Logo Search packages:      
Sourcecode: pymol version File versions  Download package

amber.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:
#-* Scott Dixon, Metaphorics, LLC
#-* 
#-*
#Z* -------------------------------------------------------------------

from chempy import feedback

import string
import copy

default_extra = { # atomic number, and normal valency (for tinker)
   # NOTE: THIS SET IS ONLY USED IF THERE ARE NO TINKER RECORDS
   # IN THE PARAMETER FILE
   # bromine 
   'BR' : [                 35 ,               1 ],
   # carbon                           
   'C'  : [                  6 ,               3 ],
   'CA' : [                  6 ,               3 ],
   'CB' : [                  6 ,               3 ],
   'CC' : [                  6 ,               3 ],
   'CF' : [                  6 ,               3 ],
   'CK' : [                  6 ,               3 ],
   'CM' : [                  6 ,               3 ],
   'CN' : [                  6 ,               3 ],
   'CQ' : [                  6 ,               3 ],
   'CR' : [                  6 ,               3 ],
   'CT' : [                  6 ,               4 ],
   'CV' : [                  6 ,               3 ],
   'CW' : [                  6 ,               3 ], 
   'CY' : [                  6 ,               2 ],
   'CX' : [                  6 ,               2 ],
   'C5' : [                  6 ,               3 ],
   'C*' : [                  6 ,               3 ],
   # calcium
   'C0' : [                 20 ,               3 ],
   # chloride
   'Cl' : [                 17 ,               1 ], 
   # fluorine
   'F'  : [                  9 ,               1 ],
   # hydrogen
   'H'  : [                  1 ,               1 ],
   'H1' : [                  1 ,               1 ],
   'H2' : [                  1 ,               1 ],
   'H3' : [                  1 ,               1 ],
   'H4' : [                  1 ,               1 ],
   'H5' : [                  1 ,               1 ],
   'HA' : [                  1 ,               1 ],
   'HC' : [                  1 ,               1 ],
   'HO' : [                  1 ,               1 ],
   'HP' : [                  1 ,               1 ],
   'HS' : [                  1 ,               1 ],
   'HW' : [                  1 ,               2 ],
   # iodine
   'I'  : [                 53 ,               1 ],
   # chloride anion
   'IM' : [                 17 ,               0 ],
   # sodium cation
   'IP' : [                 11 ,               0 ],
   # magnesium
   'MG' : [                 12 ,               0 ],
   # nitrogen
   'N'  : [                  7 ,               3 ],
   'N*' : [                  7 ,               2 ],
   'N2' : [                  7 ,               3 ],
   'N3' : [                  7 ,               4 ],
   'NA' : [                  7 ,               3 ],
   'NB' : [                  7 ,               2 ],
   'NC' : [                  7 ,               2 ],
   'NX' : [                  7 ,               2 ],
   'NZ' : [                  7 ,               3 ],
   #
   'OW' : [                  8 ,               2 ],
   'OH' : [                  8 ,               2 ],
   'OS' : [                  8 ,               2 ],
   'O'  : [                  8 ,               1 ],
   'O2' : [                  8 ,               1 ],
   'OM' : [                  8 ,               1 ],
   'OZ' : [                  8 ,               1 ],   
   'P'  : [                 15 ,               4 ],
   'S'  : [                 16 ,               2 ],
   'SO'  : [                16 ,               4 ],
   'SX'  : [                16 ,               2 ],
   'SH' : [                 16 ,               2 ],
   # copper
   'CU' : [                 29 ,               0 ],
   # iron
   'FE' : [                 26 ,               0 ],
   # lithium
   'Li' : [                  3 ,               0 ],
   # potassium
   'K'  : [                 19 ,               0 ],
   # rubidium
   'Rb' : [                 37 ,               0 ],
   # cesium
   'Cs' : [                 55 ,               0 ],
   # calcium (alternate)
   'Ca' : [                 20 ,               0 ],
   # dummy
   'X ' : [                  6 ,               1 ],
   # zinc
   'Z0' : [                 30 ,               0 ],
   'Z4' : [                 30 ,               4 ],
   'Z5' : [                 30 ,               5 ],
   }

