Package schrodinger :: Package application :: Package matsci :: Package genetic_optimization :: Module genetic_optimization :: Class CanvasKPLS

[frames] | no frames]

Class CanvasKPLS

    object --+    
             |    
ClassEvaluator --+
                 |
                CanvasKPLS

Manage Canvas KPLS jobs.

Instance Methods

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__init__(self, structs, properties, copy_models=True, fp_options_dict=None)
Create an instance.

copyCanvasKPLSModelFiles(self)
Copy the Canvas KPLS model files to the CWD.

str

makeMaestroInfile(self, struct)
Make Maestro infile.

str

makeFingerPrintInfile(self, mae_infile, name, key)
Make fingerprint infile.

float

getPropertyValue(self, property_outfile)
Get the property value.

runCanvasKPLS(self, struct)
Run the Canvas KPLS.

runIt(self)
Run it.

makeFpOptionsDict(self)
Make the fingerprint options dictionary.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

[hide private]

int, str, int or None

getFpOptions(model_file)
Return fingerprint options obtained from the given Canvas KPLS model file.

checkCanvasKPLSModelFile(model_file)
Check the given Canvas KPLS model file.

list

getValidCanvasKPLSModelFiles(property_lists)
Return file names of any valid Canvas KPLS model files.

dict

addCanvasKPLSOptions(property_string, options, name, known_name, index)
Add any Canvas KPLS options found in the given property string to the given property options dictionary.

Class Variables

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KPLS_EXT = 'kpls.tar.gz'

FP_TEXT_FILE = 'fpInfo.txt'

MODEL_OPTION = 'kpls_model'

EXTRA_OPTIONS = ['kpls_model']

CUSTOM_KEY = 'r_matsci_KPLS_%s/%s'

TG_KEY = 'r_matsci_KPLS_Tg/C'

TG_PROP = 'kpls_tg'

DIR = 'genetic_optimization/canvas_kpls_models'

PATH = '/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-...

TG_PARAMETERS = OrderedDict([('kpls_model', '/scr/buildbot/sav...

CLASS_KWARGS = OrderedDict([('kpls_tg', 'kpls_model>/scr/build...

CELSIUS = 'C'

UNKNOWN_UNITS = 'unknown'

TG_UNITS = 'C'

TAG = '_kpls'

IN_FP_EXT = '-in.fp'

OUT_EXT = '.out'

VALUE_PATTERN = re.compile(r'\s*1\s+unknown.*\s+(\d+\.?\d*)$')

ALLOWED_FP_TYPES = ['linear', 'maccs', 'radial', 'molprint2D',...

SINGLE_PRECISION = 32

DOUBLE_PRECISION = 64

FP_OPTIONS_DICT_KEY = 'fp_options_dict'

BIT_EXT = '-bit'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, structs, properties, copy_models=True, fp_options_dict=None)
(Constructor)

Create an instance.

Parameters:

structs (list of schrodinger.structure.Structure) - contains input structures for Canvas KPLS
properties (dict) - keys are (name, key) tuples with name and key the property name and structure property key to be created, values are dicts of kwargs, for example containing self.EXTRA_OPTIONS as keys
copy_models (bool) - specifies that Canvas KPLS model files specified in the properties argument be copied to the CWD, this will be necessary if wanting to make calls to .runIt in parallel (in that case it will also be necessary to call .runIt from within a subdirectory which contains all input files but this currently is not handled by this class)
fp_options_dict (dict) - fingerprint options dictionary, keys are (name, key) tuples with name and key the property name and structure property key to be created, values are (precision, fptype, atomtypes) tuples to be used in fingerprint generation

Overrides: object.__init__

makeMaestroInfile(self, struct)

Make Maestro infile.

Parameters:

struct (schrodinger.structure.Structure) - the structure for which to prepare the Maestro input file

Returns: str

the Maestro input file name

makeFingerPrintInfile(self, mae_infile, name, key)

Make fingerprint infile.

