schrodinger.application.desmond.replica_sid_generator module

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

Bases: object

ark_str(str_in)

Sanitize ARK string, by removing the doubleqoutes

export(filename=None)

Writes a file with SID results in them, so they can be read into SID gui

find_alchemistry_and_type()

Given a cms file we determine it’s component and the FEP type :return: alchemical (ref, mut) component as well as the FEP/perturbation type. :rtype: tuple(ref, mut)

get_analysis(fep_lambda)

This method generates an analysis input file, submits the analysis, and returns an ARK object with results. :param lig_rep: list of two LigandReport objects :type lig_rep: LigandReport

Parameters:perturbation_type (string) – the type of fep perturbation_type

:rtype ARK object

get_ark_results()

Function organizes and returns ARK abject

launch_SID(traj_fn, st2_fn, eaf_fn)

This method launches analyze_trajectories, a backend for SID analysis

setup_alchem_properties()
class schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport(basename, task_type, cfg=None, charge_correction=None)

Bases: object

export()
get_cms()
get_cpu_gpu_info()
get_ensemble()
get_entry_title()
get_ff()
get_job_type()
get_nwaters()
get_sim_time_ns()
get_temperature()
read_cfg(basename)
read_cms(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_number_atoms()
get_protein(asl)
get_residues()
class schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport(st, perturbation_type, leg_type, ligand_number=0, asl=None)

Bases: object

export()
getLigandFragments()

Fragments the ligand in several fragments using the murcko rules. returns the list of mappings

get_hot_atoms()

Returns number of atoms in the hot region. Depending where the rest region is set up, different property names are used.

get_mol_formula()
get_natoms()
get_resname()
get_smiles()
schrodinger.application.desmond.replica_sid_generator.find_covalent_residue_asl(ct)

Automatically find a covalent ligand ASL given a protein-ligand covalent complex :rtype: str :return: ASL string

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
schrodinger.application.desmond.replica_sid_generator.get_ref_mut_indices(cms_st)
Returns:CT ids of ref and mut

:rtype (int, int)

schrodinger.application.desmond.replica_sid_generator.is_covalent(ct, lig_atm_list)

Given ligand indices in a ct, establish if it’s covalent, if so, return the residue it is attached to.

Return type:None or str with ASL of covalent prot residue
schrodinger.application.desmond.replica_sid_generator.parse_prm_tag(tag)

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

schrodinger.application.desmond.replica_sid_generator.setup_alchem_properties(cms_st, alchem_asl, perturbation_type, leg_type)

This method sets up all alchemical selections for different types of FEPs and respected perturbation legs. :type alchem_asl: (str, str) :param alchem_asl: a tuple containing ASLs for lig1 and lig2

Parameters:
  • perturbation_type (str) – FEP_TYPE as defined in desmond.stage.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