Package schrodinger :: Package application :: Package desmond :: Module fep_edge_data :: Class FEPEdgeData

Class FEPEdgeData

object --+
         |
        FEPEdgeData

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

Instance Methods

[hide private]

__init__(self, complex_sea, solvent_sea, pv_st=None, 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 3 structures..

_init_protein_st(self, prot_st)
This method cleans up the pv file by: 1) removes non-ZOB waters 2) adds property of original indices

get_minimal_fragments_with_mutation(self)
Generates two structures of minimal fragments that contain the mutation.

_get_minimal_fragments_with_mutation(self)

ligand1_fragments(self, offset_by_receptor_natoms=True)

ligand2_fragments(self, offset_by_receptor_natoms=True)

_ligand_fragments(self, ark_obj, offset=0)
Return the dictionary of atom fragments for ligand.

_parse_sol_sid(self)

ligand1_sol_sid_rb_strain(self, stats=True)

ligand2_sol_sid_rb_strain(self, stats=True)

ligand1_cpx_sid_rb_strain(self, stats=True)

ligand2_cpx_sid_rb_strain(self, stats=True)

_get_ligand_strain(self, ark_torsion)

_get_rb_potential(self, energy, conformation)

ligand1_cpx_sid_waters(self, stats=True)

ligand2_cpx_sid_waters(self, stats=True)

ligand1_sol_sid_lighb(self, stats=True)

ligand2_sol_sid_lighb(self, stats=True)

ligand1_cpx_sid_lighb(self, stats=True)

ligand2_cpx_sid_lighb(self, stats=True)

ligand1_sol_sid_sasa(self, stats=True)

ligand2_sol_sid_sasa(self, stats=True)

ligand1_cpx_sid_sasa(self, stats=True)

ligand2_cpx_sid_sasa(self, stats=True)

ligand1_sol_sid_molsa(self, stats=True)

ligand2_sol_sid_molsa(self, stats=True)

ligand1_cpx_sid_molsa(self, stats=True)

ligand2_cpx_sid_molsa(self, stats=True)

ligand1_sol_sid_psa(self, stats=True)

ligand2_sol_sid_psa(self, stats=True)

ligand1_cpx_sid_psa(self, stats=True)

ligand2_cpx_sid_psa(self, stats=True)

ligand1_sol_sid_rgyr(self, stats=True)

ligand2_sol_sid_rgyr(self, stats=True)

ligand1_cpx_sid_rgyr(self, stats=True)

ligand2_cpx_sid_rgyr(self, stats=True)

ligand1_sol_sid_rmsd(self, stats=True)

ligand2_sol_sid_rmsd(self, stats=True)

ligand1_cpx_sid_rmsd(self, stats=True)

ligand2_cpx_sid_rmsd(self, stats=True)

numpy.array

_process_sse_data(self, data)
Process Secondary Structure elements.

_receptor_sid_sse_lambda0(self)

_receptor_sid_sse_lambda1(self)

_calculate_sse_limits(self, sse_by_res, tol=0)
This function takes a vector of residues that are in secondary structure elements (SSE), and returns their limits in the list.

tuple

_smooth_sse_limits(self, tolerance, limits)
here we're trying to to bring some tolerance to the cutoff.

(helix_limits, strand_limits)

_sse_limits(self, sse_data)
Get limits for helix and strands data

sse_limits_lambda0(self)

sse_limits_lambda1(self)

receptor_sid_rmsd_ligand_lambda0(self)
ligand1 RMSD wrt the protein

receptor_sid_rmsd_ligand_lambda1(self)
ligand2 RMSD wrt the protein

_get_receptor_backbone_atoms(self)

ResData

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

residue_tag

receptor_residue_sequence_tags(self)
A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)

_assemble_protein_b_factor(self)
Look up all backbone atoms and calculate b factors by groping them by residues

list of B-factors by residues

receptor_b_factor(self)
Returen B factor that is read from the initial structure.

receptor_sid_rmsd_backbone_lambda0(self)

receptor_sid_rmsd_backbone_lambda1(self)

receptor_sid_rmsf_backbone_lambda0(self)

receptor_sid_rmsf_backbone_lambda1(self)

_protein_sid_rmsf_backbone(self, backbone_rmsf)

