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.
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__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.. |
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_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 |
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| _get_minimal_fragments_with_mutation(self) |
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| ligand1_fragments(self,
offset_by_receptor_natoms=True) |
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| ligand2_fragments(self,
offset_by_receptor_natoms=True) |
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_ligand_fragments(self,
ark_obj,
offset=0)
Return the dictionary of atom fragments for ligand. |
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| ligand1_sol_sid_rb_strain(self,
stats=True) |
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| ligand2_sol_sid_rb_strain(self,
stats=True) |
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| ligand1_cpx_sid_rb_strain(self,
stats=True) |
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| ligand2_cpx_sid_rb_strain(self,
stats=True) |
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| _get_ligand_strain(self,
ark_torsion) |
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| _get_rb_potential(self,
energy,
conformation) |
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| ligand1_cpx_sid_waters(self,
stats=True) |
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| ligand2_cpx_sid_waters(self,
stats=True) |
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| ligand1_sol_sid_lighb(self,
stats=True) |
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| ligand2_sol_sid_lighb(self,
stats=True) |
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| ligand1_cpx_sid_lighb(self,
stats=True) |
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| ligand2_cpx_sid_lighb(self,
stats=True) |
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| ligand1_sol_sid_sasa(self,
stats=True) |
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| ligand2_sol_sid_sasa(self,
stats=True) |
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| ligand1_cpx_sid_sasa(self,
stats=True) |
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| ligand2_cpx_sid_sasa(self,
stats=True) |
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| ligand1_sol_sid_molsa(self,
stats=True) |
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| ligand2_sol_sid_molsa(self,
stats=True) |
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| ligand1_cpx_sid_molsa(self,
stats=True) |
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| ligand2_cpx_sid_molsa(self,
stats=True) |
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| ligand1_sol_sid_psa(self,
stats=True) |
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| ligand2_sol_sid_psa(self,
stats=True) |
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| ligand1_cpx_sid_psa(self,
stats=True) |
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| ligand2_cpx_sid_psa(self,
stats=True) |
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| ligand1_sol_sid_rgyr(self,
stats=True) |
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| ligand2_sol_sid_rgyr(self,
stats=True) |
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| ligand1_cpx_sid_rgyr(self,
stats=True) |
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| ligand2_cpx_sid_rgyr(self,
stats=True) |
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| ligand1_sol_sid_rmsd(self,
stats=True) |
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| ligand2_sol_sid_rmsd(self,
stats=True) |
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| ligand1_cpx_sid_rmsd(self,
stats=True) |
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| ligand2_cpx_sid_rmsd(self,
stats=True) |
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numpy.array
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| _receptor_sid_sse_lambda0(self) |
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| _receptor_sid_sse_lambda1(self) |
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_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. |
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tuple
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_smooth_sse_limits(self,
tolerance,
limits)
here we're trying to to bring some tolerance to the cutoff. |
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(helix_limits, strand_limits)
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_sse_limits(self,
sse_data)
Get limits for helix and strands data |
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| _get_receptor_backbone_atoms(self) |
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_assemble_protein_b_factor(self)
Look up all backbone atoms and calculate b factors by groping them by
residues |
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| _protein_sid_rmsf_backbone(self,
backbone_rmsf) |
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| _get_ligand_water_stats(self,
ligwat_data,
lig_frags) |
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| _get_ionic_stats(self,
polar_data,
lig_dict,
polar_prot_dict,
pv_st) |
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| _get_picat_stats(self,
picat_data,
ligand_ring_dict,
polar_prot_dict,
pi_prot_dict,
lig_dict,
pv_st) |
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| _get_pipi_stats(self,
pipi_data,
lig_frags,
ligand_ring_dict,
pi_prot_dict,
pv_st) |
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_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. |
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_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. |
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| _get_water_bridge_stats(self,
wb_data,
lig_dict,
wb_prot_dict,
pv_st) |
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_get_lig_intra_hbond_stats(self,
hb_data,
lig_dict)
This function parses internal hydrogen bonds within a ligand and
returns the statistics. |
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_get_lp_hbond_stats(self,
hb_data,
lig_dict,
prot_dict,
pv_st,
lig_st)
Get the statistics on Hydrogen bonds during the simulation. |
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_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. |
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| _get_pli_residue_profile(self,
res_data) |
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| _parse_pl_contact_data(self,
inter_type,
data,
all_cont_data) |
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| _parse_pl_hydrophobic_data(self,
inter_type,
data,
all_data) |
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| _parse_pl_metal_data(self,
data,
all_data) |
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| _parse_pl_hbond_data(self,
data,
all_data) |
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| _parse_pl_polar_data(self,
data,
all_data) |
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| _parse_pl_waterbr_data(self,
data,
all_data) |
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| _parse_pl_general_data(self,
subtype_dict,
data,
all_data) |
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str
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_parse_residue_tags(self,
keys)
Given all protein-ligand contacts; just return the protein residue
tag that are in contact with the ligand. |
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| _set_cpx_sid_protein_residues(self,
interact_dict) |
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| _pl_contact_data(self,
ark_block) |
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| _parse_sid_rms(self,
sea_obj) |
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_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. |
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_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. |
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_parse_sea(self,
sea_obj)
Given an ark object, parse the data |
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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