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

Constraints (to be created during grid generation):

List of keywords accepted by glide.py Docking class:

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  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 [hide private]
A list of Constraint objects.
read_constraints(gridfile)
Reads the receptor constraints from the specified grid file.
Variables [hide private]
  __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 [hide private]

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'])