schrodinger.application.prepwizard2.tasks module

class schrodinger.application.prepwizard2.tasks.ProteinFeature

Bases: enum.Enum

AntibodyCDR = 1
TCR = 2
schrodinger.application.prepwizard2.tasks.AA3_TO_1(aa_str)
schrodinger.application.prepwizard2.tasks.hide_non_polar_hydrogens(st)

Hide all non-polar hydrogens in the given structure; except those that overlap with other atoms.

class schrodinger.application.prepwizard2.tasks.LoggerMixin(*args, **kwargs)

Bases: object

A Mixin for a task that provides a thin wrapper for a logger

__init__(*args, **kwargs)
logger

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
info(text)

Log the text as informational.

Parameters

text (str) – the info text to log

warning(text)

Log the text as a warning.

Parameters

text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.StructureInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

struct: schrodinger.structure._structure.Structure

A parameter of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.GenerateStatesSettings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

use_epikx: bool

A parameter of the class.

epik_pH: float

A parameter of the class.

epik_pHt: float

A parameter of the class.

max_states: int

A parameter of the class.

process_detected_ligands: bool

A parameter of the class.

process_metals_and_ions: bool

A parameter of the class.

process_non_water_solvents: bool

A parameter of the class.

process_other_hets: bool

A parameter of the class.

getHetTypesToProcess()

Return a list of HetType for het types that should be processed.

epik_pHChanged

A pyqtSignal emitted by instances of the class.

epik_pHReplaced

A pyqtSignal emitted by instances of the class.

epik_pHtChanged

A pyqtSignal emitted by instances of the class.

epik_pHtReplaced

A pyqtSignal emitted by instances of the class.

max_statesChanged

A pyqtSignal emitted by instances of the class.

max_statesReplaced

A pyqtSignal emitted by instances of the class.

process_detected_ligandsChanged

A pyqtSignal emitted by instances of the class.

process_detected_ligandsReplaced

A pyqtSignal emitted by instances of the class.

process_metals_and_ionsChanged

A pyqtSignal emitted by instances of the class.

process_metals_and_ionsReplaced

A pyqtSignal emitted by instances of the class.

process_non_water_solventsChanged

A pyqtSignal emitted by instances of the class.

process_non_water_solventsReplaced

A pyqtSignal emitted by instances of the class.

process_other_hetsChanged

A pyqtSignal emitted by instances of the class.

process_other_hetsReplaced

A pyqtSignal emitted by instances of the class.

use_epikxChanged

A pyqtSignal emitted by instances of the class.

use_epikxReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.GenerateStatesInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.GenerateStatesSettings, schrodinger.application.prepwizard2.tasks.StructureInput

epik_pHChanged

A pyqtSignal emitted by instances of the class.

epik_pHReplaced

A pyqtSignal emitted by instances of the class.

epik_pHtChanged

A pyqtSignal emitted by instances of the class.

epik_pHtReplaced

A pyqtSignal emitted by instances of the class.

max_statesChanged

A pyqtSignal emitted by instances of the class.

max_statesReplaced

A pyqtSignal emitted by instances of the class.

process_detected_ligandsChanged

A pyqtSignal emitted by instances of the class.

process_detected_ligandsReplaced

A pyqtSignal emitted by instances of the class.

process_metals_and_ionsChanged

A pyqtSignal emitted by instances of the class.

process_metals_and_ionsReplaced

A pyqtSignal emitted by instances of the class.

process_non_water_solventsChanged

A pyqtSignal emitted by instances of the class.

process_non_water_solventsReplaced

A pyqtSignal emitted by instances of the class.

process_other_hetsChanged

A pyqtSignal emitted by instances of the class.

process_other_hetsReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

use_epikxChanged

A pyqtSignal emitted by instances of the class.

use_epikxReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PreprocessInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Used as input model for the PreprocessTask and the “preprocess” section of the PPWorkflowTask and PPBatchWorkflowTask tasks. Also see prepare.PrepWizardSettings which has many similarities

reference_struct: schrodinger.structure._structure.Structure

A parameter of the class.

preprocess_delete_far_waters: bool

A parameter of the class.

preprocess_watdist: float

A parameter of the class.

treat_metals: bool

A parameter of the class.