_receptor_sid_rmsf_backbone_lambda0(self)

_receptor_sid_rmsf_backbone_lambda1(self)

_parse_cpx_sid(self)

cpx_sid_lp_results(self)

_cpx_sid_lp_stats(self)

_get_ligand_water_stats(self, ligwat_data, lig_frags)

_get_ionic_stats(self, polar_data, lig_dict, polar_prot_dict, pv_st)

_get_picat_stats(self, picat_data, ligand_ring_dict, polar_prot_dict, pi_prot_dict, lig_dict, pv_st)

_get_pipi_stats(self, pipi_data, lig_frags, ligand_ring_dict, pi_prot_dict, pv_st)

_get_hydrophobic_stats(self, hphob_data, hphob_prot_dict, lig_frags, pv_st)
This function parses non-specific hydrophobic interaction and returns a list with statistics.

_get_metal_stats(self, metal_data, lig_dict, polar_prot_dict, pv_st)
This function parses protein-metal and metal-ligand interactions and returns two lists, with statistics for each type.

_get_water_bridge_stats(self, wb_data, lig_dict, wb_prot_dict, pv_st)

_get_lig_intra_hbond_stats(self, hb_data, lig_dict)
This function parses internal hydrogen bonds within a ligand and returns the statistics.

_get_lp_hbond_stats(self, hb_data, lig_dict, prot_dict, pv_st, lig_st)
Get the statistics on Hydrogen bonds during the simulation.

_fullsystem_ct(self)

cpx_sid_pl_results(self)

_cpx_sid_pl_contacts(self)
This method calculates protein-residue contacts for both lambda0 and lambda1 simulations, collates the residue information and then sets self._cpx_sid_pl_results with the results dictionaries.

_get_pli_residue_profile(self, res_data)

_parse_pl_contact_data(self, inter_type, data, all_cont_data)

__get_resname(self, tag)

_parse_pl_hydrophobic_data(self, inter_type, data, all_data)

_parse_pl_metal_data(self, data, all_data)

_parse_pl_hbond_data(self, data, all_data)

_parse_pl_polar_data(self, data, all_data)

_parse_pl_waterbr_data(self, data, all_data)

_parse_pl_general_data(self, subtype_dict, data, all_data)

str

_parse_residue_tags(self, keys)
Given all protein-ligand contacts; just return the protein residue tag that are in contact with the ligand.

str

cpx_sid_protein_residues(self)
A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation

_set_cpx_sid_protein_residues(self, interact_dict)

list

receptor_residues_interaction_ligand1(self)
A list of preotein residues that interact just with ligand1

list

receptor_residues_interaction_ligand2(self)
A list of preotein residues that interact just with ligand2

_pl_contact_data(self, ark_block)

_cpx_sid_pli_lambda0_dict(self)

_cpx_sid_pli_lambda1_dict(self)

cpx_sid_trajectory_interval_ns(self)

sol_sid_trajectory_interval_ns(self)

cpx_sid_snashot_times_ps(self)

cpx_sid_snapshot_times_ps(self)

sol_sid_snapshot_times_ps(self)

cpx_sid_number_of_frames(self)

sol_sid_number_of_frames(self)

_parse_sid_rms(self, sea_obj)

sol_timestep_list(self)

cpx_timestep_list(self)

sol_timestep_interval(self)

cpx_timestep_interval(self)

sol_delta_g_sliding_err(self)

cpx_delta_g_sliding_err(self)

sol_delta_g_sliding(self)

cpx_delta_g_sliding(self)

sol_delta_g_reverse_err(self)

cpx_delta_g_reverse_err(self)

sol_delta_g_reverse(self)

cpx_delta_g_reverse(self)

sol_delta_g_forward_err(self)

cpx_delta_g_forward_err(self)

sol_delta_g_forward_dg(self)

cpx_delta_g_forward_dg(self)

sol_delta_g_forward_bootstrap_std(self)

cpx_delta_g_forward_bootstrap_std(self)

sol_delta_g_forward_analytical_std(self)

cpx_delta_g_forward_analytical_std(self)

sol_delta_g_forward_df_per_replica(self)

cpx_delta_g_forward_df_per_replica(self)

sol_delta_g_forward(self)

cpx_delta_g_forward(self)

sol_end_time_ns(self)

