Package schrodinger :: Package application :: Package glide :: Module glide

Module glide

Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs.

The classes use the mm.mmim* wrappers to convert the keywords and values into the actual DICE input files.

Job parameters are specified by passing a dictionary of keyword/value pairs to the class initialization method. In addition, some parameters, such as constraints, can be specified by calling class methods.

Calling the writeSimplified() method will create the input file that can be passed to $SCHRODINGER/glide. The value of the JOBNAME keyword will be used as the base name for thheeh input file.

List of keywords accepted by glide.py Gridgen class:

JOBNAME (string)
RECEP_FILE (string) Path to the model file; default <jobname>.mae
GRIDFILE (string) Where to save the grids; default <jobname>.zip
GRID_CENTER (list of 3 floats) X/Y/Z coordinates for grid center
GRID_CENTER_ASL (string) Alternate way to define the grid center by computing the center from the ASL pattern match
LIGAND_MOLECULE (integer) Molecule # in RECEP_FILE for defining grid center; it will be removed from the receptor structure.
INNERBOX (list of 3 ints) Inner box size; default (10,10,10). Can also be just one int, which will be applied for x/y/z.
OUTERBOX (list of floats) Outer box size; default (30.0, 30.0, 30.0). Can also be just one float, which will be applied for x/y/z.
RECEP_VSCALE (float) Range between 0e-8 and 99999; default 1.0.
RECEP_CCUT (float) Range between 0e-8 and 10000; default 0.25.

Constraints (to be created during grid generation):

HBOND_CONSTRAINTS "hbond1 47", "hbond2 55"
METAL_CONSTRAINTS "metal1 64"
POSIT_CONSTRAINTS "label <x> <y> <z> <r>"
NOE_CONSTRAINTS "label <x> <y> <z> <rmin> <rmax>"

List of keywords accepted by glide.py Docking class:

JOBNAME (string) Jobname of the docking job.
GRIDFILE (string) Local or absolute path to gridfile.
READZIP (bool) Whether the grid files are compressed or not.
COMPRESS_POSES (bool) Whether to compress the output PV/LIB file.
LIGANDFILE (string) Local or absolute path to ligand file.
LIGFORMAT (string) Format of the input file. By default derived from ext. Supported values: 'maestro', 'sd', 'mol2', 'pdb'.
PRECISION (string) 'HTVS' | 'SP' | 'XP'
DOCKING_METHOD (string) Docking conf options. Accepted values:
- 'confgen': Dock flexibly.
- 'rigid': Dock rigidly.
- 'refineinput': Optimize and score.
- 'inplace': Score in place (do not dock).
AMIDE_MODE (string) Treatment of amide torsions. Accepted values:
- 'free': Allow free rotation of amide torsions.
- 'fixed': Only use input geometries of amide torsions.
- 'penal': Penalize non-planar amide torsions (default).
- 'trans': Allow trans conformers only.
- 'generalized': Used generalized torsion controls from torcontrol.txt.
- 'gen': Alias for 'generalized'.
AMIDE_TRANSTOL (float) Trans amide tolerance
POSE_OUTTYPE (string) Type of output file to produce. Accepted values:
- 'poseviewer': *_pv.mae file, receptor is first entry.
- 'ligandlib': *_lib.mae file, poses only.
MAXATOMS (int) Ligands with more atoms than this will be skipped.
MAXROTBONDS (int) Ligands with more rotatable bonds will be skipped.
SAMPLE_RINGS (bool) Whether to sample 5/6 membered rings.
WRITE_XP_DESC (bool) Whether to write XP descriptor information.
METAL_CUTOFF (float)
POSES_PER_LIG (int) Max number of poses to produce per ligand.
WRITEREPT (bool) Write the .rept file.
MAX_ITERATIONS (int) Max number of conjugate gradient steps; default 100.
HBOND_CUTOFF (float)
SCORING_CUTOFF (float) Scoring window for keeping initial poses; default 100.
MAXREF (int) Keep best X poses per ligand for energy minimization.
NREPORT (int) Max number of output poses to report for the job.
LIG_VSCALE (float) Scaling of van der Waals radii; default 0.80.
LIG_CCUT (float) van der Waals partial charge cutoff; default 0.15.
CV_CUTOFF (float) Reject poses with Coulomb-vdW E greater than X; default 0.0.
RINGCONFCUT (float) Energy cutoff for conformational search of rings;
DIELECTRIC (float) Distance-dependent dielectric constant; default 2.0.
POSE_RMSD (float) RMS deviation cutoff for duplicate poses; default 0.5A.
POSE_DISPLACEMENT (float) Maximum atomic displacement cutoff; default 1.3A.
POSTDOCKSTRAIN (bool) Whether to include strain correction in postdocking; default is False
FORCEFIELD (string) 'opls2001' | 'opls2005'. What forcefield to use.
FORCEPLANAR (bool) Triggers MMFFLD planarity options.

Classes

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Constraint
Class defining a docking constraint in the receptor.

DonorConstraint
H-Bond constraint that was specified as a *receptor* donor atom.

AcceptorConstraint
H-Bond constraint that was specified as a *receptor* acceptor atom.

