schrodinger.application.desmond.replica_sid_generator module

schrodinger.application.desmond.replica_sid_generator.get_cov_lig_info(cms_st)

Find ligand residue ID for covalent ligand job. The inputs should always be a complex system/complex leg. :param cms_st: Desmond system structure :type cms_st: cms.Cms

Return type:tuple(str, str, str) or tuple(None, None, None)
Returns:(chain, resname, insertion_code) information of the covalent ligand
class schrodinger.application.desmond.replica_sid_generator.AlchemAsl(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)

Bases: object

__init__(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)

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

ref_asl
mut_asl
ref_solv_asl
mut_solv_asl
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_sid_generator', '__init__': <function AlchemAsl.__init__>, 'ref_asl': <property object>, 'mut_asl': <property object>, 'ref_solv_asl': <property object>, 'mut_solv_asl': <property object>, '__dict__': <attribute '__dict__' of 'AlchemAsl' objects>, '__weakref__': <attribute '__weakref__' of 'AlchemAsl' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.replica_sid_generator'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.replica_sid_generator.setup_alchem_properties(cms_st, alchem_asl_obj, perturbation_type, leg_type)

This method sets up all alchemical selections for different types of FEPs and respected perturbation legs.

Parameters:
  • alchem_asl_obj (AlchemAsl) – AlchemAsl object
  • perturbation_type (str) – FEP_TYPE as defined in constants.FEP_TYPES
  • leg_type (str) – either a ‘solvent’ or ‘complex’
Return type:

(SmallMoleculeReport, SmallMoleculeReport), (str, str)
Returns:

two tuples of pairs: SmallMoleculeReport and full protein ASL strings
schrodinger.application.desmond.replica_sid_generator.parse_prm_tag(tag)

Given a prm tag, parse and return chain and residue ids.

class schrodinger.application.desmond.replica_sid_generator.FEPReport(basename, energy_output, task_type='lambda_hopping', n_win=12, perturbation_type=None)

Bases: object

__init__(basename, energy_output, task_type='lambda_hopping', n_win=12, perturbation_type=None)

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

setup_alchem_properties()
get_ark_results()

Function organizes and returns ARK abject

export(filename=None)

Writes a file with SID results in them, so they can be read into SID gui

ark_str(str_in)

Sanitize ARK string, by removing the doubleqoutes

launch_SID(traj_fn, st2_fn, eaf_fn)

This method launches analyze_simulation.py, a backend for SID analysis

get_analysis(fep_lambda)

This method generates an analysis input file, submits the analysis, and returns an ARK object with results.

:rtype ARK object

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_sid_generator', '__init__': <function FEPReport.__init__>, 'setup_alchem_properties': <function FEPReport.setup_alchem_properties>, '_determine_fep_leg': <function FEPReport._determine_fep_leg>, '_get_alchemical_asls': <function FEPReport._get_alchemical_asls>, 'get_ark_results': <function FEPReport.get_ark_results>, 'export': <function FEPReport.export>, 'ark_str': <function FEPReport.ark_str>, 'launch_SID': <function FEPReport.launch_SID>, 'get_analysis': <function FEPReport.get_analysis>, '__dict__': <attribute '__dict__' of 'FEPReport' objects>, '__weakref__': <attribute '__weakref__' of 'FEPReport' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.replica_sid_generator'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport(basename, task_type, perturbation_type, cfg=None)

