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Sourcecode: pymol version File versions

models.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 chempy
import copy
from cpv import *
import operator

class Base:

#------------------------------------------------------------------------------
   def update_index(self):
      if chempy.feedback['verbose']:
         print " "+str(self.__class__)+": updating indexes..."
      c = 0
      self.index = {}
      idx = self.index
      for a in self.atom:
         idx[id(a)] = c
         c = c + 1
         
#------------------------------------------------------------------------------
   def get_residues(self):
      list = []
      if self.nAtom:
         last = self.atom[0]
         c = 0
         start = 0
         for a in self.atom:
            if not a.in_same_residue(last):
               list.append((start,c))
               start = c
               last = a
            c = c + 1
         if (c-start>1):
            list.append((start,c))
      return list

#------------------------------------------------------------------------------

   def get_coord_list(self):
      lst = []
      for a in self.atom:
         lst.append(a.coord)
      return lst

#------------------------------------------------------------------------------
   def get_mass(self):
      sm = 0.0
      for a in self.atom:
         sm = sm + a.get_mass()
      return sm

#------------------------------------------------------------------------------
   def get_nuclear_charges(self):
      '''Return the sum of nuclear charges of all atoms in a molecule.'''
      sm = 0
      for a in self.atom:
         sm = sm + a.get_number()
      return sm

#------------------------------------------------------------------------------
   def list(self):
      for a in self.atom:
         print a.symbol, a.name,  a.coord
      for a in self.bond:
         print a.index
         
#------------------------------------------------------------------------------
   def get_implicit_mass(self):
      # mass calculation for implicit models

      valence = [0]*len(self.atom)
      implicit = [0]*len(self.atom)
      
      for a in self.bond:
         ai0 = a.index[0]
         ai1 = a.index[1]
         valence[ai0] = valence[ai0] + a.order
         valence[ai1] = valence[ai1] + a.order
      c = 0
      for a in self.atom:
         valence[c] = valence[c] - a.formal_charge
         implicit[c] = a.get_implicit_valence()[valence[c]]
         c = c + 1
      h_count = reduce(operator.__add__,implicit)
      hydrogen = chempy.Atom()
      hydrogen.symbol='H'
      return self.get_mass()+hydrogen.get_mass()*h_count

#------------------------------------------------------------------------------
   def assign_names(self,preserve=1):
      dct = {}
      cnt = {}
      if preserve:
         for a in self.atom:
            if a.has('name'):
               dct[a['name']] = 1
      else:
         for a in self.atom:
            if hasattr(a,'name'):
               del a.name
      for a in self.atom:
         if not a.has('name'):
            if not cnt.has_key(a.symbol):
               c = 1
            else:
               c = cnt[a.symbol]
            while 1:
               nam = a.symbol+str(c)
               c = c + 1
               if not dct.has_key(nam):
                  break
            cnt[a.symbol]=c
            a.name=nam
            dct[nam]=1
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------

class Indexed(Base):

   attr_value = {
      'nAtom' : compile('len(self.atom)','Indexed','eval'),
      'nBond' : compile('len(self.bond)','Indexed','eval'),
      }

   def __getattr__(self,attr):
      if Indexed.attr_value.has_key(attr):
         return eval(Indexed.attr_value[attr])
      else:
         raise AttributeError(attr)

#------------------------------------------------------------------------------
   def __init__(self):
      self.reset()
      
#------------------------------------------------------------------------------
   def reset(self):
      self.index = None
      self.molecule = chempy.Molecule()
      self.atom = []
      self.bond = []

#------------------------------------------------------------------------------
   def get_min_max(self):
      if len(self.atom):
         mn = copy.deepcopy(self.atom[0].coord)
         mx = copy.deepcopy(self.atom[0].coord)
         for a in self.atom:
            ac = a.coord
            if mn[0]>ac[0]: mn[0]=ac[0]
            if mn[1]>ac[1]: mn[1]=ac[1]
            if mn[2]>ac[2]: mn[2]=ac[2]
            if mx[0]<ac[0]: mx[0]=ac[0]
            if mx[1]<ac[1]: mx[1]=ac[1]
            if mx[2]<ac[2]: mx[2]=ac[2]
         return [mn,mx]
      else:
         return [[0.0,0.0,0.0],[0.0,0.0,0.0]]
      
