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__init__(self,
fep_edge_data,
basename=None,
perturbation_type=' small_molecule ' )
This class generates a PDF report for an FEP/REST (+) type of job. |
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_cleanup_temp_files(self) |
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_replica_exchange_density(self) |
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get_rest_density_plot(self,
rest_density_data,
legend=True) |
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get_rest_density_img(self,
rest_density_data,
legend=True) |
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_protein_ligand_report(self) |
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_get_lid_img(self,
stats,
lig_noh_dict,
lig_atom_dict,
ligand_st,
ligand_core_idx,
template_st=None,
template_core_idx=None,
cutoff=0.2) |
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_align_chmmol(self,
ligand_chmmol,
ligand_core_idx=None,
template_chmmol=None,
template_core_idx=None) |
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_get_aligned_chmmol(self,
ligand_st,
ligand_core_idx,
template_st=None,
template_core_idx=None) |
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_get_lid(self,
stats,
lig_noh_dict,
lig_atom_dict,
ligand_st,
ligand_core_idx,
template_st=None,
template_core_idx=None,
cutoff=0.2) |
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_get_plot_pl_bar_chart(self,
label,
data_dict0,
data_dict1,
nframes,
name_1=' Ligand 1 ' ,
name_2=' Ligand 2 ' ) |
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_create_pl_bar_fig(self,
label,
data_dict0,
data_dict1,
nframes,
pl_interactions=[ ' hb ' , ' hphb ' , ' ion ' , ' wb ' ] ,
name_1=' Ligand 1 ' ,
name_2=' Ligand 2 ' ,
fig=None,
for_print=False) |
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structure2d.structure_item
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get_2d_tors_annotated_lig_pair(self,
tors1,
tors2,
tors_from,
tors_to)
Returns structure scenes for two 2d ligands with annotations. |
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add_atom_highlight(self,
lig_item,
torsion,
color)
Add new highlight for atoms in the given torsion. |
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on_move(self,
event)
If the mouse is inside a torsion plot, highlight the 1st and 4th
atoms in that torsion in the structure. |
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create_torsions_plot(self,
fig,
tors1,
tors2,
tors_from,
tors_to,
ipage=None,
structure1_item=None,
structure2_item=None,
for_print=False)
Creates a plot for torsions using the given matplot figure. |
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get_torsions_plot(self,
tors1,
tors2,
tors_from,
tors_to,
for_print=False) |
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_get_torsion_plot_img(self,
fig,
nrows) |
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_get_annotated_2d_lig_img(self,
lig_2d_si) |
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_ligand_torsion_report(self)
Generates report which monitors Rotatable bonds |
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_get_ligand_torsion_text(self) |
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_ligand_report(self)
Generate ligand report |
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_ligand_rmsd_wrt_protein(self,
name1=' Ligand 1 ' ,
name2=' Ligand 2 ' ) |
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_get_ligand_wrt_prot_rmsd_text(self) |
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_get_ligand_wrt_prot_rmsd_plot(self,
rmsd_l0,
rmsd_l1,
ts,
ts_max,
name1,
name2) |
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_protein_report(self)
Generates the protein report (RSMD/RSMF for both end-point lambdas). |
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_get_protein_rmsf_text(self,
show_sse=False,
show_b=False,
lig_res=None)
Returns a string to be used in the PDF document |
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_add_sse_span(self,
ax,
data_limits,
color)
Setup overlay for SSE elements... |
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str
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_add_b_factor(self,
ax2,
b_data,
color,
y_range_ratio,
fsize=8)
Add B factor to the plot, on the Y2 axis. |
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_add_interacting_residues(self,
ax,
show_res,
vals,
color,
ymin=0)
Draw a vertical bar for reisdues that interact with the ligand |
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gen_protein_rmsf_image(self,
rmsf_l0,
rmsf_l1,
sse_l0,
sse_l1,
b_factor,
contact_data,
show_res_type=None) |
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image | matplotlib ax obj
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get_protein_rmsf(self,
for_print=True,
fig=None,
show_sse=False,
show_b_factor=False,
show_interacting_residues=( False, False, False) )
