schrodinger.application.lid.lid2d.compute

Module compute

Functions

get_atomic_sasa(st, iat, cutoff=7.0, scale_factor=2.32)
@return: An estimate of the atomic surface area for atom index iat in structure st.

compute_hbonds(all_hbonds, complex_st, lig_H_to_non, lig_atom_elements, pic_info, pic_center)

compute_residue_placements(all_residues, all_atoms_within_watermap, residues_hbonds, all_waters, all_metals, complex_st, rotM, ct_scale, parameters={}, rotation=None)

compute_complex_info(prot_st, ligand_st, watermap, parameters, within=4.0, molnumber=None, cofactors_st=None)

compute_molecules(residues_hbonds, pic_2d_center, generate_3d_img, best_ct3d_in_2dcoord_all, best_ct2d_all, lines, bond_to_ring, parameters, dim, all_residues, all_atoms_within_watermap, all_waters, all_metals, complex_st, rotM, ct_scale, final_image_dim, rotation=None, workspace_vm=None)

compute_ligand_atom_placements(ct2d, pic_info, pic_center, ct_atoms, rotation, sketcher_best_2D=False)

compute_pipi_stacking(all_pipi_stacking, all_ligand_atom_placements)

compute_picats(all_picats, all_ligand_atom_placements)

compute_font_sizes(image_dim)

compute_line_width(image_dim)

Variables

[hide private]

epsilons = 1e-05

DISTANCE_CUTOFF_DEFAULT = 7.0

SASA_PROBE_RADIUS = 1.4

HARD_SPHERE_S = 2.5

expected_num_atoms = {'HID': 5, 'HIE': 5, 'HIP': 5, 'HIS': 5, ...

backbone_pdb_names = set(['H', 'O'])

all_metal_atomic_numbers = {11: 'NA', 12: 'MG', 19: 'K', 20: '...

__package__ = 'schrodinger.application.lid.lid2d'

Function Details

[hide private]

get_atomic_sasa(st, iat, cutoff=7.0, scale_factor=2.32)


@return:
    An estimate of the atomic surface area for atom index iat in
    structure st.
@rtype:
    floats

@param st: 
    structure for the SASA calculation.
@type st:
    structure.Structure

@param iat:
    Atom index into st for which to calculate the atomic SASA.
@type iat:
    int

@param cutoff: 
@type cutoff:
    float 

@param scale_factor:
    Multiplier to the theoritical unoccluded atomic SASA.  Prevents
    the product of many near unity probabilities result in an A'
    surface area that is too small.  Default is 2.32
@type scale_factor:
    float

A_c = A_prime - B_prime, (A_c = 0 if A_prime < B_prime),
    where A_prime is the probability that an arbitrary point
    on the surface of atom A_c is solvent accessable (or more
    formally, outside the intersection of an adjoining sphere).
    B_prime accounts for the minimal occlusion by neighbors.

Variables Details

[hide private]

expected_num_atoms

Value:

{'HID': 5, 'HIE': 5, 'HIP': 5, 'HIS': 5, 'PHE': 6, 'TRP': 9, 'TYR': 6}

all_metal_atomic_numbers

Value:

{11: 'NA',
 12: 'MG',
 19: 'K',
 20: 'CA',
 25: 'MN',
 26: 'FE',
 27: 'CO',
 28: 'NI',
...