw()
(in
_FFIO
)
annotate()
(in
GetLabelBBXAnnotator
)
atomTypingCB()
(in
CanvasFingerprintGeneratorGUI
)
addPosfbhws()
(in
_FFIO
)
annotate()
(in
LidAnnotator
)
attach_fragment()
(in
schrodinger.structutils.build
)
addPosFrozen()
(in
Minimizer
)
annotate()
(in
SetCoordinateAnnotator
)
attach_structure()
(in
schrodinger.structutils.build
)
addPosResRow()
(in
RestraintsTab
)
ANNOTATE_ACTIONS
(in
schrodinger.application.bioluminate.actions.configs
)
attachCap()
(in
CapTermini
)
addPosRestraint()
(in
Minimizer
)
annotators
(in
schrodinger.application.lid.lid2d
)
AUTO
(in
schrodinger.protein.getpdb
)
addPredefinedCriterion()
(in
LigfilterFrame
)
answer
(in
schrodinger.application.desmond.ana
)
auto_partition()
(in
schrodinger.application.desmond.autopartition
)
addPrereq()
(in
BaseJob
)
antibody
(in
schrodinger.application.bioluminate
)
AutoColorCarbons
(in
schrodinger.application.bioluminate.pml_menus
)
addPropCriterion()
(in
LigfilterFrame
)
antibody_db_manage_gui
(in
schrodinger
)
AutoColorObjects
(in
schrodinger.application.bioluminate.pml_menus
)
addProperty()
(in
schrodinger.infra.propedit
)
ANTIBODY_NUM_TOOLBAR
(in
ViewerWindow
)
AutoColorSubMenu
(in
schrodinger.application.bioluminate.pml_menus
)
addpropop1Modified()
(in
LigfilterFrame
)
antibody_utils
(in
schrodinger.application.bioluminate
)
AutoCycleCarbonColor
(in
schrodinger.application.bioluminate.pml_menus
)
addPseudo()
(in
_FFIO
)
AntibodyNumberingToolBar
(in
schrodinger.application.bioluminate.ssv.toolbars
)
AutoCycleColor
(in
schrodinger.application.bioluminate.pml_menus
)
addPseudos()
(in
_FFIO
)
AntibodyPreset
(in
schrodinger.application.bioluminate.pml_menus
)
AUTOMATIC_CACHE_FREEING
(in
schrodinger.project
)
addQMCut()
(in
QSiteInput
)
antlr3
(in
schrodinger.application.desmond
)
autopartition
(in
schrodinger.application.desmond
)
addQMMolecule()
(in
QSiteInput
)
antlr_version
(in
BaseRecognizer
)
autoPlace()
(in
Membrane_Model
)
addRectangle()
(in
IntervalTree
)
antlr_version
(in
mexpLexer
)
autoPlaceByMolecule()
(in
Membrane_Model
)
addRectangle()
(in
IntervalTreeNode
)
antlr_version
(in
mexpParser
)
autoprojectsync_call()
(in
schrodinger.application.desmond.maestro
)
addReferenceSeries()
(in
Plotter
)
antlr_version_str
(in
BaseRecognizer
)
autosetToggled()
(in
_Pert
)
addRequiredOutputFile()
(in
_Backend
)
antlr_version_str
(in
mexpLexer
)
available_color_schemes()
(in
schrodinger.structutils.color
)
addResidue()
(in
RegionInfo
)
antlr_version_str
(in
mexpParser
)
AVAILABLE_FF
(in
_Flex
)
addResidue()
(in
sketcher
)
ANTLRFileStream
(in
schrodinger.application.desmond.antlr3.streams
)
average_energy()
(in
WaterMapAnaJob
)
addResidueAtom()
(in
sketcher
)
ANTLRInputStream
(in
schrodinger.application.desmond.antlr3.streams
)
AverageStructure
(in
schrodinger.trajectory.analysis
)
addResidueInteraction()
(in
sketcher
)
ANTLRStringStream
(in
schrodinger.application.desmond.antlr3.streams
)
addResidues()
(in
PrimeConfig
)
ANY_CONTACT
(in
StructuralInteractionFingerprintGenerator
)
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