NumericPDB.py :  » Development » PyObjC » trunk » pyobjc » PyOpenGL-2.0.2.01 » OpenGL » Demo » dek » OglSurface » Python Open Source

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Python Open Source » Development » PyObjC 
PyObjC » trunk » pyobjc » PyOpenGL 2.0.2.01 » OpenGL » Demo » dek » OglSurface » NumericPDB.py
# This is statement is required by the build system to query build info
if __name__ == '__build__':
  raise Exception

import sys
import os
import string
import Numeric
import Geometry
import copy

GUAAtoms = [ "N2", "O6", "C6", "C5", "N7", "C8", "N9", "C4", "N3", "C2", "N1" ]

def rotmat(phi, theta, psi, tx=0, ty=0, tz=0):

  s1 = Numeric.sin(phi)
  s2 = Numeric.sin(theta)
  s3 = Numeric.sin(psi)
  c1 = Numeric.cos(phi)
  c2 = Numeric.cos(theta)
  c3 = Numeric.cos(psi)

  newmat = Numeric.array([
    [ c2*c3, s2*s1*c3 - c1*s3, s2*c1*c3 + s1*s3, 0],
    [ c2*s3, s2*s1*s3 + c1*c3, s2*c1*s3 - s1*c3, 0],
    [-s2, c2*s1, c2*c1, 0],
    [tx, ty, tz, 1]])

  return newmat

def matrix_apply(crd, mat):
  o = [crd[0], crd[1], crd[2], 1.0]
  n = [0.0, 0.0, 0.0, 0.0]

  for i in range(4):
    for j in range(4):
      n[i] = n[i] + o[j] * mat[j][i]
      
  new = [None, None, None]
  
  for i in range(3):
    new[i] = (n[i]/n[3])
  return new



class PDBRecord:
  def __init__(self, type=None, anum=None, atom=None, residue=None, chain=None, rnum=None):
    self.type = type
    self.anum = anum
    self.atom = atom
    self.residue = residue
    self.chain = chain
    self.rnum = rnum



class PDB:
  def __init__(self, filename = None, crds = None, records = None, connect = None):
    if crds == None:
      crds = []
    if records == None:
      records = []
    self.records = records
    self.crds = crds
    self.connect = connect

    if filename != None:
      sys.stderr.write("Reading in new PDB %s\n" % filename)
      self.Read(filename)


## note: we read the anum here, which doesn't necessarily correspond to the actual
## record number.
  def Read(self, filename):
    pdbfile = open(filename)
    sys.stderr.write("Opened '%s' for reading as PDB\n" % filename)

    while(1):
      line = pdbfile.readline()

      if line == '':
        break

      if line[0:4] == 'ATOM' or line[0:6] == 'HETATM':
        type = string.strip(line[0:6])
        anum = string.atoi(string.strip(line[7:11]))
        atom = string.strip(line[12:17])
        residue = string.strip(line[17:20])
        chain = string.strip(line[21:22])
        rnum = string.atoi(string.strip(line[23:26]))
        x = string.atof(string.strip(line[31:38]))
        y = string.atof(string.strip(line[39:46]))
        z = string.atof(string.strip(line[47:54]))

        self.records.append(PDBRecord(type, anum, atom, residue, chain, rnum))
        self.crds.append((x,y,z))
        
    
    self.crds = Numeric.array(self.crds)

  def Write(self, filename):
    self.pdbfd=open(filename,"w")
      
    for i in range(len(self.records)):
      record = self.records[i]
      self.pdbfd.write("%-6s%5d %-4s%c%-4s%c%4d%c   %8.3f%8.3f%8.3f\n" % \
               ( record.type, record.anum, record.atom,' ', record.residue,' ', record.rnum, ' ', 
                 self.crds[i][0], self.crds[i][1], self.crds[i][2]))

    self.pdbfd.write("TER\n")

    if self.connect != None:
      for i in self.connect:
        self.pdbfd.write("CONECT")
        for j in i:
          self.pdbfd.write("%5d" % (j+1))
        self.pdbfd.write("\n")

    self.pdbfd.write("END\n")
    self.pdbfd.close()


  def Rotate(self,alpha, beta, gamma, tx, ty, tz):
    r = rotmat(alpha, beta, gamma, tx, ty, tz)
    self.RotateMatrix(r)

  def RotateMatrix(self,r):
    for i in range(len(self.crds)):
      self.crds[i] = matrix_apply(self.crds[i], r)

  def Center(self):
    center = Numeric.add.reduce(self.crds) / len(self.crds)
    self.crds = Numeric.subtract(self.crds, center)

  def Print(self):
    for i in self.records:
      print i.type, i.anum, i.atom, i.residue, i.chain, i.rnum

  def ReturnAnum(self, atom, rnum):
    for i in range(len(self.records)):
      record = self.records[i]
      if record.atom == atom and record.rnum == rnum:
         return i
    sys.stderr.write("Unable to find atom '%s' in residue %d\n" % (atom, rnum))
    return None

  def CrdByName(self, atom, res):
    x = self.ReturnAnum(atom, res)
    if x == None:
      return None
    return self.crds[x]

  def FixResNum(self):
    rnum = 1
    for i in range(len(self.records)):
      newrnum = rnum
      if i < len(self.records)-1 and \
         self.records[i+1].rnum != self.records[i].rnum:
        rnum = rnum + 1
      self.records[i].rnum = newrnum
      self.records[i].anum = i

  def Copy(self):
    crds = Numeric.array(self.crds)
    records = copy.copy(self.records)
    return PDB(None, crds, records)


  def Append(self, struct2):
    records = self.records + copy.copy(struct2.records)
    crds = Numeric.concatenate((self.crds, struct2.crds))

    return PDB(None, crds, records)

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