PEATSA.Core

All Samples(15) | Call(0) | Derive(0) | Import(15)

Contains the Core classes of the PEATSA command line tool

src/p/e/PEATDB-2.3/PEATDB/Actions.py PEATDB(Download)

 
        #get alignment for pdb seq and AA from DNA seq    
        import PEATSA.Core as Core
        if X == None:
            #we need to also provide the ref structure

                print 'rechecking mutation codes, ref prot structure has changed'                
                #get new mutation codes
                import PEATSA.Core as Core
                for p in DB.getRecs():
                    self.checkMutation(DB, p, ref, self.X)

                #print refaa
                print 'no sequence, using mutation code and ref protein seq'                 
                import PEATSA.Core as Core
                print 'Record has mutation code %s' %rec.Mutations
                mutationSet = Core.Data.MutationSet(rec.Mutations)

            if rec.aaseq == None and rec.Mutations != None:               
                print 'no sequence, using mutation code and ref protein seq'                 
                import PEATSA.Core as Core
                print 'Record has mutation code %s' %rec.Mutations
                mutationSet = Core.Data.MutationSet(rec.Mutations)

    def modelFromMutationCode(self):
        """Model directly from mutation code"""
        import PEATSA.Core as Core
        print 'Record has mutation code %s' %rec.Mutations
        mutationSet = Core.Data.MutationSet(rec.Mutations)

src/p/e/PEATDB-2.3/PEATSA/WebApp/WebScript.py PEATDB(Download)

import Data
import UtilityFunctions, Exceptions
import PEATSA.Core as Core
 
class CommandLineParser(Core.Utilities.CommandLineParser):

src/p/e/PEATDB-2.3/PEATSA/WebApp/UtilityFunctions.py PEATDB(Download)

'''Utility functions used by other WebApp classes'''
import os, MySQLdb, datetime, md5, time, random
import PEATSA.Core as Core
 
def ResourceDirectory():

src/p/e/PEATDB-2.3/PEATSA/WebApp/JobSubmission.py PEATDB(Download)

'''Contains classes and functions for processing a submission from the WebApp's main web page'''
import subprocess, os, urlparse, urllib2, string, time, StringIO, sys
import PEATSA.Core as Core
import UtilityFunctions, Exceptions, Data

src/p/e/PEATDB-2.3/PEATSA/WebApp/Exceptions.py PEATDB(Download)

#
'''Contains WebApp specific exceptions'''
import PEATSA.Core as Core
 
class DatabaseRetrievalError(Core.Exceptions.ProteinDesignToolException):

src/p/e/PEATDB-2.3/PEATSA/WebApp/Data.py PEATDB(Download)

import MySQLdb, os.path, StringIO, pickle, threading
import UtilityFunctions, Exceptions
import PEATSA.Core as Core
 
def SerializeDictionary(aDict):

src/p/e/PEATDB-2.3/PEATSA/Core/Classify.py PEATDB(Download)

import mvpa.measures.noiseperturbation
import mvpa.clfs.lars
import PEATSA.Core as Core
 
class StructureClassifier(object):

src/p/e/PEATDB-2.3/PEATDB/plugins/Summary.py PEATDB(Download)

import PEATSA.WebApp.Data
import PEATSA.WebApp.UtilityFunctions
import PEATSA.Core as Core
from PEATDB.Dialogs import MultipleValDialog
from PEATDB.Actions import DBActions

src/p/e/PEATDB-2.3/PEATDB/plugins/PEATSAplugin.py PEATDB(Download)

import PEATSA.WebApp.Data
import PEATSA.WebApp.UtilityFunctions
import PEATSA.Core as Core
from PEATDB.Dialogs import MultipleValDialog
from PEATDB.Actions import DBActions

src/p/e/PEATDB-2.3/PEATDB/plugins/PCA.py PEATDB(Download)

from mpl_toolkits.mplot3d import Axes3D
from PEATDB.Ekin.Fitting import Fitting
from PEATSA import Core

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