assign_bond_orders: bool

A parameter of the class.

use_ccd: bool

A parameter of the class.

skip_assigned_residues: bool

A parameter of the class.

class ABOOptions(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

use_ccd: bool

A parameter of the class.

skip_assigned_residues: bool

A parameter of the class.

skip_assigned_residuesChanged

A pyqtSignal emitted by instances of the class.

skip_assigned_residuesReplaced

A pyqtSignal emitted by instances of the class.

use_ccdChanged

A pyqtSignal emitted by instances of the class.

use_ccdReplaced

A pyqtSignal emitted by instances of the class.

abo_options: schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions

A parameter of the class.

add_missing_inter_residue_bonds: bool

A parameter of the class.

add_hydrogens: bool

A parameter of the class.

readd_hydrogens: bool

A parameter of the class.

add_terminal_oxygens: bool

A parameter of the class.

treat_disulfides: bool

A parameter of the class.

treat_glycosylation: bool

A parameter of the class.

treat_palmitoylation: bool

A parameter of the class.

antibody_cdr_scheme: schrodinger.infra.util.AntibodyCDRScheme

A parameter of the class.

renumber_ab_residues: bool

A parameter of the class.

tcr_cdr_scheme: schrodinger.infra.util.AntibodyCDRScheme

A parameter of the class.

renumber_tcr_residues: bool

A parameter of the class.

selenomethionines: bool

A parameter of the class.

fillsidechains: bool

A parameter of the class.

fillloops: bool

A parameter of the class.

custom_fasta_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

cap_termini: bool

A parameter of the class.

cap_termini_min_atoms: int

A parameter of the class.

run_epik: bool

A parameter of the class.

idealize_hydrogen_tf: bool

A parameter of the class.

generate_states_settings: schrodinger.application.prepwizard2.tasks.GenerateStatesSettings

A parameter of the class.

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

isDefault()

Whether the current value of this instance matches the default value.

reset()

Reset all settings except pH, which is part of the global settings.

getNumSelected()

Return the number of pre-processing steps that are enabled.

abo_optionsChanged

A pyqtSignal emitted by instances of the class.

abo_optionsReplaced

A pyqtSignal emitted by instances of the class.

add_hydrogensChanged

A pyqtSignal emitted by instances of the class.

add_hydrogensReplaced

A pyqtSignal emitted by instances of the class.

add_missing_inter_residue_bondsChanged

A pyqtSignal emitted by instances of the class.

add_missing_inter_residue_bondsReplaced

A pyqtSignal emitted by instances of the class.

add_terminal_oxygensChanged

A pyqtSignal emitted by instances of the class.

add_terminal_oxygensReplaced

A pyqtSignal emitted by instances of the class.

antibody_cdr_schemeChanged

A pyqtSignal emitted by instances of the class.

antibody_cdr_schemeReplaced

A pyqtSignal emitted by instances of the class.

assign_bond_ordersChanged

A pyqtSignal emitted by instances of the class.

assign_bond_ordersReplaced

A pyqtSignal emitted by instances of the class.

cap_terminiChanged

A pyqtSignal emitted by instances of the class.

cap_terminiReplaced

A pyqtSignal emitted by instances of the class.

cap_termini_min_atomsChanged

A pyqtSignal emitted by instances of the class.

cap_termini_min_atomsReplaced

A pyqtSignal emitted by instances of the class.

custom_fasta_fileChanged

A pyqtSignal emitted by instances of the class.

custom_fasta_fileReplaced

A pyqtSignal emitted by instances of the class.

fillloopsChanged

A pyqtSignal emitted by instances of the class.

fillloopsReplaced

A pyqtSignal emitted by instances of the class.

fillsidechainsChanged

A pyqtSignal emitted by instances of the class.

fillsidechainsReplaced

A pyqtSignal emitted by instances of the class.

generate_states_settingsChanged

A pyqtSignal emitted by instances of the class.

generate_states_settingsReplaced

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfChanged

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfReplaced

A pyqtSignal emitted by instances of the class.

preprocess_delete_far_watersChanged

A pyqtSignal emitted by instances of the class.

preprocess_delete_far_watersReplaced

A pyqtSignal emitted by instances of the class.

preprocess_watdistChanged

A pyqtSignal emitted by instances of the class.