Bases: object

__init__(basename, task_type, perturbation_type, cfg=None)

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

export()
process_salt_and_ions()
get_cms()
get_cpu_gpu_info()
get_sim_time_ns()
get_job_type()
get_ensemble()
get_temperature()
read_cms(basename)
get_nwaters()
get_entry_title()
get_ff()
read_cfg(basename)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_sid_generator', '__init__': <function FEPSimulationReport.__init__>, 'export': <function FEPSimulationReport.export>, 'process_salt_and_ions': <function FEPSimulationReport.process_salt_and_ions>, 'get_cms': <function FEPSimulationReport.get_cms>, 'get_cpu_gpu_info': <function FEPSimulationReport.get_cpu_gpu_info>, 'get_sim_time_ns': <function FEPSimulationReport.get_sim_time_ns>, 'get_job_type': <function FEPSimulationReport.get_job_type>, 'get_ensemble': <function FEPSimulationReport.get_ensemble>, 'get_temperature': <function FEPSimulationReport.get_temperature>, 'read_cms': <function FEPSimulationReport.read_cms>, 'get_nwaters': <function FEPSimulationReport.get_nwaters>, 'get_entry_title': <function FEPSimulationReport.get_entry_title>, 'get_ff': <function FEPSimulationReport.get_ff>, 'read_cfg': <function FEPSimulationReport.read_cfg>, '__dict__': <attribute '__dict__' of 'FEPSimulationReport' objects>, '__weakref__': <attribute '__weakref__' of 'FEPSimulationReport' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.replica_sid_generator'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.replica_sid_generator.ProteinReport(cms_st, prot_asl, mutation_tag=None)

Bases: object

__init__(cms_st, prot_asl, mutation_tag=None)

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

export()
get_hot_atoms()

Returns atoms in the hot region

get_residues()
get_number_atoms()
get_protein(asl)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_sid_generator', '__init__': <function ProteinReport.__init__>, 'export': <function ProteinReport.export>, 'get_hot_atoms': <function ProteinReport.get_hot_atoms>, 'get_residues': <function ProteinReport.get_residues>, 'get_number_atoms': <function ProteinReport.get_number_atoms>, 'get_protein': <function ProteinReport.get_protein>, '__dict__': <attribute '__dict__' of 'ProteinReport' objects>, '__weakref__': <attribute '__weakref__' of 'ProteinReport' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.replica_sid_generator'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport(st, perturbation_type, leg_type, ligand_number=0, asl=None, alchem_solvent_st=None, alchem_solvent_asl=None, metal_asl=None)

Bases: object

__init__(st, perturbation_type, leg_type, ligand_number=0, asl=None, alchem_solvent_st=None, alchem_solvent_asl=None, metal_asl=None)
Parameters:
  • perturbation_type (str) – one of several perturbation types
  • leg_type (str) – solvent, complex or vacuum
  • asl (str) – Asl for the ligand
  • alchem_solvent_asl (str) – Asl for alchemical solvent, can be either water or ions
  • alchem_solvent_st (Structure) – Ct of alchemical solvent, can be either water or ions
  • metal_asl (str) – Asl for the metals and ions
export()
get_alchem_solv()

Return a alchemical solvent types and number of atoms of such type

get_hot_atoms()

Returns number of atoms in the hot region. Depending where the rest region is set up, different property names are used.

getLigandFragments()

Fragments the ligand in several fragments using the murcko rules. returns the list of mappings

get_resname()
get_mol_formula()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.replica_sid_generator', '__init__': <function SmallMoleculeReport.__init__>, 'export': <function SmallMoleculeReport.export>, 'get_alchem_solv': <function SmallMoleculeReport.get_alchem_solv>, 'get_hot_atoms': <function SmallMoleculeReport.get_hot_atoms>, 'getLigandFragments': <function SmallMoleculeReport.getLigandFragments>, 'get_resname': <function SmallMoleculeReport.get_resname>, 'get_mol_formula': <function SmallMoleculeReport.get_mol_formula>, 'get_natoms': <function SmallMoleculeReport.get_natoms>, 'get_smiles': <function SmallMoleculeReport.get_smiles>, '__dict__': <attribute '__dict__' of 'SmallMoleculeReport' objects>, '__weakref__': <attribute '__weakref__' of 'SmallMoleculeReport' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.replica_sid_generator'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

get_natoms()
get_smiles()