#------------------------------------------------------------------------------
   def merge(self,other): # steals atom objects from 'other' and resets 'other'
      if chempy.feedback['actions']:
         print " "+str(self.__class__)+": merging models..."
      nAtom=self.nAtom
      self.atom.extend(other.atom)
      for b in other.bond:
         b.index[0]=b.index[0]+nAtom
         b.index[1]=b.index[1]+nAtom
         self.bond.append(b)
      other.reset()
      if self.index:
         self.update_index()

#--------------------------------------------------------------------------------
   def delete_atom(self,index):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+": deleting atom %d." % index
   
      nAtom=self.nAtom

# update index if it exists
      if self.index:
         idx = self.index
         for k in idx.keys():
            if idx[k] > index:
               idx[k] = idx[k] - 1
         del idx[id(self.atom[index])]

# delete atom
      del self.atom[index]

# delete bonds associated with this atom

      nBond = len(self.bond)
      templist = []
      for i in range(nBond):
         if index in self.bond[i].index:
            templist.append(i)
      for i in range(len(templist)):
         j = templist[i] - i
         del self.bond[j]

# re-index bond table
      for b in self.bond:
         if b.index[0] > index: 
            b.index[0] = b.index[0] - 1
         if b.index[1] > index: 
            b.index[1] = b.index[1] - 1

#--------------------------------------------------------------------------------
   def delete_list(self,list): # delete a list of indexed atoms

      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+": deleting atoms %s." % str(list)

      nAtom=self.nAtom

      lrev = copy.deepcopy(list)
      lrev.sort()
      lrev.reverse()
      
      # generate cross-reference tables
   
      o2n = {} # old to new
      if len(lrev):
         nxt = lrev.pop()
      else:
         nxt = None
      shft = 0
      for i in range(nAtom):
         if i == nxt:
            o2n[i]=-1
            if len(lrev):
               nxt = lrev.pop()
            else:
               nxt = None
            shft = shft - 1
         else:
            ixs = i + shft
            o2n[i] = ixs

      if shft:

         # delete atoms

         new_atom = []
         for i in range(nAtom):
            if o2n[i]>=0:
               new_atom.append(self.atom[i])
         self.atom = new_atom
         
         # delete bonds 

         new_bond = []   
         for b in self.bond:
            b0 = b.index[0]
            b1 = b.index[1]
            if (o2n[b0]>=0) and (o2n[b1]>=0):
               b.index[0] = o2n[b0]
               b.index[1] = o2n[b1]
               new_bond.append(b)
         self.bond = new_bond

         # update index if it exists
         if self.index:
            self.index = {}
            idx = self.index
            i = 0
            for a in self.atom:
               idx[id(a)] = i
               i = i + 1

#------------------------------------------------------------------------------
   def insert_atom(self,index,atom):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+': inserting atom "%s" before %d.' % (
            atom.name,index)

      nAtom=self.nAtom
      self.atom.insert(index,atom)
      
# re-index bond table
      for b in self.bond:
         if b.index[0] >= index: 
            b.index[0] = b.index[0] + 1
         if b.index[1] >= index: 
            b.index[1] = b.index[1] + 1

# update index if it exists
      if self.index:
         idx = self.index
         for k in idx.keys():
            if idx[k] >= index:
               idx[k] = idx[k] + 1
         idx[id(atom)] = index
         
#------------------------------------------------------------------------------
   def index_atom(self,atom):
      c = 0
      id_at = id(atom)
      for a in self.atom:
         if id(a)==id_at:
            return c
         c = c + 1
      return -1
      
#------------------------------------------------------------------------------
   def add_atom(self,atom):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+': adding atom "%s".' % atom.name
      self.atom.append(atom)
      index = self.nAtom - 1
      if self.index:
         self.index[id(atom)] = index
      return index