preprocess_watdistReplaced

A pyqtSignal emitted by instances of the class.

readd_hydrogensChanged

A pyqtSignal emitted by instances of the class.

readd_hydrogensReplaced

A pyqtSignal emitted by instances of the class.

reference_structChanged

A pyqtSignal emitted by instances of the class.

reference_structReplaced

A pyqtSignal emitted by instances of the class.

renumber_ab_residuesChanged

A pyqtSignal emitted by instances of the class.

renumber_ab_residuesReplaced

A pyqtSignal emitted by instances of the class.

renumber_tcr_residuesChanged

A pyqtSignal emitted by instances of the class.

renumber_tcr_residuesReplaced

A pyqtSignal emitted by instances of the class.

run_epikChanged

A pyqtSignal emitted by instances of the class.

run_epikReplaced

A pyqtSignal emitted by instances of the class.

selenomethioninesChanged

A pyqtSignal emitted by instances of the class.

selenomethioninesReplaced

A pyqtSignal emitted by instances of the class.

skip_assigned_residuesChanged

A pyqtSignal emitted by instances of the class.

skip_assigned_residuesReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

tcr_cdr_schemeChanged

A pyqtSignal emitted by instances of the class.

tcr_cdr_schemeReplaced

A pyqtSignal emitted by instances of the class.

treat_disulfidesChanged

A pyqtSignal emitted by instances of the class.

treat_disulfidesReplaced

A pyqtSignal emitted by instances of the class.

treat_glycosylationChanged

A pyqtSignal emitted by instances of the class.

treat_glycosylationReplaced

A pyqtSignal emitted by instances of the class.

treat_metalsChanged

A pyqtSignal emitted by instances of the class.

treat_metalsReplaced

A pyqtSignal emitted by instances of the class.

treat_palmitoylationChanged

A pyqtSignal emitted by instances of the class.

treat_palmitoylationReplaced

A pyqtSignal emitted by instances of the class.

use_ccdChanged

A pyqtSignal emitted by instances of the class.

use_ccdReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PreprocessTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.ComboSubprocessTask

input: schrodinger.application.prepwizard2.tasks.PreprocessInput

A parameter of the class.

output: List[schrodinger.structure._structure.Structure]

A parameter of the class.

validateInput()
mainFunction()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.OptimizeHBondInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Model for the “Optimize H-bond Assignments” step of the workflow tab, i.e., OptimizeHBondTask.input

samplewater: bool

A parameter of the class.

include_epik_states: bool

A parameter of the class.

xtal: bool

A parameter of the class.

simplified_pH: str

A parameter of the class.

use_propka: bool

A parameter of the class.

propka_pH: float

A parameter of the class.

label_pkas: bool

A parameter of the class.

force_list: list

A parameter of the class.

minimize_adj_h: bool

A parameter of the class.

protassign_number_sequential_cycles: int

A parameter of the class.

protassign_max_cluster_size: int

A parameter of the class.

idealize_hydrogen_tf: bool

A parameter of the class.

force_listChanged

A pyqtSignal emitted by instances of the class.

force_listReplaced

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfChanged

A pyqtSignal emitted by instances of the class.

idealize_hydrogen_tfReplaced

A pyqtSignal emitted by instances of the class.

include_epik_statesChanged

A pyqtSignal emitted by instances of the class.

include_epik_statesReplaced

A pyqtSignal emitted by instances of the class.

label_pkasChanged

A pyqtSignal emitted by instances of the class.

label_pkasReplaced

A pyqtSignal emitted by instances of the class.

minimize_adj_hChanged

A pyqtSignal emitted by instances of the class.

minimize_adj_hReplaced

A pyqtSignal emitted by instances of the class.

propka_pHChanged

A pyqtSignal emitted by instances of the class.

propka_pHReplaced

A pyqtSignal emitted by instances of the class.

protassign_max_cluster_sizeChanged

A pyqtSignal emitted by instances of the class.

protassign_max_cluster_sizeReplaced

A pyqtSignal emitted by instances of the class.

protassign_number_sequential_cyclesChanged

A pyqtSignal emitted by instances of the class.

protassign_number_sequential_cyclesReplaced

A pyqtSignal emitted by instances of the class.

samplewaterChanged

A pyqtSignal emitted by instances of the class.

