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
) or tuple(None, None)- Returns
(chain, resnum) information of the covalent ligand
- class schrodinger.application.desmond.replica_sid_generator.AlchemAsl(ref_asl: str, mut_asl: str, ref_solv_asl: Optional[str] = None, mut_solv_asl: Optional[str] = None)¶
Bases:
object
- ref_asl: str¶
- mut_asl: str¶
- ref_solv_asl: Optional[str] = None¶
- mut_solv_asl: Optional[str] = None¶
- __init__(ref_asl: str, mut_asl: str, ref_solv_asl: Optional[str] = None, mut_solv_asl: Optional[str] = None) None ¶
- schrodinger.application.desmond.replica_sid_generator.setup_alchem_properties(cms_st, alchem_asl_obj, fep_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 objectfep_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
- 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]] ¶
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)
- schrodinger.application.desmond.replica_sid_generator.write_recentered_traj(traj_fn: str, asl: str) Tuple[str, str] ¶
Center the cms/trajectory to the provided asl string. We also need to rename the CT_TYPE of ‘solute’ to ‘solvent’ to ensure proper centering. Return the new cms and trj filenames.
- 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)¶
- 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 schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport(basename, task_type, perturbation_type, cfg=None)¶
Bases:
object
- __init__(basename, task_type, perturbation_type, cfg=None)¶
- 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 schrodinger.application.desmond.replica_sid_generator.ProteinReport(cms_st, prot_asl, mutation_tag=None)¶
Bases:
object
- __init__(cms_st, prot_asl, mutation_tag=None)¶
- export()¶
- get_hot_atoms()¶
Returns atoms in the hot region
- get_residues()¶
- get_number_atoms()¶
- get_protein(asl)¶
- 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()¶
- get_natoms()¶
- get_smiles()¶