import os,sys,string,re, time
import assign_helices
import analyspdb
import display_helices
import CalcModes
import util
import settings
from MMTK import *
sys.path.append('./utilities/pyutils')
sys.path.append('./applications/tmm')

##
## tmm_start.py - initiates the calculation of the normal modes and predicts the TM alpha helical segments. 
##

def tmm_start (items, results):

    items['resultid'] = items['jobid']
    results['resultid'] = items['resultid']

    # if the user input to TMM is a pdb code, we retrieve the PDB file from the flat file
    if items['pdbcode']:
        print '...submitted pdb code:',items['pdbcode']
        results['pdbcode'] = items['pdbcode']
        #
        #Aug07: The flat db stores pdbfiles with lowercase names.
        #added convertion of pdb-code to lowercase to avoid error if user writes in upper case
        #Note: The pdb-standard specifies letters in the pdb-code to be upper case
        #
        cleaned_code = items['pdbcode'].lower()
        path = settings.PDB_PATH
        file = 'pdb'+cleaned_code+'.ent'
        filename = path + file
        try:
            filehandle = open(filename,'r')
            items['pdbstruct'] = filehandle.read()
        except:
            print 'This is not an existing pdb code'
            results['modefile_name'] = ''
            results['messages'] = 'This is not an existing pdb code'
            results['status'] = 'FAILED'
            return results
		
    else:
        print 'no pdb code entered'
        print 'checking uploaded pdbfile'

    # the pdb structure is now saved in the variable items['pdbstruct'] even though the input was a pdb code
    if items['pdbstruct']:
        if items['pdbcode'] == '':
            results['pdbcode'] = items['jobid'][0:5]
            items['pdbcode'] = items['jobid'][0:5]
                        
        print 'parsing the pdb file'
        
        # If this test is true the file that has been entered is not a pdb file
        if string.find(items['pdbstruct'],"ATOM") == -1:
            results = items
            results['pdbstruct'] = ' '
            results['modefile_name'] = ''
            results['status'] = 'FAILED'
            results['messages'] = 'The file you entered is probably not a pdb-file. Please check that you have the right file and try again from the main page.'
            return results
                
        print 'pdbfile ok'

        # Saving the pdb file to local disk
        pdbfile_name = items['pdbfilename']
        results['pdbfilename'] =  items['pdbfilename']
        pdbfile = open(pdbfile_name, 'w')
        pdbfile.write(items['pdbstruct']) 
        pdbfile.close()
        
        # Checking for the length of the structure. No structure should be larger than 20000 residues. 
        calphanb = analyspdb.analyspdb(items['pdbstruct'], items)
        
        if (calphanb > 20000):
            results['messages'] = 'This server does not support systems with more than 20000 residues'
            results['status']='FAILED'
            results['modefile_name'] = ''
            return results
        else: 
            print 'number of ca atoms:',calphanb

            ## using DSSP to find all alpha helices in the PDB structure
            print 'Assigning helices to the protein...'
            helices, residues, hydro, chains = assign_helices.AssignHelices( pdbfile_name )
            #print residues
            #print helices
            print str(len(helices)) + ' found.'
            
            ## We calculate the normal modes, unless it exist on the hard drive though...
            if items['pdbcode'] != items['jobid'][0:5]:
                exist = exists(settings.MODE_DIR, items['pdbcode'])

                ## if exist is set to 0, files will not be looked up.
                #exist = 0
                
                if exist != 0:
                    saved_nmodes = len(load(exist))
                    print 'files stores ' + str(saved_nmodes) + ' modes'
                    user_wants_nmodes = int(float(calphanb) * 3.0 * float(items['nmodes']))
                    print 'user wants ' + str(user_wants_nmodes)
                
