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mmd.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* -------------------------------------------------------------------

from chempy.models import Indexed,Connected
from chempy import Storage,Atom,Bond

import string
import copy

class MMD(Storage):
   
#---------------------------------------------------------------------------------
   def fromList(self,MMODList):

      model = Connected()
      
# get header information
      nAtom = int(MMODList[0][1:6])
      model.molecule.title = string.strip(MMODList[0][8:])
      irec = 1

# loop through atoms
      cnt = 0
      for a in range(nAtom):
         model.bond.append([])
         
      for a in range(nAtom):
         at = Atom()
         at.numeric_type = int(MMODList[irec][1:4])

# extract connectivity information
         tokens = string.splitfields(MMODList[irec][5:52])
         at.neighbor = []
         at.bondorder = []

         for i in range(6):
            if tokens[2*i] != "0":
               a2 = int(tokens[2*i])-1
               if (a2>cnt):
                  b = Bond()
                  b.index = [cnt,a2]
                  b.order = int(tokens[2*i+1])
                  model.bond[b.index[0]].append(b) # note two refs to same object
                  model.bond[b.index[1]].append(b) # note two refs to same object 
            else:
               break
         
# extract other information
         at.coord = [float(MMODList[irec][53:64]), 
            float(MMODList[irec][65:76]), float(MMODList[irec][77:88])]
         at.resi = string.strip(MMODList[irec][89:94])
         at.resi_number = int(at.resi)
         resn_code = string.strip(MMODList[irec][94:95])
         if len(resn_code): at.resn_code = resn_code
         color_code = string.strip(MMODList[irec][96:100])
         if color_code!='':
            at.color_code = int(color_code)
         else:
            at.color_code = 0
         chain = string.strip(MMODList[irec][95:96])
         if len(chain): at.chain = chain
         at.partial_charge = float(MMODList[irec][100:109])
         at.resn = MMODList[irec][119:123]
         name = string.strip(MMODList[irec][124:128])
         if len(name): at.name = name
         model.atom.append(at)
         irec = irec + 1
         cnt = cnt + 1
         
# fill in remaining datatypes
      cnt = 1
      for a in model.atom:
         a.text_type = MMOD_atom_data[a.numeric_type][0]
         a.symbol = MMOD_atom_data[a.numeric_type][1]
         a.formal_charge = MMOD_atom_data[a.numeric_type][4]
         cnt = cnt + 1
         
      return(model.convert_to_indexed())

#---------------------------------------------------------------------------------
   def updateFromList(self,model,list): # updates charges and coordinates
      nAtom = int(list[0][1:6])
      try:
         model.molecule.energy = float(list[0][58:68])/4.184 # convert to kcal
      except:
         if hasattr(model.molecule,'energy'):
            del model.molecule.energy
      if nAtom!=model.nAtom:
         raise RuntimeError(" mmd: atom count mismatch")
      c = 0
      for a in list[1:]:
         mac = model.atom[c]
         mac.coord = [float(a[53:64]), 
            float(a[65:76]), float(a[77:88])]
         mac.partial_charge = float(a[100:109])         
         c = c + 1
         
#---------------------------------------------------------------------------------
   def toList(self,model,no_blank_names=1):

      conn = copy.deepcopy(model)
      conn = conn.convert_to_connected()
      
      MMODList = []
      MMODList.append(" %5d  %-70s\n" %(conn.nAtom,conn.molecule.title))
      c = 0
      for i in conn.atom:
         
# construct neighbor list
         neighbors = 6*[0]
         bondorders = 6*[0]
         j = 0
         for b in conn.bond[c]:
            n = b.index[0]
            if n == c:
               n = b.index[1]
            neighbors[j] = n + 1
            bondorders[j] = b.order
            j = j + 1
            
