schrodinger.application.desmond.fep_edge_data module

class schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData(complex_sea, solvent_sea, pv_st=None, sol_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)

Bases: schrodinger.application.desmond.fep_edge_data.FEPEdgeData

This object stores covalent FEP related data.

atom_mapping

Return atom mapping for both ligand fragment that is used in the SID calculation. Ligands used in the solvent leg are different than those used in the complex leg. The difference is:

Complex leg – we use the side chain of the attached residue plus

the ligand.

Solvent leg – we use the peptide plus the ligand.

Returns:atom mapping for ligand1 and ligand2. The values should Return type:(list, list)

cpx_sid_lp_results

get_ligand1_atom_dict()

get_ligand2_atom_dict()

ligand1_cpx_st

ligand1_st

ligand2_cpx_st

ligand2_st

ligand_torsions

mut_st

Returns full structure of a mutated protein

receptor_sid_rmsf_backbone_lambda0

receptor_sid_rmsf_backbone_lambda1

receptor_st

receptor_title

solvent_fullsystem_ct

wt_st

Returns full structure of a WT protein

class schrodinger.application.desmond.fep_edge_data.FEPEdgeData(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule')

Bases: future.types.newobject.newobject

FEPEdgeData contains all the data related to an FEP perturbation. This includes both solvent and complex legs of the simulations as well as analysis results produced by SID.

atom_mapping

cpx_charge

cpx_charge_correction

cpx_delta_g

Returns:dG and its standard deviation Return type:float, float

cpx_delta_g_forward

cpx_delta_g_forward_analytical_std

cpx_delta_g_forward_bootstrap_std

cpx_delta_g_forward_df_per_replica

cpx_delta_g_forward_dg

cpx_delta_g_forward_err

cpx_delta_g_reverse

cpx_delta_g_reverse_err

cpx_delta_g_sliding

cpx_delta_g_sliding_err

cpx_end_time_ns

cpx_ensemble

cpx_ff

cpx_rest_exchanges

cpx_sid_lp_results

cpx_sid_number_of_frames

cpx_sid_pl_results

cpx_sid_protein_residues

A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation :rtype: str :return: a list of protein tags that interact with both ligand1 and

ligand2

cpx_sid_snapshot_times_ps

cpx_sid_snashot_times_ps

cpx_sid_trajectory_interval_ns

cpx_sim_time

Values returned in Ns (nanoseconds)

cpx_start_time_ns

cpx_temperature

cpx_timestep_interval

cpx_timestep_list

cpx_total_atoms

cpx_total_replicas

cpx_total_waters

delta_delta_g

fullsystem_ct

get_ligand1_atom_dict()

get_ligand2_atom_dict()

get_minimal_fragments_with_mutation()

Generates two structures of minimal fragments that contain the mutation. This is so we can annotate the mutations and make them searchable. :return: returns two structures of fragments that contain the mutation. :rtype : (schrodinger.structure, schrodinger.structure)

get_protein_residues_sequence_tags()

static get_smiles(st)

rtype: str return: Generate SMILES from a given ligand structure.

jobname

leg1_name

leg2_name

ligand1_atomic_mass

ligand1_charge

ligand1_cpx_asl

ligand1_cpx_sid_lighb(stats=True)

ligand1_cpx_sid_molsa(stats=True)

ligand1_cpx_sid_psa(stats=True)

ligand1_cpx_sid_rb_strain(stats=True)

ligand1_cpx_sid_rgyr(stats=True)

ligand1_cpx_sid_rmsd(stats=True)

ligand1_cpx_sid_sasa(stats=True)

ligand1_cpx_sid_waters(stats=True)

ligand1_fragments(offset_by_receptor_natoms=True)

ligand1_hash

ligand1_mol_formula

ligand1_name

ligand1_pdb_name

ligand1_rot_bonds

ligand1_smiles

ligand1_sol_asl

ligand1_sol_sid_lighb(stats=True)

ligand1_sol_sid_molsa(stats=True)

ligand1_sol_sid_psa(stats=True)

ligand1_sol_sid_rb_strain(stats=True)

ligand1_sol_sid_rgyr(stats=True)

ligand1_sol_sid_rmsd(stats=True)

ligand1_sol_sid_sasa(stats=True)

ligand1_st

Returns ligand_1 structure

ligand1_total_atoms

ligand1_total_fragments

ligand1_total_heavy

ligand1_total_hot

ligand1_total_rot_bonds

ligand2_atomic_mass

ligand2_charge

ligand2_cpx_asl

ligand2_cpx_sid_lighb(stats=True)

ligand2_cpx_sid_molsa(stats=True)

ligand2_cpx_sid_psa(stats=True)

ligand2_cpx_sid_rb_strain(stats=True)

ligand2_cpx_sid_rgyr(stats=True)

ligand2_cpx_sid_rmsd(stats=True)

ligand2_cpx_sid_sasa(stats=True)

ligand2_cpx_sid_waters(stats=True)

ligand2_fragments(offset_by_receptor_natoms=True)

ligand2_hash

ligand2_mol_formula

ligand2_name

ligand2_pdb_name

ligand2_rot_bonds

ligand2_smiles

ligand2_sol_asl

ligand2_sol_sid_lighb(stats=True)

ligand2_sol_sid_molsa(stats=True)

ligand2_sol_sid_psa(stats=True)

ligand2_sol_sid_rb_strain(stats=True)

ligand2_sol_sid_rgyr(stats=True)

ligand2_sol_sid_rmsd(stats=True)

ligand2_sol_sid_sasa(stats=True)

ligand2_st

Returns ligand_2 structure

ligand2_total_atoms

ligand2_total_fragments

ligand2_total_heavy

ligand2_total_hot

ligand2_total_rot_bonds

static ligand_name(st)

ligand_torsions

pl_contact_data0

A dictionary containing PL interactions for lambda=0

pl_contact_data1

A dictionary containing PL interactions for lambda=1

pl_interaction_similarity_matrix0

Protein-ligand interactions similarity matrix for lambda=0 sys for all available frames.