This function returns either an img or a matplotlib object of protein
RMSF plot |
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_b_factor_valid(self,
b_factor)
If b factor values are not available don't plot them |
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_gen_protein_rmsf_ax(self,
ax,
rmsf_l0,
rmsf_l1,
sse_l0,
sse_l1,
b_factor,
contact_data,
show_res_type=None,
fsize=8)
Given an matplotlib ax object, setup the plot... |
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_get_protein_rmsd_text(self) |
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_get_protein_lambda_rmsd_plot(self,
rmsd_l0,
rmsd_l1,
ts,
ts_max) |
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_get_pair_rmsd_plot(self,
val0,
val1,
ts,
ts_max,
names,
ylabel=' RMSD ($\\AA$) ' ,
y_inch=1.8,
for_print=False) |
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_create_pair_rmsd_fig(self,
val0,
val1,
ts,
ts_max,
names,
fig,
ylabel=' RMSD ($\\AA$) ' ,
for_print=False) |
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_get_sequence_viewer_image(self)
Generate protein sequence image, given a protein structure Returns a
platypus image |
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_free_energy_convergence_profiles(self) |
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_get_free_energy_convergence_text(self) |
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_gen_free_energy_convergence_table(self,
df_per_replica,
dg,
bootstrap_std,
analytical_std) |
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_gen_free_energy_convergence_plot(self,
start_time,
end_time,
dG_forward,
dG_forward_err,
dG_reverse,
dG_reverse_err,
dG_sliding,
dG_sliding_err) |
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_gen_free_energy_convergence_fig(self,
start_time,
end_time,
dG_forward,
dG_forward_err,
dG_reverse,
dG_reverse_err,
dG_sliding,
dG_sliding_err,
fig,
for_print=True) |
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_ligand_perturbation_details(self) |
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_generate_aligned_2d_lig_pair(self)
Generate *aligned* 2d images of the ligands. |
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get_2d_ligand_image(self,
lig_st) |
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_get_2d_ligand_image(self,
st) |
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_get_temp_image_fn(self,
prefix='
' ) |
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_report_fep_simulation_details(self) |
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str(self,
str_in)
This is to remove the "'s in ARK returned strings enclosed in
double quotes |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
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canvas2d.ChmMol
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_st_to_chmmol(ligand_st)
Convert ligand_st to Canvas 2d structure |
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_lid_add_lig_water_exposed(res_label,
sk,
ligand_st,
lig_noh_dict,
ligand_atoms) |
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_lid_add_water_br(res_label,
sk,
already_added_res_dict,
ligand_st,
lig_atom_dict,
lig_noh_dict,
ligand_atoms)
`res_label' for water-mediated interactions looks like this:... |
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_lid_add_hydrophobic(res_label,
sk,
already_added_res_dict)
`res_label` for non-specific hydrophobic interactions looks like this:... |
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_lid_add_picat(res_label,
sk,
already_added_res_dict,
lig_atom_dict,
ligand_atoms)
`res_label` for pi-cat interactions looks like this:... |
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_lid_add_pipi(res_label,
sk,
already_added_res_dict,
lig_atom_dict,
ligand_atoms)
`res_label` for pi-pi interactions looks like this:... |
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_lid_add_prot_metal(res_label,
sk,
already_added_metal_dict,
already_added_res_dict)
`res_label' for metal-protein mediated interactions looks like this:... |
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_lid_add_lig_metal(res_label,
sk,
already_added_metal_dict,
lig_atom_dict,
ligand_atoms)
`res_label' for metal-ligand mediated interactions looks like this:... |
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_lid_add_intramolecular_hb(res_label,
sk,
ligand_st,
lig_atom_dict,
lig_noh_dict,
ligand_atoms)
res_label for internal (intramolecular) hydrogen bonds looks like this:... |
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_lid_add_ionic(res_label,
sk,
already_added_res_dict,
lig_noh_dict,
ligand_atoms)
res_label for ionic bonds looks like this:... |
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_lid_add_hbonds(res_label,
sk,
already_added_res_dict,
ligand_st,
lig_atom_dict,
lig_noh_dict,
ligand_atoms)
res_label for hydrogen bonds looks like this:... |
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