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, str) or tuple(None, None, None) Returns:(chain, resname, insertion_code) information of the covalent ligand

class schrodinger.application.desmond.replica_sid_generator.AlchemAsl(ref_asl, mut_asl, ref_solv_asl=None, mut_solv_asl=None)

Bases: object

ref_asl

mut_asl

ref_solv_asl

mut_solv_asl

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. :type alchem_asl_obj: AlchemAsl :param alchem_asl_obj: AlchemAsl object

Parameters:

• perturbation_type (str) – FEP_TYPE as defined in desmond.const.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

schrodinger.application.desmond.replica_sid_generator.parse_prm_tag(tag)

Given a prm tag, parse and return chain and residue ids.

class schrodinger.application.desmond.replica_sid_generator.FEPReport(basename, data0, results0, data1, results1, data2, results2, task_type='lambda_hopping', n_win=12, perturbation_type=None)

Bases: object

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

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

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

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()