Package schrodinger :: Package application :: Package matsci :: Module rxn_path :: Class CheckInput

Class CheckInput

object --+
         |
        CheckInput

Check user input.

Instance Methods

[hide private]

str

checkJobName(self, job_name, logger=None)
Check job_name option.

checkInputFiles(self, inputfiles, logger)
Check input files.

list of schrodinger.structure.Structure

checkStructures(self, logger=None, *allstructures)
Check structures.

list of schrodinger.structure.Structure

checkStructurePairs(self, reorder, logger=None, *allstructures)
Check reactant and product pairs of structures.

list of floats

checkSample(self, sample, logger=None)
Check sample option.

str

checkPresumedTs(self, presumed_ts, logger=None)
Check the location of the presumed ts.

str

checkInterpolation(self, interpolation, logger=None)
Check interpolation option.

float

checkMixPrevious(self, mixprevious, logger=None)
Check mixprevious option.

str

checkGuess(self, guess, logger=None)
Check guess option.

str

checkConnectivity(self, connectivity, logger=None)
Check connectivity option.

boolean, float

checkNoRxnComplex(self, norxncomplex, vdwscale, logger=None)
Check norxncomplex and vdwscale options.

boolean

checkReorder(self, reorder, logger=None)
Check reorder option.

boolean

checkReverseInterpolation(self, reverse_interpolation, logger=None)
Check reverse interpolation option.

checkWeights(self, bondweight, angleweight, dihedralweight, cartesianweight, penaltyweight, logger=None)
Check weights, i.e.

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

Class Variables

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PAIRS = [('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ...

COMBIGLD_REPLACEMENTS = OrderedDict([('[]', ''), ('][', '-'), ...

TITLEKEY = 's_m_title'

ENTRYNAMEKEY = 's_m_entry_name'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

checkJobName(self, job_name, logger=None)

Check job_name option.

Parameters:

job_name (str) - name of job
logger (logging.getLogger) - output logger

Returns: str

job_name, name of job

checkInputFiles(self, inputfiles, logger)

Check input files.

Parameters:

inputfiles (list of str) - all provided input files
logger (logging.getLogger) - output logger

checkStructures(self, logger=None, *allstructures)

Check structures.

Parameters:

logger (logging.getLogger) - output logger
allstructures (tuple of schrodinger.structure.Structure) - all provided structures

Returns: list of schrodinger.structure.Structure

structures, updated list of structures

checkStructurePairs(self, reorder, logger=None, *allstructures)

Check reactant and product pairs of structures.

Parameters:

reorder (boolean) - normalize the atomic ordering
logger (logging.getLogger) - output logger
allstructures (tuple of schrodinger.structure.Structure) - all provided structure

Returns: list of schrodinger.structure.Structure

structures, updated list of structures

checkSample(self, sample, logger=None)

Check sample option.

Parameters:

sample (list of float) - sample points
logger (logging.getLogger) - output logger

Returns: list of floats

sample, sample points

checkPresumedTs(self, presumed_ts, logger=None)

Check the location of the presumed ts.

Parameters:

presumed_ts (str) - gives the location of the presumed ts
logger (logging.getLogger) - output logger

Returns: str

presumed_ts, the location of the presumed ts

checkInterpolation(self, interpolation, logger=None)

Check interpolation option.

Parameters:

interpolation (str) - coordinate system used for interpolating
logger (logging.getLogger) - output logger

Returns: str

interpolation, coordinate system used for interpolating

checkMixPrevious(self, mixprevious, logger=None)

Check mixprevious option.

Parameters:

mixprevious (float) - mixing weight of solution from previous path point
logger (logging.getLogger) - output logger

Returns: float

mixprevious, mixing weight of solution from previous path point

checkGuess(self, guess, logger=None)

Check guess option.

Parameters:

guess (str) - type of guess solution
logger (logging.getLogger) - output logger

Returns: str

guess, type of guess solution

checkConnectivity(self, connectivity, logger=None)

Check connectivity option.

Parameters:

connectivity (str) - type of connectivity
logger (logging.getLogger) - output logger

Returns: str

connectivity, type of connectivity

checkNoRxnComplex(self, norxncomplex, vdwscale, logger=None)

Check norxncomplex and vdwscale options.

Parameters:

norxncomplex (boolean) - disable preprocessing into a reaction complex
vdwscale (float) - scales the intermolecular distance
logger (logging.getLogger) - output logger

Returns: boolean, float

norxncomplex, vdwscale, disable preprocessing into a reaction complex and scales the intermolecular distance

checkReorder(self, reorder, logger=None)

Check reorder option.

Parameters:

reorder (boolean) - normalize the atomic ordering
logger (logging.getLogger) - output logger

Returns: boolean

reorder, normalize the atomic ordering

checkReverseInterpolation(self, reverse_interpolation, logger=None)

Check reverse interpolation option.

Parameters:

reverse_interpolation (boolean) - interpolate the reaction path in reverse
logger (logging.getLogger) - output logger

Returns: boolean

reverse_interpolation, interpolate the reaction path in reverse

checkWeights(self, bondweight, angleweight, dihedralweight, cartesianweight, penaltyweight, logger=None)

Check weights, i.e. bondweight, angleweight, dihedralweight, cartesianweight, and penaltyweight.

Parameters:

bondweight (float) - weight of the bond term
angleweight (float) - weight of the angle term
dihedralweight (float) - weight of the dihedral term
cartesianweight (float) - weight of the Cartesian term
penaltyweight (float) - weight of the bond penalty term
logger (logging.getLogger) - output logger
@rtype float, float, float, float, float

Returns:

bondweight, angleweight, dihedralweight, cartesianweight, penaltyweight, weights of the bond, angle, dihedral, Cartesian, and penalty terms

Class Variable Details

[hide private]

PAIRS

Value:

[('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ''), (' ', '_')]

COMBIGLD_REPLACEMENTS

Value:

OrderedDict([('[]', ''), ('][', '-'), ('[', ''), (']', ''), (';', ''),
 (' ', '_')])