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Sourcecode: pymol version File versions

__init__.py

import chempy
import copy
from chempy.models import Indexed

from Numeric import *
from Precision import *

class FastModel:

#------------------------------------------------------------------------------
   def __init__(self):
      self.reset()

#------------------------------------------------------------------------------
   def reset(self):
      self.nAtom = 0
      self.molecule = chempy.Molecule()
      self.txta = None
      self.inta = None
      self.flta = None
      self.crda = None
      self.bnda = None

#------------------------------------------------------------------------------
   def from_indexed(self,model):
      self.reset()
      self.nAtom = model.nAtom
      self.nBond = model.nBond
      self.molecule = copy.deepcopy(model.molecule)
      self.txta = resize(array(' ','c'),(self.nAtom,as_width))
      self.inta = zeros((self.nAtom,ai_width),Int32)
      self.flta = zeros((self.nAtom,af_width),Float)
      self.bnda = zeros((self.nBond,bi_width),Int32)
      self.crda = zeros((self.nAtom,3),Float)

      c = 0
      for a in model.atom:
         txt = "%-4s%-2s%-1s%-4s%-1s%-4s%-1s%-4s%-20s" % \
               (a.name[0:4],a.symbol[0:2],a.alt[0:1],a.resn[0:4],
                a.resn_code[0:1],a.resi[0:4],a.chain[0:1],
                a.segi[0:4],a.text_type[0:20])
         self.txta[c] = txt
         self.inta[c] = [ a.resi_number, a.hetatm, a.formal_charge,
                          a.flags, a.color_code, a.stereo, a.numeric_type ]
         self.flta[c] = [ a.b, a.q, a.partial_charge, a.vdw ]
         self.crda[c] = [ a.coord[0], a.coord[1], a.coord[2] ]
         c = c + 1

      c = 0
      for b in model.bond:
         self.bnda[c] = [ b.index[0], b.index[1], b.order, b.stereo ]
         c = c + 1

#------------------------------------------------------------------------------
   def convert_to_indexed(self):
      
      model = Indexed()
      model.molecule = copy.deepcopy(self.molecule)
      
      for c in xrange(self.nAtom):
         at = chempy.Atom()
         txta = self.txta[c]

         for attrib in ( 'name', 'symbol', 'resn', 'resn_code', 'resi',
                         'alt', 'chain', 'segi', 'text_type' ):
            ll = as[attrib]
            setattr(at,attrib,string.strip(string.join(txta[ll[0]:ll[1]],'')))

         inta = self.inta[c]
         for attrib in ( 'resi_number', 'hetatm', 'formal_charge','flags',
                         'color_code', 'stereo', 'numeric_type' ):
            setattr(at,attrib,inta[ai[attrib]])

         flta = self.flta[c]
         for attrib in ( 'b', 'q', 'partial_charge' ) :
            setattr(at,attrib,flta[af[attrib]])

         crda = self.crda[c]
         at.coord = [crda[0],crda[1],crda[2]]

         # probably need to add some checking here to eliminate values
         # which come back as defaults
         
         model.atom.append(at)
         
      for c in xrange(self.nBond):
         bnd = chempy.Bond()
         bnda = self.bnda[c]
         bnd.index = [bnda[bi_index0],bnda[bi_index1]]
         bnd.order = bnda[bi_order]
         bnd.stereo = bnda[bi_stereo]
         model.bond.append(bnd)

      return model
   
#------------------------------------------------------------------------------

# text properties

as = {}
as_width = 0

as['name'] = [ as_width ]
as_width = as_width + 4
as['name'].append(as_width)

as['symbol'] = [ as_width ]
as_width = as_width + 2
as['symbol'].append(as_width)

as['alt'] = [ as_width ]
as_width = as_width + 1
as['alt'].append(as_width)

as['resn'] = [ as_width ]
as_width = as_width + 4
as['resn'].append(as_width)

as['resn_code'] = [ as_width ]
as_width = as_width + 1
as['resn_code'].append(as_width)

as['resi'] = [ as_width ]
as_width = as_width + 4
as['resi'].append(as_width)

as['chain'] = [ as_width ]
as_width = as_width + 1
as['chain'].append(as_width)

as['segi' ] = [ as_width ]
as_width = as_width + 4
as['segi'].append(as_width)

as['text_type'] = [ as_width ]
as_width = as_width + 20
as['text_type'].append(as_width)

# integer properties

ai = {}
ai_width = 0
ai['resi_number']    = ai_width
ai_width = ai_width + 1
ai['hetatm']         = ai_width
ai_width = ai_width + 1
ai['formal_charge']  = ai_width
ai_width = ai_width + 1
ai['flags']          = ai_width
ai_width = ai_width + 1
ai['color_code']     = ai_width
ai_width = ai_width + 1
ai['stereo']         = ai_width
ai_width = ai_width + 1
ai['numeric_type']   = ai_width
ai_width = ai_width + 1

# float properties

af = {}
af_width = 0
af['b']              = af_width
af_width = af_width + 1
af['q']              = af_width
af_width = af_width + 1
af['partial_charge'] = af_width
af_width = af_width + 1
af['vdw'] = af_width
af_width = af_width + 1

# bond information

bi_index0         = 0
bi_index1         = 1
bi_order          = 2
bi_stereo         = 3
bi_width          = 4



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