source: src/ReMapDBondFileFromXYZ.py@ 5f612ee

#!/usr/bin/python
#
# Takes two pdb file and a dbond file, matches the coordinates and thus creates a mapping from old ids to new ids.

import sys, random, math, re
wrerr=sys.stderr.write
wrout=sys.stdout.write

# check arguments
if len(sys.argv) < 5:
        print "Usage: "+sys.argv[0]+" <srcPDBfile> <destXYZfile> <offsetID> <offsetXYZ> <srcDBONDfile> [destDBONDfile]" 
        sys.exit(1)

EPSILON=1e-3
CUTOFF=2.
inputsrcPDB = open(sys.argv[1], "r")
inputdestPDB = open(sys.argv[2], "r")
inputsrcDBOND = open(sys.argv[5], "r")
offsetID=int(sys.argv[3])
offsetXYZ=int(sys.argv[4])
if len(sys.argv) > 6:
        output = open(sys.argv[6],"w")
else:
        output = open(sys.argv[5]+".new", "w")

# 1. first parse both PDB files into arrays (id, element, xyz) , therewhile scan BoundaryBoxes
max = [ 0., 0., 0. ]
min = [ 0., 0., 0. ]
x = [ 0., 0., 0. ]
print "Scanning source PDB file"+sys.argv[1]+"."
srcAtoms = []
for line in inputsrcPDB:
        if "#" in line:
                continue
        if "END" in line:
                break
        if "ATOM" in line:
                entries = line.split()
                for n in range(3):
                        x[n] = float(entries[offsetXYZ+n])
                        if x[n] > max[n]:
                                max[n] = x[n]
                        if x[n] < min[n]:
                                min[n] = x[n]
                srcAtoms.append([int(entries[offsetID]), x[0], x[1], x[2]])
inputsrcPDB.close()
print "Scanning destination XYZ file"+sys.argv[2]+"."
destAtoms = []
index = 0
for line in inputdestPDB:
        entries = line.split()
        if (len(entries)<1 or (entries[0]!="O" and entries[0]!="Si" and entries[0]!="Ca")):
                continue
        for n in range(3):
                x[n] = float(entries[1+n])
                if x[n] > max[n]:
                        x[n]-=max[n]
                if x[n] < min[n]:
                        x[n]+=max[n]
        destAtoms.append([index, x[0], x[1], x[2]])
        index+=1
inputdestPDB.close()

# 2. create Linked Cell with minimum distance box length
print "Found Box bounds [%f,%f]x[%f,%f]x[%f,%f]." % (min[0],max[0],min[1],max[1],min[2],max[2])
for i in range(3):      # shift by minimum if below zero
  if min[i] < 0:
    max[i]-=min[i]
  else:
    min[i]=0
cells_x=int(math.ceil(float(max[0])/CUTOFF))
cells_y=int(math.ceil(float(max[1])/CUTOFF))
cells_z=int(math.ceil(float(max[2])/CUTOFF))
print "Number of cells in each axis direction (%f,%f,%f)." % (cells_x, cells_y, cells_z)

# 3. put each atom into its cell, lists may contain multiple atoms, mark src(0) or dest (1)
cell=[]
for i in range(cells_x):
  cell.append([])
  for j in range(cells_y):
    cell[i].append([])
    for k in range(cells_z):
      cell[i][j].append([0])
for i in range(len(srcAtoms)):
        atom = srcAtoms[i]
        print atom
        for n in range(3):
                x[n] = int(math.floor(float(atom[1+n])/CUTOFF))
        if cells_x ==x[0]:
                x[0]-=1
        if cells_y ==x[1]:
                x[1]-=1
        if cells_z ==x[2]:
                x[2]-=1
        print x
        cell[x[0]][x[1]][x[2]][0]+=1
        cell[x[0]][x[1]][x[2]].append([0,i])    # 0 means src
        print "Source atom "+str(i)+" goes to cell "+str(x[0])+","+str(x[1])+","+str(x[2])+"."
for i in range(len(destAtoms)):
        atom = destAtoms[i]
        for n in range(3):
                x[n] = int(math.floor(float(atom[1+n])/CUTOFF)) 
        cell[x[0]][x[1]][x[2]][0]+=1
        cell[x[0]][x[1]][x[2]].append([1,i])    # 1 means dest
        print "Destination atom "+str(i)+" goes to cell "+str(x[0])+","+str(x[1])+","+str(x[2])+"."