                #if exist != 0 and saved_nmodes >= (user_wants_nmodes-10):
                if exist != 0:
                    print 'Normal modes already calculated. Using file ' + exist + '.'
                    items['modefile_name'] = exist
                else:
                    print 'Calculating the normal modes...'
                    items['modefile_name'] = './scratch/'+items['jobid'] + '.mode'
                    try:
                        print 'calcing'
                        html = CalcModes.CalcModes('./scratch/'+items['jobid']+'-2.pdb', items['modefile_name'], items['nmodes'])
                        print 'done'
                        util.saveModeFile(items['modefile_name'], settings.MODE_DIR, items['pdbcode'], items['nmodes'])
                    except AttributeError:
                        print 'modes cannot be calulated'
                        results['messages'] = 'An error occurred during the calculation of the normal modes. Please contact us at <a href="mailto:contact@bioinfo.no">contact@bioinfo.no</a>'
                        results['status']='FAILED'
                        results['modefile_name'] = ''
                        return results
            else:
                try:
                    print 'calcing'
                    items['modefile_name'] = './scratch/'+items['jobid'] + '.mode'
                    html = CalcModes.CalcModes('./scratch/'+items['jobid']+'-2.pdb', items['modefile_name'], items['nmodes'])
                    print 'done'
                except AttributeError:
                    print 'modes cannot be calulated'
                    results['messages'] = 'An error occurred during the calculation of the normal modes. Please contact us at <a href="mailto:contact@bioinfo.no">contact@bioinfo.no</a>'
                    results['status']='FAILED'
                    results['modefile_name'] = ''
                    return results
                    
            ## assigning some variables that will be sent right back to zope
            print 'Finding which helices to use...'

            items['display_0'] = pdbfile_name.replace('pdb', '0.png')
            results['display_0'] = items['display_0']
            results['vmdfilename'] = pdbfile_name.replace('pdb', 'vmd')
            results['vmd'] = results['vmdfilename']
            results['chainlist'] = util.turnList(chains)
            if len(results['chainlist']) == 0:
                results['chainlist'].append('')


            
            ## This is where we find all the TM alpha helices. They are stored in the variable 'bundle'
            ## I guess we produce the VMD file here as well
            bundle, reason = display_helices.HelixWrapper( items, helices, pdbfile_name, hydro, residues, chains )

                
            ## All lists should be strings when it is sent to biaz and zope
            name_list = ['']*len(helices)
            results['bundle'], results['reason'], results['chains'], results['h_start'], results['h_end'], results['tm_helices'], results['residues'], results['h_name'] = util.convertToStrings(bundle, reason, helices, residues, name_list )

            #print "tm_helices"
            #print results['tm_helices']
            #print "h_start"
            #print results['h_start']
            #print "h_end"
            #print results['h_end']
            #print "h_name"
            #print results['h_name']
                                   
            results['jobid'] = items['jobid']
            results['modefile_name'] = items['modefile_name']

            ## Then we have to edit the VMD file to make it more convenient for the user
            edit_vmd_file(results['vmdfilename'])
                        
    else:
        results['status'] = 'FAILED'
        results['messages'] = 'Please submit a PDB file or a PDB code'
        results['modefile_name'] = ''
        return results

    return results

## Function for finding if the normal mode file of a protein exist
def exists(mode_dir, pdbcode):

    directories = ['full_set', 'half_set', 'small_set', '200']
    #directories = ['1']
    for dir in directories:
        dir = mode_dir + dir + '/'
        name = dir + pdbcode + '.mode'
        exists = 1
        try:
            about = os.stat(name)
            print "Size of file is "+str(about[6])+ " bytes"
            return name
        except OSError:
            print "File does not exist or is not accessible"
            exists = 0
    return 0
            
            

# The VMD file is allready made, but we have to change something in it... 
def edit_vmd_file( vmdfilename ):

    statefile = open(vmdfilename, 'r')
    array = []
    array = statefile.readlines()
    statefile.close()
    
    new_statefile = open(vmdfilename, 'w')
    
    c=0
    while c < len(array):

        # changes and removes a bunch of crap
        if array[c][0:7] == 'mol new':
            str = 'mol new {myPdbFile.pdb} type pdb\n'
            new_statefile.write(str)
        elif array[c][0:5] == 'save_':
            str = ''
        elif array[c][0:5] == 'rende':
            str = ''
        elif array[c][0:4] == 'quit':
            str = 'lugh'
        elif array[c][0:4] == 'scal':
            str = 'lugh'
        elif array[c][0:4] == 'colo':
            str = 'lugh'
        elif array[c][0:4] == 'axes':
            str = 'lugh'
        elif array[c][0:8] == 'mol load':
            str = 'lugh'
            #print array[c][0:8]
        else:
            #print array[c]
            new_statefile.write(array[c])
        c=c+1

    new_statefile.close()

    return