cpx_end_time_ns(self)

sol_start_time_ns(self)

cpx_start_time_ns(self)

receptor_charge(self)

receptor_total_heavy(self)

receptor_total_atom(self)

receptor_title(self)

receptor_total_residues_in_chains(self)

receptor_chain_names(self)

receptor_total_residues(self)

ligand1_total_rot_bonds(self)

ligand2_total_rot_bonds(self)

ligand1_total_fragments(self)

ligand2_total_fragments(self)

ligand1_mol_formula(self)

ligand2_mol_formula(self)

ligand1_charge(self)

ligand2_charge(self)

ligand1_atomic_mass(self)

ligand2_atomic_mass(self)

ligand1_rot_bonds(self)

ligand2_rot_bonds(self)

ligand1_total_hot(self)

ligand2_total_hot(self)

ligand1_total_heavy(self)

ligand2_total_heavy(self)

ligand1_total_atoms(self)

ligand2_total_atoms(self)

ligand1_cpx_asl(self)

ligand2_cpx_asl(self)

ligand1_pdb_name(self)

ligand2_pdb_name(self)

ligand1_smiles(self)

ligand2_smiles(self)

ligand1_name(self)

ligand2_name(self)

short_hash(self)

ligand1_hash(self)

ligand2_hash(self)

jobname(self)

delta_delta_g(self)

float, flost

sol_delta_g(self)
Returns: dG and its standard deviation

float, float

cpx_delta_g(self)
Returns: dG and its standard deviation

sol_total_replicas(self)

cpx_total_replicas(self)

sol_total_waters(self)

cpx_total_waters(self)

sol_total_atoms(self)

cpx_total_atoms(self)

sol_sim_time(self)
Values returned in Ns (nanoseconds)

cpx_sim_time(self)
Values returned in Ns (nanoseconds)

sol_temperature(self)

cpx_temperature(self)

sol_ff(self)

cpx_ff(self)

sol_ensemble(self)

cpx_ensemble(self)

sol_charge(self)

cpx_charge(self)

receptor_st(self)
Returns receptor structure

ligand1_st(self)
Returns ligand_1 structure

ligand2_st(self)
Returns ligand_2 structure

sol_rest_exchanges(self)

cpx_rest_exchanges(self)

_parse_cpx_sea(self, cpx_sea)
Since the ARK-formatted sid file contains a lot of data, in a list format, we need to parse it.

_parse_sol_sea(self, sol_sea)
Since the ARK-formatted sid file contains a lot of data, in a list format, we need to parse it.

_parse_sea(self, sea_obj)
Given an ark object, parse the data

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

Static Methods

[hide private]

_invert_frag_dict(in_dict)

_invert_dict(in_dict)

_get_unmatched_atoms(st, atom_mapping)

list, dict

_manage_multiple_frags(st, frags_dict, unmatched_frag_list)
This method checks if fragments are connected, and merges the fragments.

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

_lig_props(vals, idx_start=0, stats=True)

protein_residue(res)
Get data about the specified residue

_filter_degen_res_atoms(hbonds)
This function takes a list of hydrogen bonds and looks at the Protein Residue tag (ie: 'A:LYS_33:1HZ'), and determines if there are atoms there are equivalent hydrogen bond donors/acceptors in that residue.

_get_ligand_atom_dict(ligst)

_cpx_sid_pli_dict(ark_block)

_parse_sid(obj_sea)

_get_values(ark_obj, key1, key2)

_delta_g(ark_pair_energetics)

_write_error(msg)

_rest_exchanges(ark_obj)

Class Variables

[hide private]

_SSE_CUTOFF = 0.7

_pl_inter_names = ['H-bonds', 'Hydrophobic', 'Ionic', 'Water b...

_pl_type = {'hb': [0, 1, 9, 10], 'hphb': [2, 3, 4], 'ion': [5,...

_pl_code = {'hb': 0, 'hphb': 1, 'ion': 2, 'wb': 3}

_pl_detail_inter_type = {0: [0, '#762A83', 'Backbone donor'], ...

_pl_contact_types = ['hbonds', 'hydrophobic', 'pi_pi', 'pi_cat...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, complex_sea, solvent_sea, pv_st=None, 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 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

Overrides: object.__init__

_manage_multiple_frags(st, frags_dict, unmatched_frag_list)
Static Method

This method checks if fragments are connected, and merges the fragments.