class Parameters:

   def __init__(self,fname):
      if feedback['actions']:
         print ' '+str(self.__class__)+': loading from "%s"...' % fname
      f = open(fname)
      # skip
      l = f.readline()
      # read names & molecular weights
      self.type = []
      self.mw = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a2 = string.strip(l[0:2])
         self.type.append(a2)
         self.mw[a2] = [float(l[3:13]),string.strip(l[34:])]
      # skip 1
      l = f.readline()
      # read bonds
      self.bond = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a5 = l[0:5]
         self.bond[a5] = [float(l[5:12]),float(l[12:22]),
                          string.strip(l[22:])]
      # read angles
      self.angle = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a5 = l[0:8]
         self.angle[a5] = [float(l[8:16]),float(l[16:28]),
                          string.strip(l[28:])]
      # read torsion 
      self.torsion = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a5 = l[0:11]
         if self.torsion.has_key(a5):
            self.torsion[a5].extend(
               [int(l[11:15]),
                float(l[15:27]),
                float(l[27:36]),
                abs(int(float(l[40:52]))),
                string.strip(l[52:])])
         else:
            self.torsion[a5] = [int(l[11:15]),
                                float(l[15:27]),
                                float(l[27:36]),
                                abs(int(float(l[40:52]))),
                                string.strip(l[52:])]
      # read impropers
      self.improper = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a5 = l[0:11]
         self.improper[a5] = [float(l[15:27]),
                              float(l[27:40]),
                              abs(int(float(l[40:51]))),
                              string.strip(l[51:])]
      # skip
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
      # read vdw equivalents 
      self.vdw_eq = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         a4 = string.strip(l[0:4])
         l = l[4:]
         while len(l):
            self.vdw_eq[string.strip(l[0:4])] = a4
            l = l[4:]
      # skip
      l = string.strip(f.readline())
      # read vdw parameters
      self.vdw = {}
      while 1:
         l = string.strip(f.readline())
         if not len(l): break
         l = '  ' + l
         a4 = string.strip(l[0:4])
         self.vdw[a4] =  [float(l[4:20]),
                          float(l[20:37]),
                          string.strip(l[37:])]
         
      # read extra tinker information if present
      self.extra = {}
      while 1:
         l = f.readline()
         if not l: break
         if l[0:6] == 'TINKER':
            self.extra[string.strip(l[6:12])]  = [
               int(l[12:18]),
               int(l[18:24])]
      if not len(self.extra.keys()):
            self.extra = default_extra
      # now generate redundant equivalents
      for a in self.vdw_eq.keys():
         self.vdw[a] = self.vdw[self.vdw_eq[a]]
      for a in self.bond.keys():
         k = a[3:5]+'-'+a[0:2]
         self.bond[k] = self.bond[a]
      for a in self.angle.keys():
         k = a[6:8]+'-'+a[3:5]+'-'+a[0:2]
         self.angle[k] = self.angle[a]
         
   def dump(self):
      for b in self.type:
         print b
      kees = self.mw.keys()
      kees.sort()
      for b in kees:
         print b,self.mw[b]
      kees = self.vdw_eq.keys()
      kees.sort()
      for b in kees:
         print b,self.vdw_eq[b]
      kees = self.vdw.keys()
      kees.sort()
      for b in kees:
         print b,self.vdw[b]
      kees = self.bond.keys()
      kees.sort()
      for b in kees:
         print b,self.bond[b]
      kees = self.angle.keys()
      kees.sort()
      for b in kees:
         print b,self.angle[b]
      kees = self.torsion.keys()
      kees.sort()
      for b in kees:
         print b,self.torsion[b]
      kees = self.improper.keys()
      kees.sort()
      for b in kees:
         print b,self.improper[b]
      kees = self.vdw.keys()
      kees.sort()
      for b in kees:
         print b,self.vdw[b]
         

class Topology:

