EntDetect 1.2.0__tar.gz

entdetect-1.2.0/EntDetect/Jwalk/GridTools.py

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+# ===============================================================================
+#     This file is part of Jwalk (Python 3).
+#     
+#     Jwalk - A tool to calculate the solvent accessible surface distance (SASD) 
+#     between crosslinked residues.
+#     
+#     Copyright 2016 Josh Bullock and Birkbeck College University of London.
+# 
+#     Jwalk is available under Public Licence.
+#     This software is made available under GPL V3
+#
+#     Please cite your use of Jwalk in published work:
+#     
+#     J.Bullock, J. Schwab, K. Thalassinos, M. Topf (2016)
+#     The importance of non-accessible crosslinks and solvent accessible surface distance
+#     in modelling proteins with restraints from crosslinking mass spectrometry. 
+#     Molecular and Cellular Proteomics (15) pp.2491-2500
+#
+# ===============================================================================
+
+from numpy import zeros
+from collections import OrderedDict
+
+class Map:
+    """ 
+    
+    A class representing all information from a density map file. 
+    NOTE: Currently it can only read the CCP4/MRC  format.
+    
+    """
+
+    def __init__(self, fullMap, origin, apix, filename, header=[]):
+        """
+        
+        Read a map and its parameters in to Map class instance.
+        
+        *filename*
+            name of map file.
+        *origin*    
+            origin co-ordinates of the map (x_origin, y_origin, z_origin).
+        *apix*
+            grid spacing of map.
+        *filename*
+            filename of the Map instance
+            
+            NOTE: The *filename* 'build++copy' is reserved for copying of other Map class instances."""        
+        self.header = header
+        self.origin = origin
+        self.apix = apix
+        self.filename = filename
+        self.fullMap = fullMap
+        
+    def copy(self):
+        """
+        
+        Return:
+            copy of the Map.
+        
+        """
+        copy = Map(self.fullMap.copy(), self.origin[:], self.apix, self.filename, self.header[:])
+        return copy
+
+    def box_size(self):
+        """
+        
+        Return:
+            size of the map array, in ZYX format.
+        
+        """
+        return self.fullMap.shape
+        
+    def x_size(self):
+        """
+        
+        Return:
+            x size of the map array in x direction.
+        
+        """
+        return self.fullMap.shape[2]
+    
+    def y_size(self):
+        """
+        
+        Return:
+            y size of the map array in y direction.
+        
+        """
+        return self.fullMap.shape[1]
+    
+    def z_size(self):
+        """
+        
+        Return:
+            z size of the map array in z direction.
+        
+        """
+        return self.fullMap.shape[0]
+
+def makeGrid(struct, apix, resolution = 3, filename = "None"):
+    """
+    
+    Returns protein grid.
+    
+    Arguments:
+    
+       *struct*
+           Tempy structure instance
+       *apix*
+           angstroms per voxel
+           
+    """
+    # Build empty template map based on the size of the protein and the resolution.
+    extr = struct.get_extreme_values()
+    edge = int(2*resolution/apix)+2
+    x_size = int((extr[1]-extr[0])/apix)+edge
+    y_size = int((extr[3]-extr[2])/apix)+edge
+    z_size = int((extr[5]-extr[4])/apix)+edge
+    
+    # Origin calculated such that the centre of the map is the centre of mass of the protein.
+    x_origin = (extr[1]+extr[0])/2-(apix*x_size/2.0)
+    y_origin = (extr[3]+extr[2])/2-(apix*y_size/2.0)
+    z_origin = (extr[5]+extr[4])/2-(apix*z_size/2.0)
+    
+    newMap = zeros((z_size, y_size, x_size))
+    fullMap = Map(newMap, [x_origin, y_origin, z_origin], apix, filename)
+    return fullMap
+
+def mapGridPosition(densMap, atom):
+    
+    """
+    
+    Returns the index of the nearest pixel to an atom, and atom mass (4 values in list form).
+    
+    Arguments:
+    
+       *densMap*
+           Map instance the atom is to be placed on.
