schrodinger.application.desmond.torsion_related module

class schrodinger.application.desmond.torsion_related.TorsionPotential(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)

Bases: object

A class to contain the atom numbers for each torsion

dih = None

__init__(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)

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

set_color(col)

get_color()

set_ligand_from(lfrom)

set_ligand_to(lto)

get_angles()

set_rbpotential(rbp)

get_potential()

__str__()

Return str(self).

init_ff(st, atom_list)

This function initializes torsion force field parameters relevant to the ligand. Ligand is defined by a list of atoms.

Parameters:

• st (structure.Structure) – structure object for all molecules
• atom_list (list) – list of ligand atom indices

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.torsion_related', '__doc__': 'A class to contain the atom numbers for each torsion', 'dih': None, '__init__': <function TorsionPotential.__init__>, 'set_color': <function TorsionPotential.set_color>, 'get_color': <function TorsionPotential.get_color>, 'set_ligand_from': <function TorsionPotential.set_ligand_from>, 'set_ligand_to': <function TorsionPotential.set_ligand_to>, 'get_angles': <function TorsionPotential.get_angles>, 'set_rbpotential': <function TorsionPotential.set_rbpotential>, 'get_potential': <function TorsionPotential.get_potential>, '__str__': <function TorsionPotential.__str__>, '_convert_index_to_asl': <function TorsionPotential._convert_index_to_asl>, '_get_utt_potential': <function TorsionPotential._get_utt_potential>, '_get_energy': <function TorsionPotential._get_energy>, '_get_potential': <function TorsionPotential._get_potential>, 'init_ff': <function TorsionPotential.init_ff>, '__dict__': <attribute '__dict__' of 'TorsionPotential' objects>, '__weakref__': <attribute '__weakref__' of 'TorsionPotential' objects>})

__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.torsion_related'

__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

__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.torsion_related.BondRotator(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, prime_hmc=True, hmc_steps=20, is_fep=False)

Bases: object

perform RB scan

__init__(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, prime_hmc=True, hmc_steps=20, is_fep=False)

Parameters:is_fep – Prime license is not checkout for FEP system.

potential(conf=None, degree=True)

get potential energy corresponding to ‘conf’ :param conf: conformation in degrees to get corresponding potential :type conf: float

:rtype float

run_hmc(nsteps=20, max_confs=10)

Run Prime’s Hybrid Monte Carlo (HMC), return top output cts that will be ‘deduplicated’ by energy and rmsd. :param nsteps: Number of MC steps :param max_confs: Number of maximum conformers to return :rtype: list(structure.Structure)

prime_search_and_scan(nsteps=20)

Get best profile by using Prime HMC to generate multiple initial coordinates. Modify self.results to reflect the best profile.

getRotEnergy(offset=False)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.torsion_related', '__doc__': '\n perform RB scan\n ', '__init__': <function BondRotator.__init__>, '_has_prime': <function BondRotator._has_prime>, 'potential': <function BondRotator.potential>, 'run_hmc': <function BondRotator.run_hmc>, 'prime_search_and_scan': <function BondRotator.prime_search_and_scan>, '_scan': <function BondRotator._scan>, 'getRotEnergy': <function BondRotator.getRotEnergy>, '__dict__': <attribute '__dict__' of 'BondRotator' objects>, '__weakref__': <attribute '__weakref__' of 'BondRotator' objects>})

__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.torsion_related'

__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.torsion_related.get_old2new(st, prop='i_m_original_index')

Get dictionary for atom-level property ‘prop’ as a key, and return it’s new atom index (aid)

exception schrodinger.application.desmond.torsion_related.IncompleteFragmentError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.torsion_related', '__weakref__': <attribute '__weakref__' of 'IncompleteFragmentError' 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__

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

__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.torsion_related'

__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).

__setstate__()

__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).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.desmond.torsion_related.get_rb_potential(cms_model, lig_aids, a1, a2, a3, a4)

schrodinger.application.desmond.torsion_related.get_rb_torsions_potential(cms_model, lig_aids, a1, a2, a3, a4)