schrodinger.application.desmond.torsion_related module¶
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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
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dih
= None¶
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__init__
(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)¶ Initialize self. See help(type(self)) for accurate signature.
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set_color
(col)¶
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get_color
()¶
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set_ligand_from
(lfrom)¶
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set_ligand_to
(lto)¶
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get_angles
()¶
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set_rbpotential
(rbp)¶
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get_potential
()¶
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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
- st (
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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
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__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.
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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
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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
)
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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.
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getRotEnergy
(offset=False)¶
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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)
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exception
schrodinger.application.desmond.torsion_related.
IncompleteFragmentError
¶ Bases:
Exception
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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schrodinger.application.desmond.torsion_related.
get_rb_potential
(cms_model, lig_aids, a1, a2, a3, a4)¶
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schrodinger.application.desmond.torsion_related.
get_rb_torsions_potential
(cms_model, lig_aids, a1, a2, a3, a4)¶