Returns: list, dict: new fragment list as well as new fragment dictionary.

get_minimal_fragments_with_mutation(self)

Generates two structures of minimal fragments that contain the mutation. This is so we can annotate the mutations and make them searchable.

Returns:: returns tso structures of fragments that contain the mutation. @rtype : (schrodinger.structure, schrodinger.structure)

_ligand_fragments(self, ark_obj, offset=0)

Return the dictionary of atom fragments for ligand. The atom numbers are in the context of a protein-ligand complex, so we need to offset the atom values by the atom number in the protein/receptor.

_process_sse_data(self, data)

Process Secondary Structure elements. The input data is a list (for each frame). This list needs to be parsed (by removing '.') and casting it as array

Parameters:

data (a list containing raw SSE information from sid/eaf files) - list

Returns: numpy.array

processed SSE data in numpy array

_calculate_sse_limits(self, sse_by_res, tol=0)


This function takes a vector of residues that are in secondary
structure elements (SSE), and returns their limits in the list.
input is the following:
       sse_by_res:  [FFFTTTTTTTTFTTTTTTFFFFFFTTTTTTTFFFF]
    residue index:   1        10        20        30
    tol=0, output:  [(4,10), (12,17), (24,30)]
    tol=1, output:  [(4,17), (24,30)]
@type  sse_by_res: a list of bools if the residue is a SSE
@param sse_by_res: L{bool}
@type  tol: int
@param tol: tolerance level to smoothing out the SSE data. Default is
            zero, so no tolerance.  If tol>0 is used; then if a residue
            is inbetween two SSE residues, then those residues will be
            reported as being part of the SSE.
@rtype:  L{tuple}
@return: a list of tuples where the SSE starts and begins in terms of
         residue indices (ie: 51-63, means that a sse spans from residue
         index 51 to 63).

_smooth_sse_limits(self, tolerance, limits)

here we're trying to to bring some tolerance to the cutoff. if the number of residues <= tolerance then we merge the limits of adjacent spans. This is done so that the plots look cleaner.

Parameters:

tolerance (int) - tolerance for somoothing out the SSE limits
limits (tuple) - raw limits, without smoothing ie: [(61,70), (82-94)]

Returns: tuple

list of processed tuples

_sse_limits(self, sse_data)

Get limits for helix and strands data

Returns: (helix_limits, strand_limits): return helix and srand residue limits

sse_limits_lambda0(self)

Decorators:

@property

sse_limits_lambda1(self)

Decorators:

@property

receptor_sid_rmsd_ligand_lambda0(self)

ligand1 RMSD wrt the protein

Decorators:

@property

receptor_sid_rmsd_ligand_lambda1(self)

ligand2 RMSD wrt the protein

Decorators:

@property

protein_residue(res)
Static Method


Get data about the specified residue

@param res: The residue object to get data from
@type res: L{schrodinger.structure._Residue}

@return: A namedtuple containing the molecule number, chain,
         residue name,
and residue number
@rtype: L{ResData}

receptor_residue_sequence_list(self)

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

Returns: ResData

a list of residue objects, ordered N->C (amino to carboxy tails).

Decorators:

@property

receptor_residue_sequence_tags(self)

A residue tag looks like this: A:THR_124 (Chain:resname_resnum) if chain is not defined, use '_' (underscore)

Returns: residue_tag

a list of residue tags

Decorators:

@property

receptor_b_factor(self)

Returen B factor that is read from the initial structure. If the B factor is not defined return None

Returns: list of B-factors by residues

float

Decorators:

@property

receptor_sid_rmsd_backbone_lambda0(self)

Decorators:

@property

receptor_sid_rmsd_backbone_lambda1(self)

Decorators:

@property

receptor_sid_rmsf_backbone_lambda0(self)

Decorators:

@property

receptor_sid_rmsf_backbone_lambda1(self)

Decorators:

@property

_receptor_sid_rmsf_backbone_lambda0(self)

Decorators:

@property

_receptor_sid_rmsf_backbone_lambda1(self)

Decorators:

@property

cpx_sid_lp_results(self)

Decorators:

@property

_get_lp_hbond_stats(self, hb_data, lig_dict, prot_dict, pv_st, lig_st)

Get the statistics on Hydrogen bonds during the simulation. The function also filters out equivalent atoms on the protein & ligand and sums their contribution to yield one value.

