schrodinger.application.desmond.replica_sid_generator module¶
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schrodinger.application.desmond.replica_sid_generator.
get_cov_lig_info
(cms_st)[source]¶ 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
) or tuple(None, None)- Returns
(chain, resnum) information of the covalent ligand
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class
schrodinger.application.desmond.replica_sid_generator.
AlchemAsl
(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)[source]¶ Bases:
object
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__init__
(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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property
ref_asl
¶
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property
mut_asl
¶
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property
ref_solv_asl
¶
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property
mut_solv_asl
¶
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schrodinger.application.desmond.replica_sid_generator.
setup_alchem_properties
(cms_st, alchem_asl_obj, perturbation_type, leg_type)[source]¶ This method sets up all alchemical selections for different types of FEPs and respected perturbation legs.
- Parameters
alchem_asl_obj (
AlchemAsl
) – AlchemAsl objectperturbation_type (
str
) – FEP_TYPE as defined in constants.FEP_TYPESleg_type (
str
) – either a ‘solvent’ or ‘complex’
- Return type
(
SmallMoleculeReport
,SmallMoleculeReport
), (str
,str
)- Returns
two tuples of pairs: SmallMoleculeReport and full protein ASL strings
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schrodinger.application.desmond.replica_sid_generator.
parse_prm_tag
(cms_model: schrodinger.application.desmond.cms.Cms) → Union[Tuple[None, None, None], Tuple[str, int, str]][source]¶ Given a cms model, get the chain, resnum, and inscode of the mutated residue.
Mutated sites are parsed from the s_bioluminate_Mutations property which is a string in the format of A:33B(ALA->VAL) where A is the chain, 33 is the residue number, B in the insertion code (optional), and the mutation is from an alanine to a valine.
- In the case of
a multisite+multistep mutation (e.g. WT -> A-ALA41ILE,A-ALA43GLY)
there is no s_bioluminate_Mutations property
we must skip ligand analysis, so return (None, None, None)
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class
schrodinger.application.desmond.replica_sid_generator.
FEPReport
(basename, energy_output, task_type='lambda_hopping', n_win=12, perturbation_type=None)[source]¶ Bases:
object
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__init__
(basename, energy_output, task_type='lambda_hopping', n_win=12, perturbation_type=None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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export
(filename=None)[source]¶ Writes a file with SID results in them, so they can be read into SID gui
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class
schrodinger.application.desmond.replica_sid_generator.
FEPSimulationReport
(basename, task_type, perturbation_type, cfg=None)[source]¶ Bases:
object
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class
schrodinger.application.desmond.replica_sid_generator.
ProteinReport
(cms_st, prot_asl, mutation_tag=None)[source]¶ Bases:
object
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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)[source]¶ Bases:
object
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__init__
(st, perturbation_type, leg_type, ligand_number=0, asl=None, alchem_solvent_st=None, alchem_solvent_asl=None, metal_asl=None)[source]¶ - 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
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get_hot_atoms
()[source]¶ Returns number of atoms in the hot region. Depending where the rest region is set up, different property names are used.
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