schrodinger.application.desmond.fep_edge_data module¶

schrodinger.application.desmond.fep_edge_data.water_mol() → schrodinger.structure.Structure¶: Return a water molecule (SPC model)

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

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

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

Bases: object

sol_result¶

cpx_result¶

max_potential_energy¶

potential_energy¶: Returns potential energy that’s offset to zero

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

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')¶

Bases: object

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.

matched_tors¶

unmatched_tors¶

all_tors¶

matched_total¶

unmatched_total¶

tors_total¶

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

Bases: object

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.

static get_smiles()¶: rtype: str return: Generate SMILES from a given ligand structure.

atom_mapping¶

ligand1_fragments(offset_by_receptor_natoms=True)¶

ligand2_fragments(offset_by_receptor_natoms=True)¶

ligand1_sol_sid_rb_strain(stats=True)¶

ligand2_sol_sid_rb_strain(stats=True)¶

ligand1_cpx_sid_rb_strain(stats=True)¶

ligand2_cpx_sid_rb_strain(stats=True)¶

ligand_torsions¶

Return type:	(`FEPTorsionsContainer` object, `FEPTorsionsContainer` object)
Returns:	`FEPTorsionsContainer` objects for lambda0 and lambda1.

ligand1_cpx_sid_waters(stats=True)¶

ligand2_cpx_sid_waters(stats=True)¶

ligand1_sol_sid_lighb(stats=True)¶

ligand2_sol_sid_lighb(stats=True)¶

ligand1_cpx_sid_lighb(stats=True)¶

ligand2_cpx_sid_lighb(stats=True)¶

ligand1_sol_sid_sasa(stats=True)¶

ligand2_sol_sid_sasa(stats=True)¶

ligand1_cpx_sid_sasa(stats=True)¶

ligand2_cpx_sid_sasa(stats=True)¶

ligand1_sol_sid_molsa(stats=True)¶

ligand2_sol_sid_molsa(stats=True)¶

ligand1_cpx_sid_molsa(stats=True)¶

ligand2_cpx_sid_molsa(stats=True)¶

ligand1_sol_sid_psa(stats=True)¶

ligand2_sol_sid_psa(stats=True)¶

ligand1_cpx_sid_psa(stats=True)¶

ligand2_cpx_sid_psa(stats=True)¶

ligand1_sol_sid_rgyr(stats=True)¶

ligand2_sol_sid_rgyr(stats=True)¶

ligand1_cpx_sid_rgyr(stats=True)¶

ligand2_cpx_sid_rgyr(stats=True)¶

ligand1_sol_sid_rmsd(stats=True)¶

ligand2_sol_sid_rmsd(stats=True)¶

ligand1_cpx_sid_rmsd(stats=True)¶

ligand2_cpx_sid_rmsd(stats=True)¶

get_ligand1_atom_dict()¶

get_ligand2_atom_dict()¶

sse_limits_lambda0¶

sse_limits_lambda1¶

receptor_sid_rmsd_ligand_lambda0¶: ligand1 RMSD wrt the protein

receptor_sid_rmsd_ligand_lambda1¶: ligand2 RMSD wrt the protein

static protein_residue()¶

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_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_b_factor¶: Return 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_sid_rmsd_backbone_lambda0¶

receptor_sid_rmsd_backbone_lambda1¶

receptor_sid_rmsf_backbone_lambda0¶

receptor_sid_rmsf_backbone_lambda1¶

cpx_sid_lp_results¶

pl_contact_data0¶: A dictionary containing PL interactions for lambda=0

pl_contact_data1¶: A dictionary containing PL interactions for lambda=1

get_protein_residues_sequence_tags()¶

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.