_filter_degen_res_atoms(hbonds)
Static Method

This function takes a list of hydrogen bonds and looks at the Protein Residue tag (ie: 'A:LYS_33:1HZ'), and determines if there are atoms there are equivalent hydrogen bond donors/acceptors in that residue. If so, then the atomname is replaced by a more a more generic name. We need this for LID, in the scenarios when equivalent residue donors/acceptors interact with the same ligand atom. Multiple equivalent interactions are created in LID.

_fullsystem_ct(self)

Decorators:

@property

cpx_sid_pl_results(self)

Decorators:

@property

_parse_residue_tags(self, keys)

Given all protein-ligand contacts; just return the protein residue tag that are in contact with the ligand.

Returns: str: tags all residues in contact with the ligand

cpx_sid_protein_residues(self)

A list of protein residues that interact with both ligand1 and ligand2 throughout the simulation

Returns: str

a list of protein tags that interact with both ligand1 and ligand2

Decorators:

@property

receptor_residues_interaction_ligand1(self)

A list of preotein residues that interact just with ligand1

Returns: list

list of protein residue tags

Decorators:

@property

receptor_residues_interaction_ligand2(self)

A list of preotein residues that interact just with ligand2

Returns: list

list of protein residue tags

Decorators:

@property

_cpx_sid_pli_lambda0_dict(self)

Decorators:

@property

_cpx_sid_pli_lambda1_dict(self)

Decorators:

@property

cpx_sid_trajectory_interval_ns(self)

Decorators:

@property

sol_sid_trajectory_interval_ns(self)

Decorators:

@property

cpx_sid_snashot_times_ps(self)

Decorators:

@property

cpx_sid_snapshot_times_ps(self)

Decorators:

@property

sol_sid_snapshot_times_ps(self)

Decorators:

@property

cpx_sid_number_of_frames(self)

Decorators:

@property

sol_sid_number_of_frames(self)

Decorators:

@property

sol_timestep_list(self)

Decorators:

@property

cpx_timestep_list(self)

Decorators:

@property

sol_timestep_interval(self)

Decorators:

@property

cpx_timestep_interval(self)

Decorators:

@property

sol_delta_g_sliding_err(self)

Decorators:

@property

cpx_delta_g_sliding_err(self)

Decorators:

@property

sol_delta_g_sliding(self)

Decorators:

@property

cpx_delta_g_sliding(self)

Decorators:

@property

sol_delta_g_reverse_err(self)

Decorators:

@property

cpx_delta_g_reverse_err(self)

Decorators:

@property

sol_delta_g_reverse(self)

Decorators:

@property

cpx_delta_g_reverse(self)

Decorators:

@property

sol_delta_g_forward_err(self)

Decorators:

@property

cpx_delta_g_forward_err(self)

Decorators:

@property

sol_delta_g_forward_dg(self)

Decorators:

@property

cpx_delta_g_forward_dg(self)

Decorators:

@property

sol_delta_g_forward_bootstrap_std(self)

Decorators:

@property

cpx_delta_g_forward_bootstrap_std(self)

Decorators:

@property

sol_delta_g_forward_analytical_std(self)

Decorators:

@property

cpx_delta_g_forward_analytical_std(self)

Decorators:

@property

sol_delta_g_forward_df_per_replica(self)

Decorators:

@property

cpx_delta_g_forward_df_per_replica(self)

Decorators:

@property

sol_delta_g_forward(self)

Decorators:

@property

cpx_delta_g_forward(self)

Decorators:

@property

sol_end_time_ns(self)

Decorators:

@property

cpx_end_time_ns(self)

Decorators:

@property

sol_start_time_ns(self)

Decorators:

@property

cpx_start_time_ns(self)

Decorators:

@property

receptor_charge(self)

Decorators:

@property

receptor_total_heavy(self)

Decorators:

@property

receptor_total_atom(self)

Decorators:

@property

receptor_title(self)

Decorators:

@property

receptor_total_residues_in_chains(self)

Decorators:

@property

receptor_chain_names(self)

Decorators:

@property

receptor_total_residues(self)

Decorators:

@property

ligand1_total_rot_bonds(self)

Decorators:

@property

ligand2_total_rot_bonds(self)

Decorators:

@property

ligand1_total_fragments(self)

Decorators:

@property

ligand2_total_fragments(self)

Decorators:

@property

ligand1_mol_formula(self)

Decorators:

@property

ligand2_mol_formula(self)

Decorators:

@property

ligand1_charge(self)

Decorators:

@property

ligand2_charge(self)

Decorators:

@property

ligand1_atomic_mass(self)

Decorators:

@property

ligand2_atomic_mass(self)

Decorators:

@property

ligand1_rot_bonds(self)

Decorators:

@property

ligand2_rot_bonds(self)

Decorators:

@property

ligand1_total_hot(self)

Decorators:

@property

ligand2_total_hot(self)

Decorators:

@property

ligand1_total_heavy(self)

Decorators:

@property

ligand2_total_heavy(self)

Decorators:

@property

ligand1_total_atoms(self)

Decorators:

@property

ligand2_total_atoms(self)

Decorators:

@property

ligand1_cpx_asl(self)

Decorators:

@property

ligand2_cpx_asl(self)

Decorators:

@property

ligand1_pdb_name(self)

Decorators:

@property

ligand2_pdb_name(self)

Decorators:

@property

ligand1_smiles(self)

Decorators:

@property

ligand2_smiles(self)

Decorators:

@property

ligand1_name(self)

Decorators:

@property

ligand2_name(self)

Decorators:

@property

short_hash(self)

Decorators:

@property

ligand1_hash(self)

Decorators:

@property

ligand2_hash(self)

Decorators:

@property

jobname(self)

Decorators:

@property

delta_delta_g(self)

Decorators:

@property

sol_delta_g(self)

Returns: float, flost

dG and its standard deviation

Decorators:

@property

cpx_delta_g(self)

Returns: float, float

dG and its standard deviation

Decorators:

@property

sol_total_replicas(self)

Decorators:

@property

cpx_total_replicas(self)

Decorators:

@property

sol_total_waters(self)

Decorators:

@property

cpx_total_waters(self)

Decorators:

@property

sol_total_atoms(self)

Decorators:

@property

cpx_total_atoms(self)

Decorators:

@property

sol_sim_time(self)

Values returned in Ns (nanoseconds)

Decorators:

@property

cpx_sim_time(self)

Values returned in Ns (nanoseconds)

Decorators:

@property

sol_temperature(self)

Decorators:

@property

cpx_temperature(self)

Decorators:

@property

sol_ff(self)

Decorators:

@property

cpx_ff(self)

Decorators:

@property

sol_ensemble(self)

Decorators:

@property

cpx_ensemble(self)

Decorators:

@property

sol_charge(self)

Decorators:

@property

cpx_charge(self)

Decorators:

@property

receptor_st(self)

Returns receptor structure

Decorators:

@property

ligand1_st(self)

Returns ligand_1 structure

Decorators:

@property

ligand2_st(self)

Returns ligand_2 structure

Decorators:

@property

sol_rest_exchanges(self)

Decorators:

@property

cpx_rest_exchanges(self)

Decorators:

@property

Class Variable Details

[hide private]

_pl_inter_names

Value:

['H-bonds', 'Hydrophobic', 'Ionic', 'Water bridges']

_pl_type

Value:

{'hb': [0, 1, 9, 10], 'hphb': [2, 3, 4], 'ion': [5, 6, 11, 12], 'wb': 
[7, 8]}

_pl_detail_inter_type

Value:

{0: [0, '#762A83', 'Backbone donor'], 1: [0, '#AF8DC3', 'Backbone acce
ptor'], 9: [0, '#D9F0D3', 'Side-chain donor'], 10: [0, '#7FBF7B', 'Sid
e-chain acceptor'], 2: [1, '#FB9A99', 'Other'], 3: [1, '#33A02C', 'Pi-
Pi stacking'], 4: [1, '#B2DF8A', 'Pi-cation'], 5: [2, '#2C7BB6', 'Side
 chains'], 6: [2, '#A6BDDB', 'Backbone'], 11: [2, '#99D8C9', 'Side cha
in metal-mediated'], 12: [2, '#E5F5F9', 'Backbone metal-mediated'], 7:
 [3, '#D01C8B', 'Donor'], 8: [3, '#4DAC26', 'Acceptor']}