#------------------------------------------------------------------------------
   def add_bond(self,bond):
      if chempy.feedback['bonds']:
         print " "+str(self.__class__)+": adding bond (%d,%d)." % \
               (bond.index[0],bond.index[1])
      self.bond.append(bond)      

#------------------------------------------------------------------------------
   def remove_bond(self,index):
      if chempy.feedback['bonds']:
         print " "+str(self.__class__)+": removing bond %d." % index
      nBond=len(self.Bond)
      del self.bond[index]
      
   
#------------------------------------------------------------------------------
   def convert_to_connected(self):
      if chempy.feedback['verbose']:
         print " "+str(self.__class__)+": converting to connected model..."
      model = Connected()
      model.molecule = self.molecule
      model.atom = self.atom
      model.bond = []
      model.index = None
      for a in model.atom:
         model.bond.append([])
      for b in self.bond:
         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 
      self.reset()
      return model
#------------------------------------------------------------------------------
   def from_molobj(self,molobj): 
      self.reset()
      mol = self.molecule
      if len(molobj.title):
         mol.title = molobj.title
      if len(molobj.comments):
         mol.comments = molobj.comments
      mol.chiral = molobj.chiral
      mol.dim_code = molobj.dimcode
      for a in molobj.atom:
         at = chempy.Atom()
         at.symbol = a.symbol
         at.name = a.name
         if a.resn != chempy.Atom.defaults['resn']:
            at.resn = a.resn
         if a.resn_code != chempy.Atom.defaults['resn_code']:
            at.resn_code = a.resn_code
         at.resi = a.resi
         at.resi_number = a.resi_number
         at.b = a.b
         at.q = a.q
         at.alt = a.alt
         at.hetatm = a.hetatm
         if a.segi != chempy.Atom.defaults['segi']:
            at.segi = a.segi
         if a.chain != chempy.Atom.defaults['chain']:
            at.chain = a.chain
         at.color_code = a.color_code
         at.coord = a.coord
         at.formal_charge = a.formal_charge
         at.partial_charge = a.partial_charge
         if a.numeric_type != -99:
            at.numeric_type = a.numeric_type
         if a.text_type != 'UNKNOWN':
            at.text_type = a.text_type
         at.stereo = a.stereo
         if hasattr(a,'flags'):
            at.flags = a.flags
         if hasattr(a,'vdw'):
            at.vdw = a.vdw
         self.atom.append(at)
      for b in molobj.bond:
         bnd = chempy.Bond()
         bnd.index = [b.atom[0],b.atom[1]]
         bnd.order = b.order
         bnd.stereo = b.stereo
         self.bond.append(bnd)
#------------------------------------------------------------------------------
   def sort(self):
      if chempy.feedback['verbose']:
         print " "+__name__+": sorting..."
      if not self.index:
         self.update_index()
      old_index = self.index
      self.atom.sort()      
      self.update_index()
      xref = {}
      new_index = self.index
      for a in new_index.keys():
         xref[old_index[a]] = new_index[a]
      for b in self.bond:
         b.index[0] = xref[b.index[0]]
         b.index[1] = xref[b.index[1]]
      del old_index
      del xref

