schrodinger.application.glide.constraints module

Classes related to grid-based constraints in Glide.

class schrodinger.application.glide.constraints.Constraint(label, constype)

Bases: object

Class defining a docking constraint in the receptor.

__init__(label, constype)

property name

User-visible constraint name, as it appears in UI and in Glide input files.

type()

Return the type of the (receptor) constraint as a user-friendly string. Possible return values:

• ‘Hydrophobic’

• ‘H-bond donor’

• ‘H-bond acceptor’

• ‘Metal’

• ‘Positional’

• ‘NOE’

• ‘Metal coordination’

class schrodinger.application.glide.constraints.DonorConstraint(label, atoms=None)

Bases: _HBondConstraint

H-Bond constraint that was specified as a receptor donor atom. A ligand must have an ACCEPTOR group that is making an interaction with this atom to satisfy this constraint.

class schrodinger.application.glide.constraints.AcceptorConstraint(label, atoms=None)

Bases: _HBondConstraint

H-Bond constraint that was specified as a receptor acceptor atom. A ligand must have a DONOR group that is making an interaction with this atom to satisfy this constraint.

class schrodinger.application.glide.constraints.MetalConstraint(label, atoms=None)

Bases: Constraint

This constraint was specified as a metal receptor atom. A ligand must interact with this metal atom to satisfy this constraint.

keyword = 'METAL_CONSTRAINTS'

__init__(label, atoms=None)

atoms()

atom()

sifValue()

class schrodinger.application.glide.constraints.PositionalConstraint(label, x=None, y=None, z=None, radius=None)

Bases: Constraint

keyword = 'POSIT_CONSTRAINTS'

__init__(label, x=None, y=None, z=None, radius=None)

sifValue()

class schrodinger.application.glide.constraints.NOEConstraint(label, x=None, y=None, z=None, rmin=None, rmax=None)

Bases: Constraint

keyword = 'NOE_CONSTRAINTS'

__init__(label, x=None, y=None, z=None, rmin=None, rmax=None)

sifValue()

class schrodinger.application.glide.constraints.MetCoordConstraint(label, xmetc, ymetc, zmetc, rmetc)

Bases: Constraint

keyword = 'METCOORD_CONSTRAINTS'

sites_keyword = 'METCOORD_SITES'

__init__(label, xmetc, ymetc, zmetc, rmetc)

sifValue()

siteSifValue()

class schrodinger.application.glide.constraints.HydrophobicConstraint(label)

Bases: Constraint

__init__(label)

class schrodinger.application.glide.constraints.FeaturePattern(smarts, atoms, exclude=False, nfill=None)

Bases: object

Class defining a constraint feature pattern.

__init__(smarts, atoms, exclude=False, nfill=None)

class schrodinger.application.glide.constraints.Feature(patterns=None)

Bases: object

A list of FeaturePattern objects. Each pattern has these properties: smarts, atoms, exclude.

__init__(patterns=None)

Parameters:

patterns (list) – List of patterns associated with this feature. A shallow copy of the patterns list will be made for the new Feature object.

class schrodinger.application.glide.constraints.ConstraintGroup(parent, constraints=None, nrequired=-1)

Bases: object

Class defining a constraint group.

__init__(parent, constraints=None, nrequired=-1)

addConstraint(label)

setup(cons_labels, feature_sets)

cleanup()

Free the memory associated with this group

schrodinger.application.glide.constraints.read_constraints(gridfile)

Reads the receptor constraints from the specified grid file.

The constraints are actually read from the .cons file. The resulting constraint “type” refers to the atom type in the RECEPTOR, where applicable. Specifically, H-bond and metal-binding constraints.

The matching ligand atom for an H-bond donor receptor constraint should be an H-bond acceptor (by default). Likewire the matching ligand ato for and H-bond acceptor receptor constraint should be a donor (polar H atom).

Other constraint types don’t refer to any specific atom type (Positional, NOE), or require the same atom type in the ligand as in the receptor (Hydrophobic) so the constraint type is valid for both molecules (ligand and receptor).

To get the constraint label, simply do str(Constraint).

Parameters:

gridfile – The gridfile name; should be either a .grd or .zip file.

Return type:

A list of Constraint objects.