# 4. go through each cell and match (src, dest)-pairs by closest distance, warn if greater than EPSILON
srcMatches=0
destMatches=0
Map = {}
i=-1
j=-1
k=-1
l=-1
e=-1
r=-1
t=-1
m=-1
for i in range(cells_x):
        for j in range(cells_y):
                for k in range(cells_z):
                        
                        #go through every atom in cell
                        try:
                                for l in range(1, cell[i][j][k][0]+1):
                                        if cell[i][j][k][l][0] != 0:    # skip if it's not a src atom
                                                continue
                                        atom1=cell[i][j][k][l][1]
                                        print "Current source atom is "+str(srcAtoms[atom1][0])+"."
                                        currentPair=[atom1,-1]
                                        oldDist=0.
                                        # go through cell and all lower neighbours
                                        for e in range(i-1,i+2):
                                                #if on boarder continue periodic
                                                #if e>cells_x-1:
                                                #       e=e-cells_x
                                                if (e < 0) or (e >= cells_x):
                                                        continue
                                                for r in range(j-1,j+2):
                                                        #if on boarder continue periodic
                                                        #if r>cells_y-1:
                                                        #       r=r-cells_y
                                                        if (r < 0) or (r >= cells_y):
                                                                continue
                                                        for t in range(k-1,k+2):
                                                                #if on boarder continue periodic
                                                                #if t>cells_z-1:
                                                                #       t=t-cells_z
                                                                if (t < 0) or (t >= cells_z):
                                                                        continue
                                                                #go through all atoms in cell                           
                                                                for m in range(1, cell[e][r][t][0]+1):
                                                                        if cell[e][r][t][m][0] != 1:            # skip if it's not a dest atom
                                                                                continue
                                                                        atom2=cell[e][r][t][m][1]
                                                                        print "Current destination atom is "+str(destAtoms[atom2][0])+"."
                                                                        dist=0
                                                                        tmp=0
                                                                        for n in range(3):
                                                                                tmp = srcAtoms[atom1][1+n] - destAtoms[atom2][1+n]
                                                                                dist += tmp*tmp
                                                                        print "Squared distance between the two is "+str(dist)+"."
                                                                        if ((oldDist > dist) or ((currentPair[1] == -1) and (dist<EPSILON))):
                                                                                currentPair[1] = atom2
                                                                                oldDist = dist
                                        if currentPair[1] == -1:
                                                print"Could not find a suitable partner for srcAtom (%d,%d)!\n" % (srcAtoms[currentPair[0]][0],currentPair[1])
                                                Map[ srcAtoms[currentPair[0]][0] ] = currentPair[1]
                                        else:
                                                print "Found a suitable partner for srcAtom "+str(srcAtoms[currentPair[0]][0])+","+str(destAtoms[currentPair[1]][0])+"."
                                                srcMatches+=1
                                                destMatches+=1
                                                Map[ srcAtoms[currentPair[0]][0] ] = destAtoms[currentPair[1]][0]
                        except IndexError:
                                wrerr("Index Error: (%d,%d,%d)[%d] and (%d,%d,%d)[%d]\n" % (i,j,k,l,e,r,t,m))
                                break

# 5. print the listing
print "We have "+str(srcMatches)+" matching atoms."
print "Mapping is:"
for key in Map:
        print str(key)+" -> "+str(Map[key])
#print Map              # work also

# 6. use the listing to rewrite the dbond file, store under given filename
for line in inputsrcDBOND:
        if "#" in line:
                continue
        entries=line.split()
        flag=0
        for n in range(len(entries)):
                if int(entries[n]) == 0 or Map[ int(entries[n]) ] == -1:
                        flag=1
        if flag==1:
                continue
        for n in range(len(entries)):
                output.write("%d\t" % (Map[ int(entries[n]) ]))
        output.write("\n")
output.close()
print "We have "+str(srcMatches)+" matching atoms."
# exit