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2017-1 Schrodinger Python API
Package schrodinger :: Package application :: Package desmond :: Module fep_edge_data :: Class PRMEdgeData
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Class PRMEdgeData

 object --+    
          |    
FEPEdgeData --+
              |
             PRMEdgeData

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

Instance Methods [hide private]
 
__init__(self, complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)
@type complex_sea: C{sea} @param complex_sea: SEA object with results pertaining to the complex leg of the FEP calculation @type solvent_sea: C{sea} @param solvent_sea: SEA object with results pertaining to the solvent leg of the FEP calculation @type pv_st: L{schrodinger.Structure} @param pv_st: PoseViewer file must contain 2 or 3 structures.
 
_calc_lig_props(self)

Inherited from FEPEdgeData: get_minimal_fragments_with_mutation, ligand1_cpx_sid_lighb, ligand1_cpx_sid_molsa, ligand1_cpx_sid_psa, ligand1_cpx_sid_rb_strain, ligand1_cpx_sid_rgyr, ligand1_cpx_sid_rmsd, ligand1_cpx_sid_sasa, ligand1_cpx_sid_waters, ligand1_fragments, ligand1_sol_sid_lighb, ligand1_sol_sid_molsa, ligand1_sol_sid_psa, ligand1_sol_sid_rb_strain, ligand1_sol_sid_rgyr, ligand1_sol_sid_rmsd, ligand1_sol_sid_sasa, ligand2_cpx_sid_lighb, ligand2_cpx_sid_molsa, ligand2_cpx_sid_psa, ligand2_cpx_sid_rb_strain, ligand2_cpx_sid_rgyr, ligand2_cpx_sid_rmsd, ligand2_cpx_sid_sasa, ligand2_cpx_sid_waters, ligand2_fragments, ligand2_sol_sid_lighb, ligand2_sol_sid_molsa, ligand2_sol_sid_psa, ligand2_sol_sid_rb_strain, ligand2_sol_sid_rgyr, ligand2_sol_sid_rmsd, ligand2_sol_sid_sasa

Inherited from FEPEdgeData (private): _assemble_protein_b_factor, _calculate_sse_limits, _cpx_sid_lp_stats, _cpx_sid_pl_contacts, _get_hydrophobic_stats, _get_ionic_stats, _get_lig_intra_hbond_stats, _get_ligand_strain, _get_ligand_water_stats, _get_lp_hbond_stats, _get_metal_stats, _get_minimal_fragments_with_mutation, _get_picat_stats, _get_pipi_stats, _get_pli_residue_profile, _get_rb_potential, _get_receptor_backbone_atoms, _get_water_bridge_stats, _init_protein_st, _ligand_fragments, _parse_cpx_sea, _parse_cpx_sid, _parse_pl_contact_data, _parse_pl_general_data, _parse_pl_hbond_data, _parse_pl_hydrophobic_data, _parse_pl_metal_data, _parse_pl_polar_data, _parse_pl_waterbr_data, _parse_residue_tags, _parse_sea, _parse_sid_rms, _parse_sol_sea, _parse_sol_sid, _pl_contact_data, _pl_interaction_similarity_matrix, _process_sse_data, _receptor_sid_sse_lambda0, _receptor_sid_sse_lambda1, _set_cpx_sid_protein_residues, _smooth_sse_limits, _sse_limits

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods [hide private]
 
_protein_sid_rmsf_backbone(backbone_atoms, backbone_rmsf, st)
 
peptide_name(st)

Inherited from FEPEdgeData: get_smiles, ligand_name, protein_residue

Inherited from FEPEdgeData (private): _cpx_sid_pli_dict, _delta_g, _filter_degen_res_atoms, _get_ligand_atom_dict, _get_unmatched_atoms, _get_values, _invert_dict, _invert_frag_dict, _lig_props, _manage_multiple_frags, _parse_sid, _rest_exchanges, _write_error

Class Variables [hide private]

Inherited from FEPEdgeData (private): _SSE_CUTOFF, _pl_code, _pl_contact_types, _pl_detail_inter_type, _pl_inter_names, _pl_type

Properties [hide private]
  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
  ligand1_sol_asl
  ligand2_sol_asl
  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
  wt_name
  mut_name
ResData wt_residue_sequence_list
Return a list of residue objects (ResData) in amino-to-carboxy order.
residue_tag wt_residue_sequence_tags
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)
ResData mut_residue_sequence_list
Return a list of residue objects (ResData) in amino-to-carboxy order.
residue_tag mut_residue_sequence_tags
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)