#------------------------------------------------------------------------------
   def get_internal_tuples(self):
      # generates raw atom sets needed to construct an internal coordinate
      # description of the molecule
      model = self
      # get a connected version too
      cmodel = copy.deepcopy(model).convert_to_connected()
      center = [0.0,0.0,0.0]
      nAtom = model.nAtom
      to_go = nAtom
      done = {}
      if to_go<3:
         z_set = [(0),(1,0)]
      else:
         # get center of molecule
         for a in model.atom:
            center = add(center,a.coord)
         center = scale(center,1.0/nAtom)
         # find most central multivalent atom
         min_a = -1
         c = 0
         for a in model.atom:
            if len(cmodel.bond[c])>1: # must have at least two neighbors
               d = distance(a.coord,center)
               if min_a < 0:
                  min_d = d
                  min_a = c
               elif d<min_d:
                  min_d=d
                  min_a=c
            c = c + 1
         fst = min_a
         # make this our first atom
         z_set = [( fst, )]
         done[fst] = 1
         to_go = to_go - 1
         # for the second atom, try to choose different multivalent neighbor
         nxt = -1
         for b in cmodel.bond[fst]:
            nbr = b.index[0]
            if nbr == fst:
               nbr = b.index[1]
            if len(cmodel.bond[nbr])>1:
               nxt = nbr
               break
         # safety, choose any neighbor
         if nxt<0:
            nbr = b.index[0]
            if nbr == fst:
               nbr = b.index[1]
            nxt = nbr
         z_set.append((nxt,fst))
         done[nxt] = 1
         to_go = to_go - 1
         # for the third atom, choose a different multivalent neighbor
         trd = -1
         for b in cmodel.bond[fst]:
            nbr = b.index[0]
            if nbr == fst:
               nbr = b.index[1]
            if len(cmodel.bond[nbr])>1:
               if not done.has_key(nbr):
                  trd = nbr
                  break
         # safety, choose any unchosen neighbor
         if trd<0:
            for b in cmodel.bond[fst]:
               nbr = b.index[0]
               if nbr == fst:
                  nbr = b.index[1]
               if not done.has_key(nbr):
                  trd = nbr
                  break
         z_set.append((trd,fst,nxt))
         done[trd] = 1
         result = 1
         to_go = to_go - 1
         if to_go:
            # now find all torsions in the molecule
            tors = {}
            for b in model.bond: # use bond as center of torsion
               a1 = b.index[0]
               a2 = b.index[1]
               for c in cmodel.bond[a1]: 
                  a0 = c.index[0] 
                  if a0 not in (a1,a2): # outside atom
                     for d in cmodel.bond[a2]:
                        a3 = d.index[0] 
                        if a3 not in (a0,a1,a2): # outside atom
                           if a0 < a3:
                              to = (a0,a1,a2,a3)
                           else:
                              to = (a3,a2,a1,a0)                        
                           tors[to] = 1
                        a3 = d.index[1] 
                        if a3 not in (a0,a1,a2): # outside atom
                           if a0 < a3:
                              to = (a0,a1,a2,a3)
                           else:
                              to = (a3,a2,a1,a0)
                           tors[to] = 1
                  a0 = c.index[1] 
                  if a0 not in (a1,a2): # outside atom
                     for d in cmodel.bond[a2]:
                        a3 = d.index[0] 
                        if a3 not in (a0,a1,a2): # outside atom
                           if a0 < a3:
                              to = (a0,a1,a2,a3)
                           else:
                              to = (a3,a2,a1,a0)                        
                           tors[to] = 1
                        a3 = d.index[1] 
                        if a3 not in (a0,a1,a2): # outside atom
                           if a0 < a3:
                              to = (a0,a1,a2,a3)
                           else:
                              to = (a3,a2,a1,a0)                        
                           tors[to] = 1
            if len(tors.keys()):
               # choose remaining atoms based on existing atoms using torsion
               while to_go:
                  for tor in tors.keys():
                     a0 = tor[0]
                     a1 = tor[1]
                     a2 = tor[2]
                     a3 = tor[3]
                     dh0 = done.has_key(a0)
                     dh1 = done.has_key(a1)
                     dh2 = done.has_key(a2)
                     dh3 = done.has_key(a3)
                     if ( (not dh0) and dh1 and dh2 and dh3 ):
                        z_set.append((a0,a1,a2,a3))
                        done[a0] = 1
                        to_go = to_go - 1
                     elif ( dh0 and dh1 and dh2 and (not dh3) ):
                        z_set.append((a3,a2,a1,a0))
                        done[a3] = 1
                        to_go = to_go - 1
            else: # for molecules with no torsions (dichloromethane, etc.)
               # we have to generate torsions which include one virtual
               # bond
               for b in cmodel.bond[fst]:
                  nbr = b.index[0]
                  if nbr in [fst,nxt,trd]:
                     nbr = b.index[1]
                  if not done.has_key(nbr):
                     z_set.append((nbr,trd,fst,nxt))
                     to_go = to_go - 1
                     done[nbr] = 1
      return z_set
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
class Connected(Base):

