mordred.surface_area

surface area subpackage.

$ python -m mordred.surface_area -h
usage: python -m mordred.surface_area [-h] [-s R] [-l L] FILE

positional arguments:
  FILE                  input sdf/mol file

optional arguments:
  -h, --help            show this help message and exit
  -s R, --solvent-radius R
                        solvent radius (default: 1.4)
  -l L, --mesh-level L  mesh level (default: 5)
class mordred.surface_area.SurfaceArea(radiuses, xyzs, level=4)[source]

Bases: object

calculate solvent accessible surface area.

Parameters:

  • radiuses (np.ndarray(dtype=float, shape=(N,))) – atomic radius + solvent radius vector

  • xyzs (np.ndarray(dtype=float, shape=(N, 3))) – atomic position matrix

  • level (int) –

    mesh level. subdivide icosahedron n-1 times.

    \[N_{\rm points} = 5 \times 4^{level} - 8\]

atomic_sa(i)[source]

Calculate atomic surface area.

Parameters:

i (int) – atom index

Return type:

float

surface_area()[source]

Calculate all atomic surface area.

Return type:

[float]

classmethod from_mol(mol, conformer=-1, solvent_radius=1.4, level=4)[source]

Construct SurfaceArea from rdkit Mol type.

Parameters:

  • mol (rdkit.Chem.Mol) – input molecule

  • conformer (int) – conformer id

  • solvent_radius (float) – solvent radius

  • level (int) – mesh level

Return type:

SurfaceArea

classmethod from_pdb(pdb, solvent_radius=1.4, level=3)[source]