pl_interaction_similarity_matrix1

Protein-ligand interactions similarity matrix for lambda=1 sys for all available frames.

static protein_residue(res)

Get data about the specified residue

Parameters:res (schrodinger.structure._Residue) – The residue object to get data from Returns:A namedtuple containing the molecule number, chain, residue name,

and residue number :rtype: ResData

receptor_b_factor

Returen B factor that is read from the initial structure. If the B factor is not defined return None :rtype: list of B-factors by residues :return: float

receptor_chain_names

receptor_charge

receptor_residue_sequence_list

Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy

tails).

Return type:ResData

receptor_residue_sequence_tags

A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype: residue_tag

receptor_residues_interaction_ligand1

A list of preotein residues that interact just with ligand1 :rtype: list :return: list of protein residue tags

receptor_residues_interaction_ligand2

A list of preotein residues that interact just with ligand2 :rtype: list :return: list of protein residue tags

receptor_sid_rmsd_backbone_lambda0

receptor_sid_rmsd_backbone_lambda1

receptor_sid_rmsd_ligand_lambda0

ligand1 RMSD wrt the protein

receptor_sid_rmsd_ligand_lambda1

ligand2 RMSD wrt the protein

receptor_sid_rmsf_backbone_lambda0

receptor_sid_rmsf_backbone_lambda1

receptor_st

Returns receptor structure

receptor_title

receptor_total_atom

receptor_total_heavy

receptor_total_residues

receptor_total_residues_in_chains

short_hash

sol_charge

sol_charge_correction

sol_delta_g

Returns:dG and its standard deviation Return type:float, float

sol_delta_g_forward

sol_delta_g_forward_analytical_std

sol_delta_g_forward_bootstrap_std

sol_delta_g_forward_df_per_replica

sol_delta_g_forward_dg

sol_delta_g_forward_err

sol_delta_g_reverse

sol_delta_g_reverse_err

sol_delta_g_sliding

sol_delta_g_sliding_err

sol_end_time_ns

sol_ensemble

sol_ff

sol_rest_exchanges

sol_sid_number_of_frames

sol_sid_snapshot_times_ps

sol_sid_trajectory_interval_ns

sol_sim_time

Values returned in Ns (nanoseconds)

sol_start_time_ns

sol_temperature

sol_timestep_interval

sol_timestep_list

sol_total_atoms

sol_total_replicas

sol_total_waters

sse_limits_lambda0

sse_limits_lambda1

class schrodinger.application.desmond.fep_edge_data.FEPTorsions(ark_sol=None, ark_cpx=None, sol_idx_offset=0, cpx_idx_offset=0)

cpx_result

max_potential_energy

plot(ax, color='gray', for_print=False, pot_tick_pos='right', hist_tick_pos='Bottom')

potential_energy

Returns potential energy that’s offset to zero

sol_result

class schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer(sol_torsions_sea_list, cpx_torsions_sea_list, sol_idx_offset=0, cpx_idx_offset=0, perturbation_type='small_molecule')

Class that stores torsions for a single ligand. These torsions are from both solvent and complex legs of the simulations, corresponding to a single lambda value.

all_tors

matched_tors

matched_total

tors_total

unmatched_tors

unmatched_total

class schrodinger.application.desmond.fep_edge_data.PRMEdgeData(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)

Bases: schrodinger.application.desmond.fep_edge_data.FEPEdgeData

PRMEdgeData is an object that stores Protein Residue Mutation related data. And inherits from FEPEdgeData.

atom_mapping

cpx_sid_lp_results

get_protein_residues_sequence_tags()

ligand1_st

ligand2_st

ligand_st_mol_formula

ligand_torsions

mut_frag_st

mut_name

mut_residue_sequence_list

Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy

tails).

Return type:ResData

mut_residue_sequence_tags

A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype: residue_tag

mut_st

Returns full structure of a mutated protein

static peptide_name(st)

prm_name

receptor_sid_rmsf_backbone_lambda0

receptor_sid_rmsf_backbone_lambda1

receptor_st

solvent_fullsystem_ct

wt_frag_st

wt_name

wt_residue_sequence_list

Return a list of residue objects (ResData) in amino-to-carboxy order. :return: a list of residue objects, ordered N->C (amino to carboxy

tails).

Return type:ResData

wt_residue_sequence_tags

A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use ‘_’ (underscore) :return: a list of residue tags :rtype: residue_tag

wt_st

Returns full structure of a WT protein

class schrodinger.application.desmond.fep_edge_data.ResData

Bases: schrodinger.application.desmond.fep_edge_data.ResData

A class to store the molecule number, chain, name, and number of a residue

fullName()

Return a string of the residue data formatted as chain:resname_resnum

Returns:The formatted residue data Return type:str

nameNum()

Return the residue name and number formatted as resname_resnum

Returns:The formatted residue data Return type:str

schrodinger.application.desmond.fep_edge_data.tag_protein(proteinA, proteinB)

This is function was adopted from:

scisol.leadoptmap.protein_fep_mapper.tag_protein

This proceeds in several steps for mutation of protein A -> protein B Loop over all other atoms in the two full length proteins and assign 1:1 atom mapping. For the mutated residue, it might put some wrong numbers in, but it is fine as the correct value will later overwrite them.

:param proteinA : protein A :type proteinA : structure :param proteinB : protein B :type proteinB : structure