_pl_contact_types

Value:

['hbonds', 'hydrophobic', 'pi_pi', 'pi_cat', 'polar', 'water_br', 'met
al']

Class FEPEdgeData

__init__(self, complex_sea, solvent_sea, pv_st=None, atom_mapping=None) (Constructor)

_manage_multiple_frags(st, frags_dict, unmatched_frag_list) Static Method

get_minimal_fragments_with_mutation(self)

_ligand_fragments(self, ark_obj, offset=0)

_process_sse_data(self, data)

_calculate_sse_limits(self, sse_by_res, tol=0)

_smooth_sse_limits(self, tolerance, limits)

_sse_limits(self, sse_data)

sse_limits_lambda0(self)

sse_limits_lambda1(self)

receptor_sid_rmsd_ligand_lambda0(self)

receptor_sid_rmsd_ligand_lambda1(self)

protein_residue(res) Static Method

receptor_residue_sequence_list(self)

receptor_residue_sequence_tags(self)

receptor_b_factor(self)

receptor_sid_rmsd_backbone_lambda0(self)

receptor_sid_rmsd_backbone_lambda1(self)

receptor_sid_rmsf_backbone_lambda0(self)

receptor_sid_rmsf_backbone_lambda1(self)

_receptor_sid_rmsf_backbone_lambda0(self)

_receptor_sid_rmsf_backbone_lambda1(self)

cpx_sid_lp_results(self)

_get_lp_hbond_stats(self, hb_data, lig_dict, prot_dict, pv_st, lig_st)

_filter_degen_res_atoms(hbonds) Static Method

_fullsystem_ct(self)

cpx_sid_pl_results(self)

_parse_residue_tags(self, keys)

cpx_sid_protein_residues(self)

receptor_residues_interaction_ligand1(self)

receptor_residues_interaction_ligand2(self)

_cpx_sid_pli_lambda0_dict(self)

_cpx_sid_pli_lambda1_dict(self)

cpx_sid_trajectory_interval_ns(self)

sol_sid_trajectory_interval_ns(self)

cpx_sid_snashot_times_ps(self)

cpx_sid_snapshot_times_ps(self)

sol_sid_snapshot_times_ps(self)

cpx_sid_number_of_frames(self)

sol_sid_number_of_frames(self)

sol_timestep_list(self)

cpx_timestep_list(self)

sol_timestep_interval(self)

cpx_timestep_interval(self)

sol_delta_g_sliding_err(self)

cpx_delta_g_sliding_err(self)

sol_delta_g_sliding(self)

cpx_delta_g_sliding(self)

sol_delta_g_reverse_err(self)

cpx_delta_g_reverse_err(self)

sol_delta_g_reverse(self)

cpx_delta_g_reverse(self)

sol_delta_g_forward_err(self)

cpx_delta_g_forward_err(self)

sol_delta_g_forward_dg(self)

cpx_delta_g_forward_dg(self)

sol_delta_g_forward_bootstrap_std(self)

cpx_delta_g_forward_bootstrap_std(self)

sol_delta_g_forward_analytical_std(self)

cpx_delta_g_forward_analytical_std(self)

sol_delta_g_forward_df_per_replica(self)

cpx_delta_g_forward_df_per_replica(self)

sol_delta_g_forward(self)

cpx_delta_g_forward(self)

sol_end_time_ns(self)

cpx_end_time_ns(self)

sol_start_time_ns(self)

cpx_start_time_ns(self)

receptor_charge(self)

receptor_total_heavy(self)

receptor_total_atom(self)

receptor_title(self)

receptor_total_residues_in_chains(self)

receptor_chain_names(self)

receptor_total_residues(self)

ligand1_total_rot_bonds(self)

ligand2_total_rot_bonds(self)

ligand1_total_fragments(self)

ligand2_total_fragments(self)

init(self, complex_sea, solvent_sea, pv_st=None, atom_mapping=None)
(Constructor)

_manage_multiple_frags(st, frags_dict, unmatched_frag_list)
Static Method

protein_residue(res)
Static Method

_filter_degen_res_atoms(hbonds)
Static Method