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sdf.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

import string
import re
import copy

from chempy import io

class SDFRec:
   
   def __init__(self,sdflist):
      getkee = re.compile("^>\s+<([^>]*)>")
      gettag = re.compile("^>\s+<[^>]*>\s+\((.*)\)")
      ll = len(sdflist)
      if ll<4:
         print " SDFRec: invalid SDF record format #1"
         raise RuntimeError
      self.kees = ['MOL'] # separate key list to preserve order
      self.data = {}
      self.ref_code = {}
      self.data['MOL'] = []
      mol = self.data['MOL']
      l = 0
      while l<ll:
         mol.append(sdflist[l])
         if sdflist[l][0:6]=='M  END':
            break;
         if sdflist[l][0:1]=='>':
            mol[len(mol)-1]='M  END\n'
            sdflist.insert(l,'M  END\n')
            ll=len(sdflist)
            break;
         l = l + 1
         if l>=ll:
            print " SDFRec: invalid SDF record format #2"
            raise RuntimeError
      while l<ll:
         if sdflist[l][0]=='>':
            sl = sdflist[l]
            kee_match = getkee.match(sl)
            if not kee_match:
               print " SDFRec: invalid SDF record format #3"
               raise RuntimeError
            kee = kee_match.group(1)
            self.kees.append(kee)
            ref_code_match = gettag.match(sl)
            if ref_code_match:
               self.ref_code[kee] = ref_code_match.group(1)
            else:
               self.ref_code[kee] = ''
            self.data[kee] = []
            sd = self.data[kee]
            l = l + 1
            while l<ll:
               if len(string.strip(sdflist[l]))!=0:
                  sd.append(sdflist[l])
                  l = l + 1
               else:
                  break;
         else:
            l = l + 1

   def toList(self):
      r = []
      for k in self.kees:
         if k!='MOL':
            if self.ref_code[k]!='':
               r.append(">  <"+k+"> ("+self.ref_code[k]+")\n")
            else:
               r.append(">  <"+k+">\n")               
         for a in self.data[k]:
            r.append(a)
         if k!='MOL':
            r.append("\n")
      return r

   def get(self,kee):
      if self.data.has_key(kee):
         return self.data[kee]
      else:
         return None

   def get_single(self,kee): # automatic stripping
      if self.data.has_key(kee):
         sdk = self.data[kee]
         if len(sdk):
            return string.strip(sdk[0])
         else:
            return None
      else:
         return None
         
   def set_single(self,kee,data,ref_code=None): # adds LF
      self.set(kee,[data+'\n'],ref_code)
      
   def get_model(self):
      return io.mol.fromList(self.get('MOL'))
      
   def set_model(self,model):
      self.set('MOL',io.mol.toList(model))
               
   def set(self,kee,data,ref_code=None):
      if kee not in self.kees:
         self.kees.append(kee)
         self.ref_code[kee]=''
      if ref_code!=None:
         self.ref_code[kee]=ref_code
      self.data[kee] = copy.deepcopy(data)

   def delete(self,kee):
      self.kees.remove(kee)
      del self.data[kee]

class SDF:
   
   def __init__(*args):
      mode = 'r'
      if len(args)<2:
         raise ValueError
      self = args[0]
      fname = args[1]
      if len(args)==3:
         mode = args[2]
      self.mode = mode
      self.at_eof = 0
      if mode not in ('w','r','wa','pf','url'):
         print " SDF: bad mode"
         return None
      if mode=='pf': # pseudofile
         self.file = fname
      elif (mode[0:1]=='r') and (string.find(fname,':')>1):
         # does this look like a URL? (but not a DOS path)
         from urllib import urlopen
         self.file = urlopen(fname)
      else:
         self.file = open(fname,mode)

   def write(self,rec):
      lst = rec.toList()
      for a in lst:
         self.file.write(a)
      self.file.write('$$$$\n')
      
   def read(self): # returns SDFRec or None at end of file
      cur = []
      while 1:
         s = self.file.readline()
         if not s:
            return None
         elif s[0:4]==r'$$$$':
            return SDFRec(cur)
         else:
            cur.append(s)
         
   def close(self):
      self.file.close()
      
   

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