propka.ligand
Ligand atom typing
This module contains the assign_sybyl_type()
function to analyze
all propka.atom.Atom
in terms of SYBYL atom types (see
ALL_SYBYL_TYPES
).
Module Attributes
SYBYL atom types |
|
PROPKA input types |
Functions
|
Test whether a group of atoms are planar. |
|
Assign Sybyl type to atom. |
|
Identify the atoms in a ring |
|
Determine whether group of atoms form aromatic ring. |
|
Finds out if atom forms a plane together with its bonded atoms. |
|
Determine if atom is a member of a ring. |
|
Set atom type.. |
- propka.ligand.ALL_SYBYL_TYPES = ['C.3', 'H', 'C.2', 'H.spc', 'C.1', 'H.t3p', 'C.ar', 'LP', 'C.cat', 'Du', 'N.3', 'Du.C', 'N.2', 'Any', 'N.1', 'Hal', 'N.ar', 'Het', 'N.am', 'Hev', 'N.pl3', 'Li', 'N.4', 'Na', 'O.3', 'Mg', 'O.2', 'Al', 'O.co2', 'Si', 'O.spc', 'K', 'O.t3p', 'Ca', 'S.3', 'Cr.th', 'S.2', 'Cr.oh', 'S.O', 'Mn', 'S.O2', 'Fe', 'P.3', 'Co.oh', 'F', 'Cu', 'Cl', 'Zn', 'Br', 'Se', 'I', 'Mo', 'Sn']
SYBYL atom types
- propka.ligand.PROPKA_INPUT_TYPES = ['1P', '1N', '2P', '2N', 'C3', 'H', 'C2', 'Hsp', 'C1', 'Ht3', 'Car', 'LP', 'Cca', 'Du', 'N3', 'DuC', 'N2', 'Any', 'N1', 'Hal', 'Nar', 'Het', 'Nam', 'Hev', 'Npl', 'Li', 'N4', 'Na', 'O3', 'Mg', 'O2', 'Al', 'Oco', 'Si', 'Osp', 'K', 'Ot3', 'Ca', 'S3', 'Crt', 'S2', 'Cro', 'SO', 'Mn', 'SO2', 'Fe', 'P3', 'Coo', 'F', 'Cu', 'Cl', 'Zn', 'Br', 'Se', 'I', 'Mo', 'Sn']
PROPKA input types
- propka.ligand.are_atoms_planar(atoms)[source]
Test whether a group of atoms are planar.
- Parameters:
atoms – list of atoms
- Returns:
Boolean
- propka.ligand.assign_sybyl_type(atom)[source]
Assign Sybyl type to atom.
- Parameters:
atom – atom to assign
- propka.ligand.identify_ring(this_atom, original_atom, number, past_atoms)[source]
Identify the atoms in a ring
- Parameters:
this_atom – atom to test
original_atom – some other atom
number – number of atoms
past_atoms – atoms that have already been found
- Returns:
list of atoms
- propka.ligand.is_aromatic_ring(atoms)[source]
Determine whether group of atoms form aromatic ring.
- Parameters:
atoms – list of atoms to test
- Returns:
Boolean
- propka.ligand.is_planar(atom)[source]
Finds out if atom forms a plane together with its bonded atoms.
- Parameters:
atom – atom to test
- Returns:
Boolean