samplewaterReplaced

A pyqtSignal emitted by instances of the class.

simplified_pHChanged

A pyqtSignal emitted by instances of the class.

simplified_pHReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

use_propkaChanged

A pyqtSignal emitted by instances of the class.

use_propkaReplaced

A pyqtSignal emitted by instances of the class.

xtalChanged

A pyqtSignal emitted by instances of the class.

xtalReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.OptimizeHBondTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.SubprocessCmdTask

A task optimized H-Bonds, i.e., to run the protein assignment (protassign)

input: schrodinger.application.prepwizard2.tasks.OptimizeHBondInput

A parameter of the class.

output: schrodinger.structure._structure.Structure

A parameter of the class.

message: str

A parameter of the class.

validateInput()
setInitialStatus()
prepareInput()
makeCmd()

Create the command to run ProtAssign without job control (-NOJOBID)

runCmd(cmd)
processOutput()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

messageChanged

A pyqtSignal emitted by instances of the class.

messageReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.CleanupInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Model for the “Clean Up” step of the workflow tab

run_impref: bool

A parameter of the class.

force_field: str

A parameter of the class.

rmsd: float

A parameter of the class.

fixheavy: bool

A parameter of the class.

delete_far_waters: bool

A parameter of the class.

watdist: float

A parameter of the class.

delete_nonbridging_waters: bool

A parameter of the class.

delwater_hbond_cutoff: int

A parameter of the class.

delete_far_watersChanged

A pyqtSignal emitted by instances of the class.

delete_far_watersReplaced

A pyqtSignal emitted by instances of the class.

delete_nonbridging_watersChanged

A pyqtSignal emitted by instances of the class.

delete_nonbridging_watersReplaced

A pyqtSignal emitted by instances of the class.

delwater_hbond_cutoffChanged

A pyqtSignal emitted by instances of the class.

delwater_hbond_cutoffReplaced

A pyqtSignal emitted by instances of the class.

fixheavyChanged

A pyqtSignal emitted by instances of the class.

fixheavyReplaced

A pyqtSignal emitted by instances of the class.

force_fieldChanged

A pyqtSignal emitted by instances of the class.

force_fieldReplaced

A pyqtSignal emitted by instances of the class.

rmsdChanged

A pyqtSignal emitted by instances of the class.

rmsdReplaced

A pyqtSignal emitted by instances of the class.

run_imprefChanged

A pyqtSignal emitted by instances of the class.

run_imprefReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

watdistChanged

A pyqtSignal emitted by instances of the class.

watdistReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.DeleteWatersTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.BlockingFunctionTask

A task that may run water deletion and restrained minimization on a protein

input: schrodinger.application.prepwizard2.tasks.CleanupInput

A parameter of the class.

output: schrodinger.structure._structure.Structure

A parameter of the class.

validateInput()
mainFunction()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.CleanupTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.BlockingFunctionTask

A task that may run water deletion and restrained minimization on a protein

input: schrodinger.application.prepwizard2.tasks.CleanupInput

A parameter of the class.

output: schrodinger.structure._structure.Structure

A parameter of the class.

valence_error: bool

A parameter of the class.

validateInput()
mainFunction()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

valence_errorChanged

A pyqtSignal emitted by instances of the class.

valence_errorReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPWorkflowSettings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Settings for PPW workflow auto task.

preprocess: schrodinger.application.prepwizard2.tasks.PreprocessInput

A parameter of the class.

hbond: schrodinger.application.prepwizard2.tasks.OptimizeHBondInput

A parameter of the class.

cleanup: schrodinger.application.prepwizard2.tasks.CleanupInput

A parameter of the class.

do_preprocess: bool

A parameter of the class.

do_hbond: bool

A parameter of the class.

do_cleanup: bool

A parameter of the class.

use_pdb_ph_if_available: bool

A parameter of the class.

cleanupChanged

A pyqtSignal emitted by instances of the class.

cleanupReplaced

A pyqtSignal emitted by instances of the class.

do_cleanupChanged

A pyqtSignal emitted by instances of the class.

do_cleanupReplaced

A pyqtSignal emitted by instances of the class.

do_hbondChanged

A pyqtSignal emitted by instances of the class.