   def __init__(self,model):
      self.model = model
      if feedback['actions']:
         print ' '+str(self.__class__)+': searching...'
      # get a connected version too
      cmodel = copy.deepcopy(model).convert_to_connected()
      # find atom types in molecule
      self.present = {}
      for a in model.atom:
         self.present[a.text_type] = 1
      # copy bonds
      self.bond = {}
      for b in model.bond:
         a0 = b.index[0]
         a1 = b.index[1]
         if a0 < a1:
            self.bond[(a0,a1)] = 1
         else:
            self.bond[(a1,a0)] = 1
      # find angles
      self.angle = {}
      ang = self.angle
      for b in model.bond:
         a0 = b.index[0]
         a1 = b.index[1]
         for c in cmodel.bond[a0]: # a0 in center
            a2 = c.index[0] 
            if a2 not in (a0,a1): # outside atom
               if a1 < a2:
                  an = (a1,a0,a2)
               else:
                  an = (a2,a0,a1)                  
               ang[an] = 1
            a2 = c.index[1]
            if a2 not in (a0,a1): # outside atom
               if a1 < a2:
                  an = (a1,a0,a2)
               else:
                  an = (a2,a0,a1)                  
               ang[an] = 1
         for c in cmodel.bond[a1]: # a1 in center
            a2 = c.index[0] 
            if a2 not in (a0,a1): # outside atom
               if a0 < a2:
                  an = (a0,a1,a2)
               else:
                  an = (a2,a1,a0)                  
               ang[an] = 1
            a2 = c.index[1]
            if a2 not in (a0,a1): # outside atom
               if a0 < a2:
                  an = (a0,a1,a2)
               else:
                  an = (a2,a1,a0)                  
               ang[an] = 1
      # find torsions
      self.torsion = {}
      tors = self.torsion
      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
      # find impropers (only autogenerates for atoms with 3 bonds)
      self.improper = {}
      impr = self.improper
      a2 = 0
      for a in model.atom: # a2 is the center atom 
         bnd = cmodel.bond[a2]
         if len(bnd) == 3:
            lst = []
            for b in bnd:
               at = b.index[0]
               if at == a2:
                  at = b.index[1]
               lst.append(at)
            lst.sort()
            impr[(lst[0],lst[1],a2,lst[2])] = 1
         a2 = a2 + 1
         
      if feedback['actions']:
         print ' '+str(self.__class__)+': found:'
         print ' '+str(self.__class__)+':    types       %6d' % (
            len(self.present.keys()))
         print ' '+str(self.__class__)+':    bonds       %6d' % (
            len(self.bond.keys()))
         print ' '+str(self.__class__)+':    angles      %6d' % (
            len(self.angle.keys()))
         print ' '+str(self.__class__)+':    torsions    %6d' % (
            len(self.torsion.keys()))
         print ' '+str(self.__class__)+':    impropers   %6d' % (
            len(self.improper.keys()))

   def dump(self):
      kees = self.present.keys()
      kees.sort()
      for b in kees:
         print b
      kees = self.bond.keys()
      kees.sort()
      for b in kees:
         print b
      kees = self.angle.keys()
      kees.sort()
      for b in kees:
         print b
      kees = self.torsion.keys()
      kees.sort()
      for b in kees:
         print b
      kees = self.improper.keys()
      kees.sort()
      for b in kees:
         print b

   def get_list(self):
      return [self.bond.keys(),
              self.angle.keys(),
              self.torsion.keys(),
              self.improper.keys()]

class Subset:
   
   def __init__(self,par,top):
      if feedback['actions']:
         print ' '+str(self.__class__)+': applying parameter set to topology...'
      self.model = top.model
      self.present = copy.deepcopy(top.present)
      atype = []
      for a in self.model.atom:
         atype.append(a.text_type)
      # extra tinker info (atomic number, valency)
      self.miss_extra = []
      self.extra = {}
      s_extra = self.extra
      present = top.present
      p_extra = par.extra
      for kee in present.keys():
         if p_extra.has_key(kee):
            s_extra[kee] = p_extra[kee]
         else:
            self.miss_extra.append(kee)
      # molecular weight
      self.miss_mw = []
      self.mw = {}
      s_mw = self.mw
      present = top.present
      p_mw = par.mw
      for kee in present.keys():
         if p_mw.has_key(kee):
            s_mw[kee] = p_mw[kee]
         else:
            self.miss_mw.append(kee)
            
