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Molecule.py
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Molecule.py
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import re
import numpy, random
class Molecule:
def __init__(self, pdbfile, pdbcode=None, includeH=True):
""" Initialise molecule with pdb filename and code (set to pdbfile if missing).
The molecule is read from pdbfile. """
self.initialized = False
self.load (pdbfile, pdbcode, includeH=includeH)
def load(self, pdbfile, pdbcode=None, includeH=True):
""" Load molecule from PDB file pdbfile. pdbcode is set to pdbfile if missing """
self.pdbfile = pdbfile
if pdbcode is None:
self.pdbcode = pdbfile
else:
self.pdbcode = pdbcode
# Does not handle file-not-found exceptions: this is done up-front
f = open (pdbfile, "r")
lines = f.readlines ()
f.close ()
self.atomcoords = []
self.atmnames = []
self.atmsymbols = []
self.resnames = []
self.resnum = []
self.atmkeys = []
self._residueInfo = dict ()
self._residuenames = dict ()
self._atomInfo = []
count = -1
reH = re.compile ('H')
for line in lines:
line = line.strip ()
# Filter for ATOM
if not ((line[0:4] == 'ATOM')): continue
coords = [float (line[30:38]), float (line[38:46]), float (line[46:54])]
name = line[12:16]
symbol = line[13:14]
resname = line[17:20]
resID = int (line[22:26])
# Account for PDB files in which the element symbol is shifted from column 14
# VMD writes such PDB files, ptraj does not
# Fully compliant PDB files should also have the element in columns 77-78
# Option "nowrap" to ptraj's "trajout" command may well control this behaviour
if ((symbol != 'H') and reH.match (name)): symbol = 'H'
if not includeH and (symbol == 'H'): continue
count = count + 1
self.atomcoords.append (coords)
self.atmnames.append (name)
self.atmsymbols.append (symbol)
self.atmkeys.append (0)
self.resnames.append (resname)
self.resnum.append (resID)
self._atomInfo.append (dict (id=count, coords=coords, name=name, symbol=symbol, residue=resID, residue_name=resname,key=0))
if not self._residueInfo.has_key (resID):
self._residueInfo[resID] = dict (id=resID, atomID=[], name=resname)
self._residuenames[resID] = dict (id=resID, name=resname)
self._residueInfo[resID]['atomID'].append (count)
self.nAtoms = len (self.atmnames)
self.nCoords = 3 * self.nAtoms
self.framebytes = (self.nCoords) * 8 + (
self.nCoords / 10 + 1) # Numeric fields + EOL characters (in crd format)
if self.nCoords % 10 == 0: self.framebytes -= 1 # Special case if ncoords exactly divisible by 10
self.moltype = None
self.initialized = True
def numAtoms(self):
""" Returns number of atoms in molecule """
return self.nAtoms
def numCoords(self):
""" Returns number of coordinates in molecule """
return self.nCoords
def numResidues(self):
""" Returns number of residues in molecule """
resIDs = set (self.resnum)
return len (resIDs)
def coordinates(self):
for atom in self._atomInfo:
yield atom["coords"]
def atoms(self):
for atom in self._atomInfo:
yield atom
def getResidueInformation(self, resIDs=None, atomIDs=None):
""" Return residue information for a list of residue IDs or a list of atom IDs
Information returned is dictionary with resID, resName, and list of atomIDs
"""
if resIDs is None:
resIDs = set ()
else:
resIDs = set (resIDs)
if atomIDs is not None:
for i in atomIDs:
resIDs.add (self._atomInfo[i]["residue"])
return self.getResidueInformation (resIDs=resIDs)
resIDs = list (resIDs)
resIDs.sort ()
str=''
for res in resIDs:
str=str+self._residueInfo[res]["name"]
print self._shortenResidue (str)
str = ''
return dict ((resID, self._residueInfo[resID]) for resID in resIDs)
def getAtomInformation(self, resIDs=None, atomIDs=None):
""" Return atom information for a list of residue IDs or a list of atom IDs
Information returned is dictionary with atomID, name, symbol, coords, key and resID
"""
if atomIDs is None:
atomIDs = set ()
else:
atomIDs = set (atomIDs)
if resIDs is not None:
for i in resIDs:
atomIDs.update (self._residueInfo[i]['atomID'])
return self.getAtomInformation (atomIDs=atomIDs)
atomIDs = list (atomIDs)
atomIDs.sort ()
return dict ((atomID, self._atomInfo[atomID]) for atomID in atomIDs)
def __str__(self):
s = ["PDB file %s" % self.pdbfile]
s.append ("Number of atoms: %d" % self.numAtoms ())
s.append ("Number of residues: %d" % self.numResidues ())
return "\n\t".join (s) + "\n"
def __del__(self):
pass
def calc_geom_center(self):
fX = 0.0
fY = 0.0
fZ = 0.0
for coord in self.atomcoords:
fX = fX + coord[0]
fY = fY + coord[1]
fZ = fZ + coord[2]
fX = fX / self.nAtoms
fY = fY / self.nAtoms
fZ = fZ / self.nAtoms
center = (fX, fY, fZ)
return center
def calc_main_axis(self):
""" Calcs sym. (3,3)-matrix of main moment
( sum(y_i**2+z_i**2) sum(-x_i*y_i) sum(-x_i*z_i) )
( sum(-x_i*y_i) sum(x_i**2+z_i**2) sum(-y_i*z_i) )
( sum(-x_i*z_i) sum(-y_i*z_i) sum(x_i**2+y_i**2) )
and determines its eigen vectors.