Inherited from FEPEdgeData: cpx_charge, cpx_charge_correction, cpx_delta_g, 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, cpx_sid_snapshot_times_ps, cpx_sid_snashot_times_ps, cpx_sid_trajectory_interval_ns, cpx_sim_time, 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, jobname, leg1_name, leg2_name, ligand1_atomic_mass, ligand1_charge, ligand1_cpx_asl, ligand1_hash, ligand1_mol_formula, ligand1_name, ligand1_pdb_name, ligand1_rot_bonds, ligand1_smiles, 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_hash, ligand2_mol_formula, ligand2_name, ligand2_pdb_name, ligand2_rot_bonds, ligand2_smiles, ligand2_total_atoms, ligand2_total_fragments, ligand2_total_heavy, ligand2_total_hot, ligand2_total_rot_bonds, pl_contact_data0, pl_contact_data1, pl_interaction_similarity_matrix0, pl_interaction_similarity_matrix1, receptor_b_factor, receptor_chain_names, receptor_charge, receptor_residue_sequence_list, receptor_residue_sequence_tags, receptor_residues_interaction_ligand1, receptor_residues_interaction_ligand2, receptor_sid_rmsd_backbone_lambda0, receptor_sid_rmsd_backbone_lambda1, receptor_sid_rmsd_ligand_lambda0, receptor_sid_rmsd_ligand_lambda1, 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, 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, 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

Inherited from FEPEdgeData (private): _cpx_sid_pli_lambda0_dict, _cpx_sid_pli_lambda1_dict, _receptor_sid_rmsf_backbone_lambda0, _receptor_sid_rmsf_backbone_lambda1

Inherited from object: __class__

Method Details [hide private]

__init__(self, complex_sea, solvent_sea, pv_st=None, atom_mapping=None, perturbation_type='small_molecule', frag_atom_mapping=None)
(Constructor)

  

@type   complex_sea: C{sea}
@param  complex_sea: SEA object with results pertaining to the complex
                     leg of the FEP calculation
@type   solvent_sea: C{sea}
@param  solvent_sea: SEA object with results pertaining to the solvent
                     leg of the FEP calculation
@type         pv_st: L{schrodinger.Structure}
@param        pv_st: PoseViewer file must contain 2 or 3 structures.
                     [receptor, lig1, lig2]; otherwise it's None
@type  atom_mapping: L{L{int}, L{int}}
@param atom_mapping: mapping of ligand2 to ligand1 atoms
@type  frag_atom_mapping: L{L{int}, L{int}}
@param frag_atom_mapping: mapping of frag1 and frag2 atoms
Overrides: object.__init__

_protein_sid_rmsf_backbone(backbone_atoms, backbone_rmsf, st)
Static Method

 
Overrides: FEPEdgeData._protein_sid_rmsf_backbone

Property Details [hide private]

wt_st

Returns full structure of a WT protein

Get Method:
unreachable.wt_st(self) - Returns full structure of a WT protein

mut_st

Returns full structure of a mutated protein

Get Method:
unreachable.mut_st(self) - Returns full structure of a mutated protein

ligand1_st

Returns ligand_1 structure

Get Method:
unreachable.ligand1_st(self)

ligand2_st

Returns ligand_2 structure

Get Method:
unreachable.ligand2_st(self)

receptor_st

Returns receptor structure

Get Method:
unreachable.receptor_st(self)

ligand1_sol_asl

Get Method:
unreachable.ligand1_sol_asl(self)

ligand2_sol_asl

Get Method:
unreachable.ligand2_sol_asl(self)

wt_frag_st

Get Method:
unreachable.wt_frag_st(self)

mut_frag_st

Get Method:
unreachable.mut_frag_st(self)

solvent_fullsystem_ct

Get Method:
unreachable.solvent_fullsystem_ct(self)

ligand_st_mol_formula

Get Method:
unreachable.ligand_st_mol_formula(self)

prm_name

Get Method:
unreachable.prm_name(self)

receptor_sid_rmsf_backbone_lambda0

Get Method:
unreachable.receptor_sid_rmsf_backbone_lambda0(self)

receptor_sid_rmsf_backbone_lambda1

Get Method:
unreachable.receptor_sid_rmsf_backbone_lambda1(self)

ligand_torsions

Get Method:
unreachable.ligand_torsions(self)

wt_name

Get Method:
unreachable.wt_name(self)

mut_name

Get Method:
unreachable.mut_name(self)

wt_residue_sequence_list

Return a list of residue objects (ResData) in amino-to-carboxy order.

Get Method:
unreachable.wt_residue_sequence_list(self) - Return a list of residue objects (ResData) in amino-to-carboxy order.
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)

Get Method:
unreachable.wt_residue_sequence_tags(self) - A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)
Type:
residue_tag

mut_residue_sequence_list

Return a list of residue objects (ResData) in amino-to-carboxy order.

Get Method:
unreachable.mut_residue_sequence_list(self) - Return a list of residue objects (ResData) in amino-to-carboxy order.
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)

Get Method:
unreachable.mut_residue_sequence_tags(self) - A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)
Type:
residue_tag

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2017-1 Schrodinger Python API
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