schrodinger.application.desmond.replica_sid_generator module¶
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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
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class
schrodinger.application.desmond.replica_sid_generator.
AlchemAsl
(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)¶ Bases:
object
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__init__
(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)¶ Initialize self. See help(type(self)) for accurate signature.
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ref_asl
¶
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mut_asl
¶
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ref_solv_asl
¶
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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)¶ 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
- alchem_asl_obj (
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schrodinger.application.desmond.replica_sid_generator.
parse_prm_tag
(tag)¶ Given a prm tag, parse and return chain and residue ids.
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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)¶ Bases:
object
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__init__
(basename, energy_output, task_type='lambda_hopping', n_win=12, perturbation_type=None)¶ Initialize self. See help(type(self)) for accurate signature.
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setup_alchem_properties
()¶
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get_ark_results
()¶ Function organizes and returns ARK abject
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export
(filename=None)¶ Writes a file with SID results in them, so they can be read into SID gui
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ark_str
(str_in)¶ Sanitize ARK string, by removing the doubleqoutes
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launch_SID
(traj_fn, st2_fn, eaf_fn)¶ This method launches analyze_simulation.py, a backend for SID analysis
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get_analysis
(fep_lambda)¶ This method generates an analysis input file, submits the analysis, and returns an ARK object with results.
:rtype
ARK object
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class
schrodinger.application.desmond.replica_sid_generator.
FEPSimulationReport
(basename, task_type, perturbation_type, cfg=None)¶ Bases:
object
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__init__
(basename, task_type, perturbation_type, cfg=None)¶ Initialize self. See help(type(self)) for accurate signature.
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export
()¶
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process_salt_and_ions
()¶
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get_cms
()¶
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get_cpu_gpu_info
()¶
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get_sim_time_ns
()¶
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get_job_type
()¶
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get_ensemble
()¶
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get_temperature
()¶
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read_cms
(basename)¶
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get_nwaters
()¶
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get_entry_title
()¶
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get_ff
()¶
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read_cfg
(basename)¶
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class
schrodinger.application.desmond.replica_sid_generator.
ProteinReport
(cms_st, prot_asl, mutation_tag=None)¶ Bases:
object
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__init__
(cms_st, prot_asl, mutation_tag=None)¶ Initialize self. See help(type(self)) for accurate signature.
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export
()¶
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get_hot_atoms
()¶ Returns atoms in the hot region
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get_residues
()¶
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get_number_atoms
()¶
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get_protein
(asl)¶
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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)¶ 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)¶ 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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export
()¶
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get_alchem_solv
()¶ Return a alchemical solvent types and number of atoms of such type
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get_hot_atoms
()¶ 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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getLigandFragments
()¶ Fragments the ligand in several fragments using the murcko rules. returns the list of mappings
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get_resname
()¶
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get_mol_formula
()¶
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get_natoms
()¶
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get_smiles
()¶
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