"""
#Clarify why the above step has been done
c0, c1, c2 = self.calc_geom_center ()
M = numpy.zeros ((3, 3), dtype=float)
M = [[0] * 3, [0] * 3, [0] * 3]
for x in self.atomcoords:
xi = x[0] - c0
yi = x[1] - c1
zi = x[2] - c2
M[0][0] = M[0][0] + xi * xi
M[0][1] = M[0][1] + xi * yi
M[0][2] = M[0][2] + xi * zi
M[1][1] = M[1][1] + yi * yi
M[1][2] = M[1][2] + yi * zi
M[2][2] = M[2][2] + zi * zi
M[1][0] = M[0][1]
M[2][0] = M[0][2]
M[2][1] = M[1][2]
M = numpy.array (M)
d = sum (numpy.diag (M))
M = -M
M[0, 0] = M[0, 0] + d
M[1, 1] = M[1, 1] + d
M[2, 2] = M[2, 2] + d
eigenVals, eigenVecs = numpy.linalg.eig (M)
eigenVecs = eigenVecs.transpose ()
return eigenVecs
def get_transf_matrix(self):
# This function gets out the transformation matrix which is needed to
# transform the main axis of the protein to the x-, y-, z- axis.We use
# this kind of transformation when we want to put our protein within a
# grid which has minimum volume.
main_axis = self.calc_main_axis ()
# aux_mat = zeros((3,3), Float)
# for i in (0,1,2):
# for j in (0,1,2):
# aux_mat[i][j] = main_axis[j][i]
#
# rot_mat = zeros((3,3), Float)
# rot_mat = inverse(aux_mat)
# return rot_mat
return main_axis
def transform_molecule(self, transf_mat):
""" Apply transformation matrix to coordinates of molecule and return transformed coordinates.
The molecule is unchanged. """
#Understand how the transformation is working
transf_molecule = []
for ind in self.atomcoords:
transf_coord = [0.0, 0.0, 0.0]
for i in (0, 1, 2):
transf_coord[0] = transf_coord[0] + transf_mat[0][i] * ind[i]
transf_coord[1] = transf_coord[1] + transf_mat[1][i] * ind[i]
transf_coord[2] = transf_coord[2] + transf_mat[2][i] * ind[i]
transf_molecule.append (transf_coord)
return transf_molecule
# Function will be used for PPIAnalyzer by C. Pfleger
# returns for a given coordinate set (atoms) a list of residue names and residue identifier
def get_res_name_ident(self, list_of_coord): # pragma: no cover
list_of_resi = ['', ''] # residue name / residue identifier
for i in range (len (self.atomcoords)):
coord = self.atomcoords[i]
if coord in list_of_coord: #problemo
print "Bin ich hier?"
akt_res_name = self.resnames[i] # !# Possibly out one indent ..
akt_res_iden = self.resnum[i]
help = [akt_res_name, akt_res_iden]
if help not in list_of_resi:
list_of_resi.extend (help)
help = None
return list_of_resi
def write_transf_molecule(self, filename, transf_coord): # pragma: no cover
file = open (filename, 'w')
atom_number = 0
for ind in transf_coord:
alt_loc = ' '
res_name = self.resnames[atom_number]
chain_id = ' '
res_num = self.resnum[atom_number]
icode = ' '
occupancy = 0.0
temp_factor = 0.0
seg_id = 'XXXX'
ele_symbol = 'XX'
charge = 'XX'
atom_name = self.atmnames[atom_number]
atom_number = atom_number + 1
print self.id
print >> file, ('ATOM %5i %4s%s%3s %s%4i%s %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s') % (
atom_number, atom_name, alt_loc, res_name, chain_id, res_num, icode, ind[0], ind[1], ind[2], occupancy,
temp_factor, seg_id, ele_symbol, charge)
file.close ()
def _shortenResidue(self, str):
d = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q', 'LYS': 'K',
'ILE': 'I', 'PRO': 'P', 'THR': 'T', 'PHE': 'F', 'ASN': 'N',
'GLY': 'G', 'HIS': 'H', 'LEU': 'L', 'ARG': 'R', 'TRP': 'W',
'ALA': 'A', 'VAL': 'V', 'GLU': 'E', 'TYR': 'Y', 'MET': 'M'}
if len (str) % 3 != 0:
raise ValueError ('Input length should be a multiple of three')
y = ''
for i in range (len (str) / 3):
y += d[str[3 * i:3 * i + 3]]
return y