4.3.3. propka.ligand

4.3.3.1. 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

ALL_SYBYL_TYPES	SYBYL atom types
PROPKA_INPUT_TYPES	PROPKA input types

Functions

are_atoms_planar(atoms)	Test whether a group of atoms are planar.
assign_sybyl_type(atom)	Assign Sybyl type to atom.
identify_ring(this_atom, original_atom, …)	Identify the atoms in a ring
is_aromatic_ring(atoms)	Determine whether group of atoms form aromatic ring.
is_planar(atom)	Finds out if atom forms a plane together with its bonded atoms.
is_ring_member(atom)	Determine if atom is a member of a ring.
set_type(atom, type_)	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)

Test whether a group of atoms are planar.

Parameters

atoms – list of atoms

Returns

Boolean

propka.ligand.assign_sybyl_type(atom)

Assign Sybyl type to atom.

Parameters

atom – atom to assign

propka.ligand.identify_ring(this_atom, original_atom, number, past_atoms)

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)

Determine whether group of atoms form aromatic ring.

Parameters

atoms – list of atoms to test

Returns

Boolean

propka.ligand.is_planar(atom)

Finds out if atom forms a plane together with its bonded atoms.

Parameters

atom – atom to test

Returns

Boolean

propka.ligand.is_ring_member(atom)

Determine if atom is a member of a ring.

Parameters

atom – atom to test

Returns

list of atoms

propka.ligand.set_type(atom, type_)

Set atom type..

Parameters

• atom – atom to set

• type – type value to set