Package schrodinger :: Package structutils :: Module assignbondorders

Module assignbondorders


A module to assign bond orders based on molecular geometry.

Assigns double and triple bonds to structures based on molecular geometry
(bond length, bond angles, and dihedral angles). Useful when importing
ligands from PDBs into Maestro.   Please check the output structure for
errors and compare it to the molecular formula. If this script assigns
bond orders incorrectly to a reasonable structure, please email the
maestro file of the structure to help@schrodinger.com.

Functions:

There is a single public function:

    assignbondorders.assign_st(input_st, atoms=None, neutralize=False, problem_only=False, skip_assigned_residues=True)
        Assigns bond orders to atom list [atoms] of structure input_st and
        returns a list of bonds that were adjusted. Bond orders are assigned for
        all atoms if the atoms list is empty or not specified.

Copyright (c) Schrodinger, LLC. All rights reserved.

Classes

[hide private]

AssignBondOrders

Functions

[hide private]

debug(txt)
For general debug messages

debuggroup(msg)
For debugging group bond assignments

debugbonders(msg)
For debugging aromatic ring assignments

debugbond(msg)
For debugging code that calculates bond "scores"

warning(msg)

get_single_bond_length(a1, a2)
Returns ideal length of a single-order bond between specified atoms.

get_neighbors(st, atom)
Returns a list of atoms that <atom> is bound to.

calculate_average_angle(st, atom_num)
Calculates the average of all bond angles around the input atom.

calculate_dihedral(st, a1, a2)
Calculates the average dihedral angle of the bond between the specified atoms.

order_ring_or_chain(st, atoms)
This function orders the atoms in the ring or chain by bonding order.

do_rings_share_atoms(r1, r2)

get_rings_in_group(ring, rings_to_check)

get_ring_atom_coords(st, ring_atoms)
Get the coordinates of the ring atoms as a numpy array.

get_edge_normals(ring_atom_coords)
Get vectors normal to the planes described by each ring-edge and the center of the ring.

calculate_planarity(st, ring_atoms)
Calculate the ring planarity.

_residue_atom_subset(res, atoms)
Return atoms of the residue residue which are also in the specified <atoms> list.

assign_st(st, atoms=None, neutralize=False, problem_only=False, skip_assigned_residues=True)
Performs the assign-bond-order algorithm on the supplied structure.

_genBondsDict(st, atoms)
Generates the state dictionary for the specified st.

orders_assigned(st, atoms=None, all=False)
Returns True if all bond orders are OK in the specified structure.

Variables

[hide private]

DEBUG = False
hash(x)

logger = log.get_output_logger("schrodinger.structutils.assign...

DEBUG_AROMATIC = True
hash(x)

DEBUG_BOND_SCORE = True
hash(x)

DEBUG_GROUP = True
hash(x)

DOUBLE_BOND_THRESHOLD = 5.0

MAX_VALENCE = [0, 1, 1, 1, 2, 6, 4, 4, 2, 1, 1, 1, 2, 8, 8, 8,...

ATOM_RADII_DICT = {1: 0.23, 5: 0.83, 6: 0.68, 7: 0.68, 8: 0.68...

ASSIGNED_AROMATIC = 0
hash(x)

NOT_AROMATIC = 1

NOT_ASSIGNED = 2

__package__ = 'schrodinger.structutils'

Function Details

[hide private]

get_single_bond_length(a1, a2)

Returns ideal length of a single-order bond between specified atoms. If either of the atoms is non-common, returns 0.0.

calculate_average_angle(st, atom_num)

Calculates the average of all bond angles around the input atom. Returns 0 if the angle can not be calculated. Close to 109 degrees = tetrahedral Close to 120 degrees = planar Close to 180 degrees = linear

calculate_dihedral(st, a1, a2)

Calculates the average dihedral angle of the bond between the specified atoms. Close to 0 (zero) is likely to be double bond.

get_ring_atom_coords(st, ring_atoms)

Get the coordinates of the ring atoms as a numpy array.

If st has periodic boundary conditions (PBC), the coordinates returned will all be in the frame of reference of the first atom in ring_atoms.

get_edge_normals(ring_atom_coords)

Get vectors normal to the planes described by each ring-edge and the center of the ring.

Assumes that atoms are in order.

calculate_planarity(st, ring_atoms)

Calculate the ring planarity.

Very planar rings have a planarity of < 1.

Assumes that atoms are in order.

_residue_atom_subset(res, atoms)

Return atoms of the residue residue which are also in the specified <atoms> list. Will return an empty list if this residue already has bond orders assigned.

assign_st(st, atoms=None, neutralize=False, problem_only=False, skip_assigned_residues=True)


Performs the assign-bond-order algorithm on the supplied structure.
If the atom list is specified, only those atoms are fixed.
neutralize   - protonate carboxylic acids.
problem_only - assign only to atoms with PDB convert problem of 4
               (orange atoms). Not compatible with <atoms> argument.
skip_assigned_residues - If True, bond orders are not assigned to
                         residues that have double or triple bonds,
                         even if that residue's atoms are in <atoms>.
                         Not compatible with <problem_only> option.

Returns a list of (atom1, atom2, order) for every bond whose order was
altered.

orders_assigned(st, atoms=None, all=False)

Returns True if all bond orders are OK in the specified structure. Can be given a list of atoms to check bond orders of. If not list is specified and all flag is set to True, all atoms are checked; otherwise only atoms with a PDB convert error (appear orange in Maestro) are checked. NOTE: atoms and all options are mutually exclusinve.

Variables Details

[hide private]

logger

Value:

log.get_output_logger("schrodinger.structutils.assignbondorders")

MAX_VALENCE

Value:

[0,
 1,
 1,
 1,
 2,
 6,
 4,
 4,
...

ATOM_RADII_DICT

Value:

{1: 0.23,
 5: 0.83,
 6: 0.68,
 7: 0.68,
 8: 0.68,
 9: 0.64,
 14: 1.2,
 15: 1.05,
...