      # van der waals
      self.miss_vdw = []
      self.vdw = {}
      s_vdw = self.vdw
      present = top.present
      p_vdw = par.vdw
      for kee in present.keys():
         if p_vdw.has_key(kee):
            s_vdw[kee] = p_vdw[kee]
         else:
            self.miss_vdw.append(kee)
      # bonds
      self.miss_bond = []
      self.bond = {}
      s_bond = self.bond
      bond = top.bond
      p_bond = par.bond
      for a in bond.keys():
         kee = "%-2s-%-2s" % (atype[a[0]],atype[a[1]])
         if p_bond.has_key(kee):
            s_bond[kee] = p_bond[kee]
         else:
            self.miss_bond.append((a,kee))
      # angles
      self.miss_angle = []
      self.angle = {}
      s_angle = self.angle
      angle = top.angle
      p_angle = par.angle
      for a in angle.keys():
         kee = "%-2s-%-2s-%-2s" % (atype[a[0]],atype[a[1]],atype[a[2]])
         if p_angle.has_key(kee):
            s_angle[kee] = p_angle[kee]
         else:
            self.miss_angle.append((a,kee))
      # torsions      
      self.miss_torsion = []
      self.torsion = {}
      s_torsion = self.torsion
      torsion = top.torsion
      p_torsion = par.torsion
      for a in torsion.keys():
         at0=atype[a[0]]
         at1=atype[a[1]]
         at2=atype[a[2]] # center atom
         at3=atype[a[3]]
         while 1: # not a real loop, just "else" avoidance
            kee1 = "%-2s-%-2s-%-2s-%-2s" % (at0,at1,at2,at3)
            if p_torsion.has_key(kee1):
               s_torsion[kee1] = p_torsion[kee1]
               break
            kee2 = "%-2s-%-2s-%-2s-%-2s" % (at3,at2,at1,at0)
            if p_torsion.has_key(kee2):
               s_torsion[kee2] = p_torsion[kee2]
               break
            kee = "X -%-2s-%-2s-X " % (at1,at2)
            if p_torsion.has_key(kee):
               s_torsion[kee1] = p_torsion[kee]
               break
            kee = "X -%-2s-%-2s-X " % (at2,at1)
            if p_torsion.has_key(kee): 
               s_torsion[kee2] = p_torsion[kee]
               break
            self.miss_torsion.append((a,kee1))
            break
      # impropers      
      self.miss_improper = []
      self.improper = {}
      s_improper = self.improper
      improper = top.improper
      p_improper = par.improper
      for a in improper.keys():
         at0=atype[a[0]]
         at1=atype[a[1]]
         at2=atype[a[2]] # center atom
         at3=atype[a[3]]
         while 1: # not a real loop, just "else" avoidance

            kee1 = "%-2s-%-2s-%-2s-%-2s" % (at1,at3,at2,at0)
            if p_improper.has_key(kee1):
               s_improper[kee1] = p_improper[kee1]
               break
            kee2 = "%-2s-%-2s-%-2s-%-2s" % (at3,at1,at2,at0)
            if p_improper.has_key(kee2):
               s_improper[kee2] = p_improper[kee2]
               break

            kee3 = "%-2s-%-2s-%-2s-%-2s" % (at0,at3,at2,at1)
            if p_improper.has_key(kee3):
               s_improper[kee3] = p_improper[kee3]
               break
            kee4 = "%-2s-%-2s-%-2s-%-2s" % (at3,at0,at2,at1)
            if p_improper.has_key(kee4):
               s_improper[kee4] = p_improper[kee4]
               break

            kee5 = "%-2s-%-2s-%-2s-%-2s" % (at0,at1,at2,at3)
            if p_improper.has_key(kee5):
               s_improper[kee5] = p_improper[kee5]
               break
            kee6 = "%-2s-%-2s-%-2s-%-2s" % (at1,at0,at2,at3)
            if p_improper.has_key(kee6):
               s_improper[kee6] = p_improper[kee6]
               break