MetalConstraint
This constraint was specified as a metal receptor atom.

PositionalConstraint

NOEConstraint

HydrophobicConstraint

FeaturePattern
Class defining a constraint feature pattern.

ConstraintGroup
Class defining a constraint group.

GlideJob
Class for writing Glide input files - either Gridgen or Docking.

Gridgen
Class for writing Glide Grid Generation input files.

Dock
Class for generating Glide docking input files.

Functions

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A list of Constraint objects.

read_constraints(gridfile)
Reads the receptor constraints from the specified grid file.

Variables

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__doc__ = ...

DEBUG = False

HYDROPHOBIC = 'Hydrophobic'

HBOND_DONOR = 'H-bond donor'

HBOND_ACCEPTOR = 'H-bond acceptor'

METAL = 'Metal'

POSITIONAL = 'Positional'

NOE = 'NOE'

NA = 'NA'

mmim_cons_types = ['NA', 'Hydrophobic', 'H-bond donor', 'H-bon...

FREE = 'free'

FIXED = 'fixed'

PENALIZE = 'penal'

TRANS = 'trans'

HTVS = 'HTVS'

SP = 'SP'

XP = 'XP'

PV = 'poseviewer'

LIB = 'ligandlib'

PV_SD = 'poseviewer_sd'

LIB_SD = 'ligandlib_sd'

ALL = -1

_gridgen_specs = '\nJOBTYPE = string(default=\'GRIDG...

gridgen_specs = ['', 'JOBTYPE = string(default=\'GRI...

_docking_specs = '\nJOBTYPE = string(default=\'DOCKI...

docking_specs = ['', 'JOBTYPE = string(default=\'DOC...

_special_keys = ['JOBTYPE', 'INNERBOX', 'OUTERBOX', 'NREQUIRED...

_old_keywords = {'COREATOMS': 'CORE_ATOMS', 'CORE_DEF': 'CORE_...

torcons_section_allowed_keywords = set(['ALL', 'ATOMS', 'SMART...

__package__ = 'schrodinger.application.glide'

l = ''

Function Details

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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.

Returns: A list of Constraint objects.

Variables Details

[hide private]

doc

Value:

"""
Classes for creating Grid Generation and Ligand Docking DICE (Impact) 
input
files from user-friendly keyword/value pairs.

The classes use the mm.mmim* wrappers to convert the keywords and valu
es into
the actual DICE input files.
...

mmim_cons_types

Value:

['NA',
 'Hydrophobic',
 'H-bond donor',
 'H-bond acceptor',
 'NA',
 'Metal',
 'Positional',
 'NOE',
...

_gridgen_specs

Value:

'''
JOBTYPE           = string(default=\'GRIDGEN\')
RECEP_FILE        = string(default=None)
JOBNAME           = string(default=None)
GRID_CENTER       = float_list(default=None)     # list of floats (x,y
,z)
GRID_CENTER_ASL   = string(default=None)
LIGAND_MOLECULE   = integer(default=None) 
...

gridgen_specs

Value:

['',
 'JOBTYPE           = string(default=\'GRIDGEN\')',
 'RECEP_FILE        = string(default=None)',
 'JOBNAME           = string(default=None)',
 'GRID_CENTER       = float_list(default=None)     # list of floats (x
,y,z)',
 'GRID_CENTER_ASL   = string(default=None)',
 'LIGAND_MOLECULE   = integer(default=None) ',
...

_docking_specs

Value:

'''
JOBTYPE           = string(default=\'DOCKING\')
JOBNAME           = string(default=None)
GRIDFILE          = string(default=None)
LIGANDFILE        = string(default=None)
LIGFORMAT         = option(\'maestro\', \'sd\', \'mol2\', \'pdb\', def
ault=None) 
                    # MMIM default is to derive from extension
...

docking_specs

Value:

['',
 'JOBTYPE           = string(default=\'DOCKING\')',
 'JOBNAME           = string(default=None)',
 'GRIDFILE          = string(default=None)',
 'LIGANDFILE        = string(default=None)',
 'LIGFORMAT         = option(\'maestro\', \'sd\', \'mol2\', \'pdb\', d
efault=None) ',
 '                    # MMIM default is to derive from extension',
...

_special_keys

Value:

['JOBTYPE',
 'INNERBOX',
 'OUTERBOX',
 'NREQUIRED_CONS',
 'USE_CONS',
 'PRECISION',
 'READBASE',
 'READZIP',
...

_old_keywords

Value:

{'COREATOMS': 'CORE_ATOMS',
 'CORE_DEF': 'CORE_DEFINITION',
 'LIGAND_SOURCE': 'LIGSOURCE',
 'LIGCCUT': 'LIG_CCUT',
 'LVDW': 'LIG_VSCALE',
 'MODEL_FILE': 'RECEP_FILE',
 'OUTTYPE': 'POSE_OUTTYPE',
 'POSTDOCKNPOSE': 'POSTDOCK_NPOSE',
...

torcons_section_allowed_keywords

Value:

set(['ALL', 'ATOMS', 'SMARTS', 'TORVAL', 'USEVAL'])