fullsystem_ct¶

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

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

cpx_sid_trajectory_interval_ns¶

sol_sid_trajectory_interval_ns¶

cpx_sid_snashot_times_ps¶

cpx_sid_snapshot_times_ps¶

sol_sid_snapshot_times_ps¶

cpx_sid_number_of_frames¶

sol_sid_number_of_frames¶

leg1_name¶

leg2_name¶

sol_timestep_list¶

cpx_timestep_list¶

sol_timestep_interval¶

cpx_timestep_interval¶

sol_delta_g_sliding_err¶

cpx_delta_g_sliding_err¶

sol_delta_g_sliding¶

cpx_delta_g_sliding¶

sol_delta_g_reverse_err¶

cpx_delta_g_reverse_err¶

sol_delta_g_reverse¶

cpx_delta_g_reverse¶

sol_delta_g_forward_err¶

cpx_delta_g_forward_err¶

sol_delta_g_forward_dg¶

cpx_delta_g_forward_dg¶

sol_delta_g_forward_bootstrap_std¶

cpx_delta_g_forward_bootstrap_std¶

sol_delta_g_forward_analytical_std¶

cpx_delta_g_forward_analytical_std¶

sol_delta_g_forward_df_per_replica¶

cpx_delta_g_forward_df_per_replica¶

sol_delta_g_forward¶

cpx_delta_g_forward¶

sol_end_time_ns¶

cpx_end_time_ns¶

sol_start_time_ns¶

cpx_start_time_ns¶

receptor_charge¶

receptor_total_heavy¶

receptor_total_atom¶

receptor_title¶

receptor_total_residues_in_chains¶

receptor_chain_names¶

receptor_total_residues¶

ligand1_total_rot_bonds¶

ligand2_total_rot_bonds¶

ligand1_total_fragments¶

ligand2_total_fragments¶

ligand1_mol_formula¶

ligand2_mol_formula¶

ligand1_charge¶

ligand2_charge¶

ligand1_alchemical_mols¶

ligand2_alchemical_mols¶

ligand1_alchemical_atom_total¶

ligand2_alchemical_atom_total¶

ligand1_atomic_mass¶

ligand2_atomic_mass¶

ligand1_rot_bonds¶

ligand2_rot_bonds¶

ligand1_total_hot¶

ligand2_total_hot¶

ligand1_total_heavy¶

ligand2_total_heavy¶

ligand1_total_atoms¶

ligand2_total_atoms¶

ligand1_cpx_asl¶

ligand2_cpx_asl¶

ligand1_sol_asl¶

ligand2_sol_asl¶

ligand1_pdb_name¶

ligand2_pdb_name¶

ligand1_smiles¶

ligand2_smiles¶

static ligand_name()¶

ligand1_name¶

ligand2_name¶

short_hash¶

ligand1_hash¶

ligand2_hash¶

jobname¶

delta_delta_g¶

sol_delta_g¶

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

cpx_delta_g¶

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

sol_total_replicas¶

cpx_total_replicas¶

sol_total_waters¶

cpx_total_waters¶

sol_total_atoms¶

cpx_total_atoms¶

sol_sim_time¶: Values returned in Ns (nanoseconds)

cpx_sim_time¶: Values returned in Ns (nanoseconds)

sol_temperature¶

cpx_temperature¶

sol_ff¶

cpx_ff¶

sol_ensemble¶

cpx_ensemble¶

sol_charge¶

cpx_charge¶

sol_salt_molecules¶

cpx_salt_molecules¶

sol_salt_info¶

cpx_salt_info¶

receptor_st¶: Returns receptor structure

ligand1_st¶: Returns ligand_1 structure

ligand2_st¶: Returns ligand_2 structure

sol_rest_exchanges¶

cpx_rest_exchanges¶

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.

wt_st¶: Returns full structure of a WT protein

mut_st¶: Returns full structure of a mutated protein

ligand1_st¶: Returns ligand_1 structure

ligand2_st¶: Returns ligand_2 structure

receptor_st¶: Returns receptor structure

wt_frag_st¶

mut_frag_st¶

solvent_fullsystem_ct¶

ligand_st_mol_formula¶

prm_name¶

receptor_sid_rmsf_backbone_lambda0¶

receptor_sid_rmsf_backbone_lambda1¶

ligand_torsions¶

Return type:	(`FEPTorsionsContainer` object, `FEPTorsionsContainer` object)
Returns:	`FEPTorsionsContainer` objects for lambda0 and lambda1.

static peptide_name()¶

wt_name¶

mut_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

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

get_protein_residues_sequence_tags()¶

cpx_sid_lp_results¶

atom_mapping¶

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.

wt_st¶: Returns full structure of a WT protein

mut_st¶: Returns full structure of a mutated protein

receptor_st¶: Returns receptor structure

ligand1_cpx_st¶

ligand2_cpx_st¶

ligand1_st¶: Returns ligand_1 structure

ligand2_st¶: Returns ligand_2 structure

solvent_fullsystem_ct¶

receptor_sid_rmsf_backbone_lambda0¶

receptor_sid_rmsf_backbone_lambda1¶

ligand_torsions¶

Return type:	(`FEPTorsionsContainer` object, `FEPTorsionsContainer` object)
Returns:	`FEPTorsionsContainer` objects for lambda0 and lambda1.

receptor_title¶

cpx_sid_lp_results¶

get_ligand1_atom_dict()¶

get_ligand2_atom_dict()¶

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`)

class schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData(complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='metalloprotein')¶

Bases: schrodinger.application.desmond.fep_edge_data.FEPEdgeData

This object stores Metalloprotein FEP related data.

fullsystem_ct¶

Return type:	`schrodinger.structure.Structure`
Returns:	The full system structure.

receptor_st¶

Return type:	`schrodinger.structure.Structure`
Returns:	The receptor structure.

ligand1_st¶

Return type:	`schrodinger.structure.Structure`
Returns:	The ligand1 structure.

ligand2_st¶

Return type:	`schrodinger.structure.Structure`
Returns:	The ligand2 structure.

ligand_torsions¶

Return type:	(`FEPTorsionsContainer` object, `FEPTorsionsContainer` object)
Returns:	`FEPTorsionsContainer` objects for lambda0 and lambda1.

receptor_sid_rmsf_backbone_lambda0¶

Return type:	List[float]
Returns:	The RMSF for each receptor residue in lambda0.

receptor_sid_rmsf_backbone_lambda1¶

Return type:	List[float]
Returns:	The RMSF for each receptor residue in lambda1.