do_hbondReplaced

A pyqtSignal emitted by instances of the class.

do_preprocessChanged

A pyqtSignal emitted by instances of the class.

do_preprocessReplaced

A pyqtSignal emitted by instances of the class.

hbondChanged

A pyqtSignal emitted by instances of the class.

hbondReplaced

A pyqtSignal emitted by instances of the class.

preprocessChanged

A pyqtSignal emitted by instances of the class.

preprocessReplaced

A pyqtSignal emitted by instances of the class.

use_pdb_ph_if_availableChanged

A pyqtSignal emitted by instances of the class.

use_pdb_ph_if_availableReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPWorkflowInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.StructureInput, schrodinger.application.prepwizard2.tasks.PPWorkflowSettings

Settings and structure input for PPW workflow tasks.

cleanupChanged

A pyqtSignal emitted by instances of the class.

cleanupReplaced

A pyqtSignal emitted by instances of the class.

do_cleanupChanged

A pyqtSignal emitted by instances of the class.

do_cleanupReplaced

A pyqtSignal emitted by instances of the class.

do_hbondChanged

A pyqtSignal emitted by instances of the class.

do_hbondReplaced

A pyqtSignal emitted by instances of the class.

do_preprocessChanged

A pyqtSignal emitted by instances of the class.

do_preprocessReplaced

A pyqtSignal emitted by instances of the class.

hbondChanged

A pyqtSignal emitted by instances of the class.

hbondReplaced

A pyqtSignal emitted by instances of the class.

preprocessChanged

A pyqtSignal emitted by instances of the class.

preprocessReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

use_pdb_ph_if_availableChanged

A pyqtSignal emitted by instances of the class.

use_pdb_ph_if_availableReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPWorkflowOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

structs: List[schrodinger.structure._structure.Structure]

A parameter of the class.

postprocess_valence_error: bool

A parameter of the class.

postprocess_valence_errorChanged

A pyqtSignal emitted by instances of the class.

postprocess_valence_errorReplaced

A pyqtSignal emitted by instances of the class.

structsChanged

A pyqtSignal emitted by instances of the class.

structsReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPWorkflowTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.jobtasks.ComboJobTask

Runs the entire workflow. Intended to be created by PPBatchWorkflowTask.

input: schrodinger.application.prepwizard2.tasks.PPWorkflowInput

A parameter of the class.

output: schrodinger.application.prepwizard2.tasks.PPWorkflowOutput

A parameter of the class.

mainFunction()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

struct_file: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

settings: schrodinger.application.prepwizard2.tasks.PPWorkflowSettings

A parameter of the class.

settingsChanged

A pyqtSignal emitted by instances of the class.

settingsReplaced

A pyqtSignal emitted by instances of the class.

struct_fileChanged

A pyqtSignal emitted by instances of the class.

struct_fileReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.jobtasks.CmdJobTask

Task for the auto PPW2 workflow, both single structure and batch. This task runs the $SCHRODINGER/utilities/prepwizard driver.

input: schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput

A parameter of the class.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks._CmdJobTaskOutput

output_filename: schrodinger.tasks.tasks.TaskFile

A parameter of the class.

incorporation_fileChanged

A pyqtSignal emitted by instances of the class.

incorporation_fileReplaced

A pyqtSignal emitted by instances of the class.

log_fileChanged

A pyqtSignal emitted by instances of the class.

log_fileReplaced

A pyqtSignal emitted by instances of the class.

output_filenameChanged

A pyqtSignal emitted by instances of the class.

output_filenameReplaced

A pyqtSignal emitted by instances of the class.

output_filesChanged

A pyqtSignal emitted by instances of the class.

output_filesReplaced

A pyqtSignal emitted by instances of the class.

class JobConfig(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.JobConfig

incorporation

A parameter of the class.

host_settings: schrodinger.tasks.jobtasks.HostSettings

A parameter of the class.

host_settingsChanged

A pyqtSignal emitted by instances of the class.

host_settingsReplaced

A pyqtSignal emitted by instances of the class.

incorporationChanged

A pyqtSignal emitted by instances of the class.

incorporationReplaced

A pyqtSignal emitted by instances of the class.

jobnameChanged

A pyqtSignal emitted by instances of the class.