Parameters:

mae_infile (str) - the Maestro input file name
name (str) - the property name
key (str) - the structure property key

Returns: str

the Canvas fingerprint input file name

Raises:

RuntimeError - if canvasFPGen fails

getPropertyValue(self, property_outfile)

Get the property value.

Parameters:

property_outfile (str) - the Canvas KPLS output file

Returns: float

the property value

Raises:

RuntimeError - if property output file doesn't exist or doesn't contain the property value

runCanvasKPLS(self, struct)

Run the Canvas KPLS.

Parameters:

struct (schrodinger.structure.Structure) - the structure on which to run Canvas KPLS

Raises:

RuntimeError - if canvasKPLS fails

runIt(self)

Run it.

Raises:

RuntimeError - for any issue

Overrides: ClassEvaluator.runIt

getFpOptions(model_file)
Static Method

Return fingerprint options obtained from the given Canvas KPLS model file.

Parameters:

model_file (str) - the name of the Canvas KPLS model file

Returns: int, str, int or None

contains (1) precision, (2) fingerprint type, and (3) atom type if present

Raises:

RuntimeError - if there is anything wrong with the Canvas KPLS model file

checkCanvasKPLSModelFile(model_file)
Static Method

Check the given Canvas KPLS model file.

Parameters:

model_file (str) - the name of the Canvas KPLS model file

Raises:

RuntimeError - if there is anything wrong with the Canvas KPLS model file

getValidCanvasKPLSModelFiles(property_lists)
Static Method

Return file names of any valid Canvas KPLS model files.

Parameters:

property_lists (list) - contains lists of property specifications

Returns: list

file names of valid Canvas KPLS model files

addCanvasKPLSOptions(property_string, options, name, known_name, index)
Static Method

Add any Canvas KPLS options found in the given property string to the given property options dictionary.

Parameters:

property_string (str) - the string representation of the property specifications, containing options as '<option_substring>=<value>'
options (dict) - contains property options
name (str) - the property name
known_name (bool) - if the given property name is a known name
index (int) - the property index

Returns: dict

the given property options with Canvas KPLS options added

Raises:

UnknownNameError - if the name is not allowed to be unknown
IncompleteExtraOptionsError - if the provided Canvas KPLS options are incomplete

Class Variable Details

[hide private]

PATH

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/data/genet
ic_optimization/canvas_kpls_models'

TG_PARAMETERS

Value:

OrderedDict([('kpls_model', '/scr/buildbot/savedbuilds/NB/2016-4/build
-126/mmshare-v3.6/data/genetic_optimization/canvas_kpls_models/Tg250.k
pls.tar.gz')])

CLASS_KWARGS

Value:

OrderedDict([('kpls_tg', 'kpls_model>/scr/buildbot/savedbuilds/NB/2016
-4/build-126/mmshare-v3.6/data/genetic_optimization/canvas_kpls_models
/Tg250.kpls.tar.gz')])

ALLOWED_FP_TYPES

Value:

['linear',
 'maccs',
 'radial',
 'molprint2D',
 'torsion',
 'pairwise',
 'triplet',
 'quartet',
...

Class CanvasKPLS

__init__(self, structs, properties, copy_models=True, fp_options_dict=None) (Constructor)

makeMaestroInfile(self, struct)

makeFingerPrintInfile(self, mae_infile, name, key)

getPropertyValue(self, property_outfile)

runCanvasKPLS(self, struct)

runIt(self)

getFpOptions(model_file) Static Method

checkCanvasKPLSModelFile(model_file) Static Method

getValidCanvasKPLSModelFiles(property_lists) Static Method

addCanvasKPLSOptions(property_string, options, name, known_name, index) Static Method

PATH

TG_PARAMETERS

CLASS_KWARGS

ALLOWED_FP_TYPES

init(self, structs, properties, copy_models=True, fp_options_dict=None)
(Constructor)

getFpOptions(model_file)
Static Method

checkCanvasKPLSModelFile(model_file)
Static Method

getValidCanvasKPLSModelFiles(property_lists)
Static Method

addCanvasKPLSOptions(property_string, options, name, known_name, index)
Static Method