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Constraint Class defining a docking constraint in the receptor. |
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DonorConstraint H-Bond constraint that was specified as a *receptor* donor atom. |
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AcceptorConstraint H-Bond constraint that was specified as a *receptor* acceptor atom. |
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MetalConstraint This constraint was specified as a metal receptor atom. |
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PositionalConstraint | |||
NOEConstraint | |||
MetCoordConstraint | |||
HydrophobicConstraint | |||
FeaturePattern Class defining a constraint feature pattern. |
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ConstraintGroup Class defining a constraint group. |
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GlideJob Class for writing Glide input files - either Gridgen or Docking. |
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Gridgen Class for writing Glide Grid Generation input files. |
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Dock Class for generating Glide docking input files. |
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A list of Constraint objects. |
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float |
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tuple of lists, e.g. ([10, 10, 10], [-5.9863, -1.887 , -0.2703]) |
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__doc__ =
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DEBUG = os.environ.has_key('SCHRODINGER_PYTHON_DEBUG')
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HYDROPHOBIC = 'Hydrophobic'
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HBOND_DONOR = 'H-bond donor'
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HBOND_ACCEPTOR = 'H-bond acceptor'
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METAL = 'Metal'
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POSITIONAL = 'Positional'
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NOE = 'NOE'
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METCOORD = 'Metal coordination'
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NA = 'NA'
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mmim_cons_types = [NA, HYDROPHOBIC, HBOND_DONOR, HBOND_ACCEPTO
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FREE = 'free'
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FIXED = 'fixed'
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PENALIZE = 'penal'
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TRANS = 'trans'
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HTVS = 'HTVS'
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SP = 'SP'
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XP = 'XP'
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PV = 'poseviewer'
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LIB = 'ligandlib'
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PV_SD = 'poseviewer_sd'
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LIB_SD = 'ligandlib_sd'
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ALL = -1
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extra_specs = {}
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_special_keys = set(['JOBTYPE', 'INNERBOX', 'OUTERBOX', 'NREQU
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_old_keywords = {}
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torcons_section_allowed_keywords = set(['ALL', 'SMARTS', 'ATOM
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consgroup_section_allowed_keywords = set(['USE_CONS', 'NREQUIR
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mmim_to_inputconfig_type_map = {'boolean': 'boolean', 'boolean
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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).
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Read mmim_keywords.json and return a list of objects. The read_yaml() name was retained for compatibility. |
Return a string with the specification of the mmim keywords that are valid for the jobtypes given. Jobtypes should be an iterable with items such as 'docking', 'multi_docking', or 'gridgen'. Keywords for jobtype 'all' are always included. By default, undocumented keywords are not included in the return value, but that behavior can be overridden by setting 'include_undocumented' to True. |
Return a list of validation specs for a given jobtype (e.g., 'docking' or 'gridgen') or list of jobtypes. This includes not only the keywords returned by keyword_spec(jobtype), but also some extra keywords that are supported by glide.py but not by mmim. |
Given a list of (x, y, z) coordinates for all atoms in a ligand, calculate the ligand size. This value should be added to the innerbox to get the default outerbox.
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Gets the default box size for a grid. This returns the outer and inner box lengths.
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Return a Gridgen or Dock object given an SIF input filename or keyword dictionary. If it is a filename, use it to set JOBNAME (e.g. for "dir/myjob.in", set it to "myjob"). |
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__doc__
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mmim_cons_types
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_special_keys
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torcons_section_allowed_keywords
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consgroup_section_allowed_keywords
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mmim_to_inputconfig_type_map
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Trees | Indices | Help |
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