+       *atom*
+           Atom instance.
+           
+    """
+    origin = densMap.origin
+    apix = densMap.apix
+    box_size = densMap.box_size()
+    x_pos = int(round((atom.x-origin[0])/apix,0))
+    y_pos = int(round((atom.y-origin[1])/apix,0))
+    z_pos = int(round((atom.z-origin[2])/apix,0))
+    
+    if((densMap.x_size() > x_pos >= 0) and (densMap.y_size() > y_pos >= 0) and (densMap.z_size() > z_pos >= 0)):
+        return (x_pos, y_pos, z_pos, atom.mass)
+    else:
+        return 0
+
+def mark_CAlphas(densMap, prot, aa1, aa2):
+    """
+    
+    Returns ordered dictionaries containing {residue_number, chain, residue name : x, y, z}
+    for both aa1 and aa2.
+    
+    Arguments:
+    
+       *densMap*
+           Protein grid
+       *prot*
+           Tempy structure instance
+        *aa1*
+            Residue type 1
+        *aa2*
+            Residue type 2
+           
+    """
+    
+    aa1_CA = OrderedDict()
+    aa2_CA = OrderedDict()
+    
+    for atom in prot.atomList:
+       
+            if atom.res == aa1: 
+                
+                if atom.atom_name == 'CA':
+                    pos = mapGridPosition(densMap, atom)
+                    aa1_CA[atom.res_no,atom.chain,atom.res]=[pos[0],pos[1],pos[2]]
+                    
+            if atom.res == aa2:
+                if atom.atom_name == 'CA':
+                    pos = mapGridPosition(densMap, atom)
+                    aa2_CA[atom.res_no,atom.chain,atom.res]=[pos[0],pos[1],pos[2]]
+        
+            
+    return aa1_CA, aa2_CA
+
+def process_input_crosslinks(uv_xl):
+    """Processes crosslink input .txt file and returns list of residues and crosslinked pairs"""
+
+    aa1 = []
+    aa2 = []
+    crosslink_pairs = []
+    #c = 0
+    count = 0
+    with open(uv_xl) as xl_in:
+        for line in xl_in:
+            count +=1
+            col = line.split("|")
+            try:
+                chain1 = col[1].rstrip()
+                chain1 = chain1.lstrip()
+                chain2 = col[3].rstrip()
+                chain2 = chain2.lstrip()
+            except:
+                print("ERROR: formatting error on line {} : {}".format(str(count),line))
+                exit(1)
+            # if no chain is given
+            if len(chain1) == 0:
+                chain1 = " "
+            if len(chain2) == 0:
+                chain2 = " "
+                
+            aa1.append([int(col[0]),chain1])
+            aa2.append([int(col[2]),chain2])
+            
+            crosslink_pairs.append([(int(col[0]),chain1),(int(col[2]),chain2)])
+            '''
+            if (int(col[0]),chain1,c) in xl_pair:
+                c +=1
+            xl_pair[int(col[0]),chain1,c] = [int(col[2]),chain2,c]
+            '''
+            
+    return aa1, aa2 , crosslink_pairs
+
+def mark_CAlphas_pairs(densMap, prot, uv_xl):
+    
+    """
+    Processes input txt file. Checks each atom is in the structure and returns
+    the pairs of crosslinks as well as the Calpha positions on the grid.