   attr_value = {
      'nAtom' : compile('len(self.atom)','Connected','eval'),
      }

   def __getattr__(self,attr):
      if Connected.attr_value.has_key(attr):
         return eval(Connected.attr_value[attr])
      else:
         raise AttributeError(attr)
      
#------------------------------------------------------------------------------
   def __init__(self):
      self.reset()
  
#------------------------------------------------------------------------------
   def reset(self):
      self.index = None
      self.molecule = chempy.Molecule()
      self.atom = []
      self.bond = []
      
#------------------------------------------------------------------------------
   def convert_to_indexed(self):
      if chempy.feedback['verbose']:
         print " "+str(self.__class__)+": converting to indexed model..."
      indexed = Indexed()
      indexed.atom = self.atom
      indexed.molecule = self.molecule
      c = 0 
      for a in self.bond:
         for b in a:
            if b.index[0] == c:
               indexed.bond.append(b)
         c = c + 1
      self.reset()
      return indexed

#------------------------------------------------------------------------------
   def insert_atom(self,index,atom):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+': inserting atom "%s" before %d.' % (
            atom.name,index)

      nAtom=self.nAtom
      self.atom.insert(index,atom)
      
# re-index bond table
      for a in self.bonds:
         for b in a:
            if b.index[0] >= index:
               b.index[0] = b.index[0] + 1
            if b.index[1] >= index:
               b.index[1] = b.index[1] + 1

# update index if it exists
      if self.index:
         idx = self.index
         for k in idx.keys():
            if idx[k] >= index:
               idx[k] = idx[k] + 1
         idx[id(atom)] = index

#------------------------------------------------------------------------------
   def delete_atom(self,index):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+": deleting atom %d." % index

      nAtom=self.nAtom

# update index if it exists
      if self.index:
         idx = self.index
         for k in idx.keys():
            if idx[k] > index:
               idx[k] = idx[k] - 1
         del idx[id(self.atom[index])]

# delete atom
      del self.atom[index]

# delete bonds associated with this atom

      nBond = len(self.bond)

      for a in self.bond:
         i = 0
         templist = []
         for b in a:
            if index in b.index:
               templist.append(i)
            i = i + 1
         for i in range(len(templist)):
            j = templist[i] - i
            del a[j]

# re-index bond table
      for b in self.bond:
         if b.index[0] > index: 
            b.index[0] = b.index[0] - 1
         if b.index[1] > index: 
            b.index[1] = b.index[1] - 1

#------------------------------------------------------------------------------
   def add_atom(self,atom):
      if chempy.feedback['atoms']:
         print " "+str(self.__class__)+': adding atom "%s".' % atom.name
      self.atom.append(atom)
      self.bond.append([])
      index = self.nAtom - 1
      if self.index:
         self.index[id(atom)] = index
      return index

#------------------------------------------------------------------------------
   def sort(self):
      if chempy.feedback['verbose']:
         print " "+__name__+": sorting..."
      if not self.index:
         self.update_index()
      old_index = self.index
      self.atom.sort()      
      self.update_index()
      xref = {}
      new_index = self.index
      for a in new_index.keys():
         xref[old_index[a]] = new_index[a]
      new_bond = [None] * self.nAtom
      c = 0
      tmp_list = []
      for a in self.bond:
         for b in a:
            if c==b.index[0]:
               tmp_list.append(b)
         new_bond[xref[c]] = a
         c = c + 1
      for b in tmp_list:
         b.index[0] = xref[b.index[0]]
         b.index[1] = xref[b.index[1]]
      del self.bond
      self.bond = new_bond
      del old_index
      del xref
      




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