# assemble output line
         if i.numeric_type>0:
            tline = " %3d" % (i.numeric_type)
         else:
            tline = " %3d" % 64
         for j in range(6): 
            tline = tline + " %5d %1d" % (neighbors[j], bondorders[j])
         tline = tline + " %11.6f %11.6f %11.6f " % (i.coord[0], 
            i.coord[1], i.coord[2])
         name = i.name
         if not len(name):
            if no_blank_names:
               name = "%s%d" % (i.symbol,c+1)
               name = name[0:4]
         tline = tline + "%5d%1s%1s%4d%9.5f%9.5f %-4s %4s\n" % \
            (i.resi_number,i.resn_code, i.chain, i.color_code,
             i.partial_charge, i.partial_charge, i.resn, name)
         MMODList.append(tline)
         c = c + 1
         
      return(MMODList)


#---------------------------------------------------------------------------------
'#Ntype Atype Elem Hybr Att Chg\n',
MMOD_atom_data = {
   1: ['C1','C' ,'sp' , 2, 0],
   2: ['C2','C' ,'sp2', 3, 0],
   3: ['C3','C' ,'sp3', 4, 0],
   4: ['CA','C' ,'sp3', 3, 0],
   5: ['CB','C' ,'sp3', 2, 0],
   6: ['CC','C' ,'sp3', 1, 0],
   7: ['CD','C' ,'sp2', 2, 0],
   8: ['CE','C' ,'sp2', 1, 0],
   9: ['CF','C' ,'sp' , 1, 0],
  10: ['CM','C' ,'unk',-1,-1],
  11: ['CP','C' ,'unk',-1, 1],
  12: ['CR','C' ,'unk',-1, 0],
  14: ['C0','C' ,'unk',-1, 0],
  15: ['O2','O' ,'sp2', 1, 0],
  16: ['O3','O' ,'sp3', 2, 0],
  17: ['OA','O' ,'sp3', 1, 0],
  18: ['OM','O' ,'sp3', 1,-1],
  19: ['OW','O' ,'sp3', 0, 0],
  20: ['OP','O' ,'sp2', 2, 1],
  21: ['OQ','O' ,'sp3', 3, 1],
  23: ['O0','O' ,'unk',-1, 0],
  24: ['N1','N' ,'sp' , 1, 0],
  25: ['N2','N' ,'sp2', 2, 0],
  26: ['N3','N' ,'sp3', 3, 0],
  27: ['NA','N' ,'sp3', 2, 0],
  28: ['NB','N' ,'sp3', 1, 0],
  29: ['NC','N' ,'sp3', 0, 0],
  30: ['ND','N' ,'sp2', 1, 0],
  31: ['N4','N' ,'sp2', 3, 1],
  32: ['N5','N' ,'sp3', 4, 1],
  33: ['NE','N' ,'sp3', 3, 1],
  34: ['NF','N' ,'sp3', 2, 1],
  35: ['NG','N' ,'sp3', 1, 1],
  36: ['NH','N' ,'sp2', 2, 1],
  37: ['NI','N' ,'sp2', 1, 1],
  40: ['N0','N' ,'unk',-1, 0],
  41: ['H1','H' ,'s'  , 1, 0],
  42: ['H2','H' ,'s'  , 1, 0],
  43: ['H3','H' ,'s'  , 1, 0],
  44: ['H4','H' ,'s'  , 0, 0],
  45: ['H5','H' ,'s'  , 0, 0],
  48: ['H0','H' ,'s'  ,-1, 0],
  49: ['S1','S' ,'sp3', 2, 0],
  50: ['SA','S' ,'sp3', 1, 0],
  51: ['SM','S' ,'sp3', 0,-1],
  52: ['S0','S' ,'unk',-1, 0],
  53: ['P0','P' ,'unk',-1, 0],
  54: ['B2','B' ,'sp2', 2, 0],
  55: ['B3','B' ,'sp3', 3, 0],
  56: ['F0','F' ,'sp3', 1, 0],
  57: ['Cl','Cl','sp3', 1, 0],
  58: ['Br','Br','sp3', 1, 0],
  59: ['I0','I' ,'sp3', 1, 0],
  60: ['Si','Si','unk',-1, 0],
  61: ['Du','Du','unk',-1, 0],
  62: ['Du','Du','unk',-1, 0],
  63: ['Lp','Lp','unk', 1, 0],
  64: ['Du','Du','unk',-1, 0]};


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