            kee = "X -%-2s-%-2s-%-2s" % (at3,at2,at0)
            if p_improper.has_key(kee):
               s_improper[kee1] = p_improper[kee]
               break
            kee = "X -%-2s-%-2s-%-2s" % (at1,at2,at0)
            if p_improper.has_key(kee):
               s_improper[kee2] = p_improper[kee]
               break
            kee = "X -%-2s-%-2s-%-2s" % (at3,at2,at1)
            if p_improper.has_key(kee):
               s_improper[kee3] = p_improper[kee]
               break
            kee = "X -%-2s-%-2s-%-2s" % (at0,at2,at1)
            if p_improper.has_key(kee):
               s_improper[kee4] = p_improper[kee]
               break
            kee = "X -%-2s-%-2s-%-2s" % (at1,at2,at3)
            if p_improper.has_key(kee):
               s_improper[kee5] = p_improper[kee]
               break
            kee = "X -%-2s-%-2s-%-2s" % (at0,at2,at3)
            if p_improper.has_key(kee):
               s_improper[kee6] = p_improper[kee]
               break

            kee = "X -X -%-2s-%-2s" % (at2,at0)
            if p_improper.has_key(kee):
               s_improper[kee1] = p_improper[kee]
               break
            kee = "X -X -%-2s-%-2s" % (at2,at1)
            if p_improper.has_key(kee):
               s_improper[kee3] = p_improper[kee]
               break
            kee = "X -X -%-2s-%-2s" % (at2,at3)
            if p_improper.has_key(kee):
               s_improper[kee5] = p_improper[kee]
               break
            self.miss_improper.append((a,kee1))
            break

      if feedback['actions']:
         print ' '+str(self.__class__)+': missing:'
         print ' '+str(self.__class__)+':    mol. wts.         %6d' % (
            len(self.miss_mw))
         print ' '+str(self.__class__)+':    vdw               %6d' % (
            len(self.miss_vdw))
         print ' '+str(self.__class__)+':    bonds             %6d' % (
            len(self.miss_bond))
         print ' '+str(self.__class__)+':    angles            %6d' % (
            len(self.miss_angle))
         print ' '+str(self.__class__)+':    torsions          %6d' % (
            len(self.miss_torsion))
         print ' '+str(self.__class__)+':    impropers         %6d (usually okay)' % (
            len(self.miss_improper))
         print ' '+str(self.__class__)+':    extra tinker info %6d' % (
            len(self.miss_extra))
      
   def dump(self):
      kees = self.mw.keys()
      kees.sort()
      for b in kees:
         print b,self.mw[b]
      kees = self.bond.keys()
      kees.sort()
      for b in kees:
         print b,self.bond[b]
      kees = self.angle.keys()
      kees.sort()
      for b in kees:
         print b,self.angle[b]
      kees = self.torsion.keys()
      kees.sort()
      for b in kees:
         print b,self.torsion[b]
      kees = self.improper.keys()
      kees.sort()
      for b in kees:
         print b,self.improper[b]
      kees = self.vdw.keys()
      kees.sort()
      for b in kees:
         print b,self.vdw[b]

   def dump_missing(self,impropers=0):
      if len(self.miss_mw):
         print ' '+str(self.__class__)+': missing molecular weights...'
      for b in self.miss_mw:
         print " ",b
      if len(self.miss_vdw):
         print ' '+str(self.__class__)+': missing van der Waalss...'
      for b in self.miss_vdw:
         print " ",b
      if len(self.miss_bond):
         print ' '+str(self.__class__)+': missing bonds...'
      for b in self.miss_bond:
         print " ",b
      if len(self.miss_angle):
         print ' '+str(self.__class__)+': missing angless...'
      for b in self.miss_angle:
         print " ",b
      if len(self.miss_torsion):
         print ' '+str(self.__class__)+': missing torsions...'
      for b in self.miss_torsion:
         print " ",b
      if impropers:
         if len(self.miss_improper):
            print ' '+str(self.__class__)+': missing impropers...'
         for b in self.miss_improper:
            print " ",b

