Class PhpMOEConverter

object --+
         |
        PhpMOEConverter

Instance Methods

[hide private]

(PhpHypoAdaptor, str)

createPhaseHypothesis(self, ph4_file)
Reads a MOE pharmacophore file, creating a Phase hypothesis from relevant information.

list of dict

_readMOEFile(self, ph4_file)
Reads a MOE pharmacophore file, returning feature data as list of pharmacophore site data organized by header indexed dictionaries.

list of dict

_formInputData(self, count, headers, input_list)
Creates a dictionary from MOE ph4 data, supplied as a number of entries, headers with header types, and a list of all input values in order.

_castMOEType(self, value, MOE_type)
Casts raw MOE pharmacophore strings.

(list of PhpSite, str)

_extractPhaseSites(self, feature_data)
Extracts feature data from raw data dictionary read from MOE file into PhpSites suitable for populating a Phase hypothesis.

(list of PhpSite, list of str)

_checkSiteProjectedPoints(self, sites)
Checks that sites have appropriate projected points, updating the sites if possible.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

createPhaseHypothesis(self, ph4_file)

Reads a MOE pharmacophore file, creating a Phase hypothesis from relevant information.

Parameters:

ph4_file (str) - path to MOE .ph4 file to read

Returns: (PhpHypoAdaptor, str)

tuple containing the Phase hypothesis adapted from the MOE input file, and a string with any conversion warnings

_readMOEFile(self, ph4_file)

Reads a MOE pharmacophore file, returning feature data as list of pharmacophore site data organized by header indexed dictionaries.

Parameters:

ph4_file (str) - path to MOE .ph4 file to read

Returns: list of dict

list of feature data dictionaries

_formInputData(self, count, headers, input_list)

Creates a dictionary from MOE ph4 data, supplied as a number of entries, headers with header types, and a list of all input values in order.

Parameters:

count (int) - number of entries to create
headers (list of tuples) - (header, header type) pairs
input_list (list of str) - list of all inputs in a given section of MOE file

Returns: list of dict

list of dictionaries containing cast data indexed by header

_castMOEType(self, value, MOE_type)

Casts raw MOE pharmacophore strings.

Parameters:

value (str) - value read from MOE text
MOE_type (str) - value type (tt, t, r, i, ix)

Returns:

value cast to corresponding type (str, int, float, hex)

_extractPhaseSites(self, feature_data)

Extracts feature data from raw data dictionary read from MOE file into PhpSites suitable for populating a Phase hypothesis.

Parameters:

feature_data (list of dict) - list of MOE data dictionaries

Returns: (list of PhpSite, str)

list of Phase sites, warning message

_checkSiteProjectedPoints(self, sites)

Checks that sites have appropriate projected points, updating the sites if possible.

Parameters:

sites (list of PhpSite) - Phase sites to check static fragment projected coords

Returns: (list of PhpSite, list of str)

updated Phase sites, any update warnings