jobnameReplaced

A pyqtSignal emitted by instances of the class.

viewnameChanged

A pyqtSignal emitted by instances of the class.

viewnameReplaced

A pyqtSignal emitted by instances of the class.

makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

job_config: JobConfig

A parameter of the class.

job_configChanged

A pyqtSignal emitted by instances of the class.

job_configReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

output: parameters.CompoundParam

A parameter of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.GenerateStatesTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.ComboSubprocessTask

A task that will run epik to generate states

input: schrodinger.application.prepwizard2.tasks.GenerateStatesInput

A parameter of the class.

output: List[schrodinger.structure._structure.Structure]

A parameter of the class.

validateInput()
validateLicenses()
mainFunction()
applyHetStates(applied_states, state_sts, no_hets_recep_st, all_recep_metals)

For each complex in <applied_states>, apply states for another het, based on the het states in <state_sts>. Return list of new complexes.

calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.ProteinRefinementInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

force_field: str

A parameter of the class.

rmsd: float

A parameter of the class.

fixheavy: bool

A parameter of the class.

fixheavyChanged

A pyqtSignal emitted by instances of the class.

fixheavyReplaced

A pyqtSignal emitted by instances of the class.

force_fieldChanged

A pyqtSignal emitted by instances of the class.

force_fieldReplaced

A pyqtSignal emitted by instances of the class.

rmsdChanged

A pyqtSignal emitted by instances of the class.

rmsdReplaced

A pyqtSignal emitted by instances of the class.

structChanged

A pyqtSignal emitted by instances of the class.

structReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.prepwizard2.tasks.ProteinRefinementTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.SubprocessCmdTask

A task to run the protein refinement (restrained minimization, i.e., impref)

input: schrodinger.application.prepwizard2.tasks.ProteinRefinementInput

A parameter of the class.

output: schrodinger.structure._structure.Structure

A parameter of the class.

validateInput()
prepareInput()
makeCmd()

Create the command to run impref not under job control (-NOJOBID)

processOutput()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

schrodinger.application.prepwizard2.tasks.update_params(to_params, from_params)

Update the to_params with the values in from_params.

Parameters
schrodinger.application.prepwizard2.tasks.generate_annotation(task)

Return the annotation text to use for a finished task.

Parameters

task (schrodinger.tasks.tasks.AbstractTask) – the task

Returns

the note to use

Return type

str

schrodinger.application.prepwizard2.tasks.annotate_entry_title(st, annotation)

Annotates the structure title by putting a note on the structure title, only if it is the ANNOTATIONS.

Will replace the existing note at the end of the title, if one is found. If no exact match is found at the end, the new note is appended.

Parameters

  • st (structure.Structure) – the new structure which needs annotated title

  • annotation (str) – one of the known annotation strings

schrodinger.application.prepwizard2.tasks.get_chain_sequences(st: schrodinger.structure._structure.Structure, custom_fasta_file: str = None) → Dict[str, str]

Get a dictionary which maps the residue sequence of a chain to the chain name using a fasta file or the SEQRES information in the structure.

@param st: structure to process

@param custom_fasta_file: FASTA file to read sequences from. If not specified, the SEQRES block from the structure will be used.

@return: a dictionary where the key is the chain name and the value is a string of one letter codes for the amino acids in that chain.

schrodinger.application.prepwizard2.tasks.find_missing_peptide_bonds(st: schrodinger.structure._structure.Structure, seq_by_chain: Dict[str, str]) → List[Tuple[schrodinger.structure._structure.Residue]]

Find sequence-adjacent residues that are not connected by a peptide bond.

For each continuous segment in each chain, align that sequence to the expected sequence and infer if there are peptide bonds that are missing from the structure.

@param st: Structure to process.

@param seq_by_chain: dictionary where the key is the chain name, and the value is a string of the one letter residue codes for the residues in that chain.

@return: a list of residues of the structure which are next to each other in sequence but are not connected with a bond.

schrodinger.application.prepwizard2.tasks.add_peptide_bond(st: schrodinger.structure._structure.Structure, res1: schrodinger.structure._structure.Residue, res2: schrodinger.structure._structure.Residue) → bool

Adds a bond from res1(N) atom to res2(C) atom.

Returns True if the bond was added, or False if either atom is missing.