   def complete(self):
      if not ( len(self.miss_mw) or
               len(self.miss_vdw) or
               len(self.miss_bond) or
               len(self.miss_angle) or
               len(self.miss_torsion) ):
         return 1
      else:
         return 0

   def assign_types(self):
      c = 0
      self.mapping = {}
      map = self.mapping
      kees = self.present.keys()
      label = []
      type = []
      kees.sort()
      for a in kees:
         c = c + 1
         st = str(c)
         label.append(st)
         type.append(a)
         map[a] = st
      # assign numeric types 
      for a in self.model.atom:
         a.numeric_type = map[a.text_type]
      
   def write_tinker_prm(self,fname,proofread=None,smooth=None):
      c = 0
      self.mapping = {}
      map = self.mapping
      kees = self.present.keys()
      label = []
      type = []
      kees.sort()
      if proofread:
         for a in kees:
            label.append(a)
            type.append(a)
            map[a] = a
      else:
         for a in kees:
            c = c + 1
            st = str(c)
            label.append(st)
            type.append(a)
            map[a] = st
      # assign numeric types as per the parameter we're writing
      for a in self.model.atom:
         a.numeric_type = map[a.text_type]
      f = open(fname,'w')
      if smooth:
         f.write('''
forcefield              SMOOTH AMBER
vdwtype                 GAUSSIAN
gausstype               LJ-2
''')
      else:
         f.write('''
forcefield              AMBER95
vdwtype                 LENNARD-JONES
''')
      f.write('''
radiusrule              ARITHMETIC
radiustype              R-MIN
radiussize              RADIUS
epsilonrule             GEOMETRIC
vdw-14-use
vdw-scale               2.0
chg-14-use
chg-scale               1.2
dielectric              1.0
''')

      # types
      for c in range(len(self.present)):
         at = type[c]
         f.write("atom %6s %6s    %-2s      %-25s %3d %10.3f%6d\n" % (
            label[c],label[c],at,'"'+self.mw[at][1][0:23]+'"',
            self.extra[at][0],
            self.mw[at][0],self.extra[at][1]))
      # van der waals
      for c in range(len(self.present)):
         at = type[c]
         f.write("vdw   %8s          %10.4f %10.4f\n" % (
            map[at],self.vdw[at][0],self.vdw[at][1]))
      # bonds
      bond = {}
      for a in self.bond.keys():
         kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
         bond[kee] = a
      kees = bond.keys()
      kees.sort()
      for a in kees:
         kee = bond[a]
         f.write("bond    %6s%5s     %10.1f %10.4f\n" % (
            a[0],a[1],self.bond[kee][0],self.bond[kee][1]))
      # angles
      angle = {}
      for a in self.angle.keys():
         kee = (map[string.strip(a[0:2])],
                map[string.strip(a[3:5])],
                map[string.strip(a[6:8])],                
                )
         angle[kee] = a
      kees = angle.keys()
      kees.sort()
      for a in kees:
         kee = angle[a]
         f.write("angle    %5s%5s%5s%9.2f    %8.2f\n" % (
            a[0],a[1],a[2],self.angle[kee][0],self.angle[kee][1]))
      # impropers
      if not smooth:
         improper = {}
         for a in self.improper.keys():
            kee = (map[string.strip(a[0:2])],
                   map[string.strip(a[3:5])],
                   map[string.strip(a[6:8])],
                   map[string.strip(a[9:11])],                                
                   )
            improper[kee] = a
         kees = improper.keys()
         kees.sort()
         for a in kees:
            kee = improper[a]
            f.write("imptors  %5s%5s%5s%5s     %10.3f%7.1f%3d\n" % (
               a[0],a[1],a[2],a[3],self.improper[kee][0],
               self.improper[kee][1],self.improper[kee][2]))
      else:
         improper = {}
         for a in self.improper.keys():
            kee = (map[string.strip(a[0:2])],
                   map[string.strip(a[3:5])],
                   map[string.strip(a[6:8])],
                   map[string.strip(a[9:11])],                                
                   )
            improper[kee] = a
         kees = improper.keys()
         kees.sort()
         for a in kees:
            kee = improper[a]
            f.write("improper %5s%5s%5s%5s      %10.2f       0.00\n" % (
               a[2],a[0],a[1],a[3],self.improper[kee][0]*3.5))
      # torsions
      torsion = {}
      for a in self.torsion.keys():
         kee = (map[string.strip(a[0:2])],
                map[string.strip(a[3:5])],
                map[string.strip(a[6:8])],
                map[string.strip(a[9:11])],                                
                )
         torsion[kee] = a
      kees = torsion.keys()
      kees.sort()
      for a in kees:
         kee = torsion[a]
         st = "torsion  %5s%5s%5s%5s     " % (
            a[0],a[1],a[2],a[3])
         lst = self.torsion[kee]
         div = lst[0]
         lst = lst[1:]
         while len(lst):
            st = st + "%10.3f%7.1f%3d  " % (
               lst[0]/div,lst[1],lst[2])
            lst = lst[5:]
         while len(st)>79:
            st = string.replace(st,'  ',' ')
         f.write(st+"\n")
      # null charge records
      for c in range(len(self.present)):
         a = label[c]
         f.write("charge  %6s    %10.4f\n" % (a,0.0))
      f.close()


   def get_list(self):
      list = []
      c = 0
      self.mapping = {}
      map = self.mapping
      kees = self.present.keys()
      label = []
      type = []
      kees.sort()
      for a in kees:
         c = c + 1
         st = str(c)
         type.append(a)
         map[a] = c
      # assign numeric types as per the parameter we're writing
      for a in self.model.atom:
         a.numeric_type = map[a.text_type]
      # types
      typ_list = []
      for c in range(len(self.present)):
         at = type[c]
         typ_list.append((map[at],self.extra[at][0],self.mw[at][0],self.extra[at][1]))
      list.append(typ_list)
      # van der waals
      vdw_list = []
      for c in range(len(self.present)):
         at = type[c]
         vdw_list.append((map[at],self.vdw[at][0],self.vdw[at][1]))
      list.append(vdw_list)
      # bonds
      bnd_list = []
      bond = {}
      for a in self.bond.keys():
         kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
         bond[kee] = a
      kees = bond.keys()
      kees.sort()
      for a in kees:
         kee = bond[a]
         bnd_list.append((a[0],a[1],self.bond[kee][0],self.bond[kee][1]))
      list.append(bnd_list)
      # angles
      ang_list = []
      angle = {}
      for a in self.angle.keys():
         kee = (map[string.strip(a[0:2])],
                map[string.strip(a[3:5])],
                map[string.strip(a[6:8])],                
                )
         angle[kee] = a
      kees = angle.keys()
      kees.sort()
      for a in kees:
         kee = angle[a]
         ang_list.append((a[0],a[1],a[2],self.angle[kee][0],self.angle[kee][1]))
      list.append(ang_list)
      # impropers
      imp_list = []
      improper = {}
      for a in self.improper.keys():
         kee = (map[string.strip(a[0:2])],
                map[string.strip(a[3:5])],
                map[string.strip(a[6:8])],
                map[string.strip(a[9:11])],                                
                )
         improper[kee] = a
      kees = improper.keys()
      kees.sort()
      for a in kees:
         kee = improper[a]
         imp_list.append((a[0],a[1],a[2],a[3],self.improper[kee][0],
            self.improper[kee][1],self.improper[kee][2]))
      list.append(imp_list)
      # torsions
      tor_list = []
      torsion = {}
      for a in self.torsion.keys():
         kee = (map[string.strip(a[0:2])],
                map[string.strip(a[3:5])],
                map[string.strip(a[6:8])],
                map[string.strip(a[9:11])],                                
                )
         torsion[kee] = a
      kees = torsion.keys()
      kees.sort()
      for a in kees:
         kee = torsion[a]
         tor = [ a[0],a[1],a[2],a[3] ]
         lst = self.torsion[kee]
         div = lst[0]
         lst = lst[1:]
         while len(lst):
            tor.extend([lst[0]/div,lst[1],lst[2]])
            lst = lst[5:]
         tor_list.append(tor)
      list.append(tor_list)
      return list

Generated by  Doxygen 1.6.0   Back to index