+    
+    Arguments:
+        *densMap*
+            grid that encompasses protein
+        *prot*
+            .pdb file
+        *uv_xl*
+             .txt input file
+    
+    """
+    
+    # process txt file
+    aa1, aa2, crosslink_pairs = process_input_crosslinks(uv_xl)
+    # crosslink_pairs is a list of [crosslinked aa1, aa2]
+        
+    aa1_CA = OrderedDict()
+    aa2_CA = OrderedDict()
+
+    atom_check = []
+    
+    for atom in prot.atomList:    
+        if [atom.res_no,atom.chain] in aa1:
+            if atom.atom_name == "CA":
+                pos = mapGridPosition(densMap, atom)
+                aa1_CA[atom.res_no,atom.chain,atom.res]=[pos[0],pos[1],pos[2]]
+                atom_check.append([atom.res_no,atom.chain])
+        if [atom.res_no,atom.chain] in aa2:
+            if atom.atom_name == "CA":
+                pos = mapGridPosition(densMap, atom)
+                aa2_CA[atom.res_no,atom.chain,atom.res]=[pos[0],pos[1],pos[2]]
+                atom_check.append([atom.res_no,atom.chain])
+    
+    # check that all the residues listed are in the structure
+    rem_x = []
+    
+    for x in aa1:
+        if x not in atom_check:
+            print("ERROR ! Residue {} - {} not in pdb structure - please check input files".format(x[0], x[1]))
+            rem_x.append((x[0], x[1]))
+    for x in aa2:
+        if x not in atom_check:
+            print("ERROR ! Residue {} - {} not in pdb structure - please check input files".format(x[0], x[1]))
+            rem_x.append((x[0], x[1]))
+        
+    # remove crosslinks from crosslink_pairs if one or both residues are not in structure
+    index_to_delete = []
+    
+    for i in range(len(crosslink_pairs)):
+        [x1, x2] = crosslink_pairs[i]
+        if x1 in rem_x:
+            index_to_delete.append(i)
+        elif x2 in rem_x:
+            index_to_delete.append(i)
+    
+    crosslink_pairs_hold = []
+    for i in range(len(crosslink_pairs)):
+        if i not in index_to_delete:
+            crosslink_pairs_hold.append(crosslink_pairs[i])
+            
+    # append residue name to crosslink_pairs_final
+    
+    aa_d = {}
+    
+    for a in aa1_CA:
+        aa_d[a[0],a[1]]= a
+    for a in aa2_CA:
+        aa_d[a[0],a[1]]= a
+        
+    crosslink_pairs_final = []
+    for x1, x2 in crosslink_pairs_hold:
+        crosslink_pairs_final.append([aa_d[x1],aa_d[x2]])
+        
+    return crosslink_pairs_final, aa1_CA, aa2_CA
+                 
+def generate_solvent_accessible_surface(densMap,prot,aa1_CA, aa2_CA):
+    
+    """
+    
+    Returns masked array which functions as solvent accessible surface
+    
+    Arguments:
+    
+       *densMap*
+           Protein Grid
+       *prot*
+           Tempy structure instance
+        *aa1_CA*
+           voxel positions of each C_alpha atom of interest
+        *aa2_CA*
+           voxel positions of each C_alpha atom of interest
+           
+    """
+    # store different radii for each atom and calculate the voxel spheres for each
+    sphere = {}
+    radius = {}
+    
+    C = 0.8
+    
+    radius['CA'] = 1.73 + C
+    radius['S'] = 1.67 + C
+    radius['N'] = 1.43 + C
+    radius['OH'] = 1.30 + C
+    
+    for r in radius:
+        
+        sphere[r] = []
+        rad = int(round(radius[r]/densMap.apix))
+        
+        for x in range(-rad,rad+1):
+            for y in range(-rad,rad+1):
+                for z in range(-rad,rad+1):
+                    if (x**2 + y**2 + z**2) <= (rad**2):
+                        sphere[r].append([x,y,z])
+    
+    backbone = ['N','CA','C','O']                         
+    
+    # generate solvent accessible surface
+    
+    for atom in prot.atomList:
+        
+        pos = mapGridPosition(densMap, atom)
+            
+        if pos:
+            # don't place side chain atoms of residues of interest in the surface
+            if ((atom.res_no,atom.chain,atom.res) in aa1_CA and atom.atom_name not in backbone) or (
+            (atom.res_no,atom.chain,atom.res) in aa2_CA and atom.atom_name not in backbone):
+                pass
+            # for each atom, expand the corresponding voxel sphere around it to create solvent accessible surface
+            else:
+                if atom.atom_name[:1] == 'C':
+                    for (x,y,z) in sphere['CA']:
+                        if((densMap.x_size() > (pos[0]+x) >= 0) and (densMap.y_size() > (pos[1]+y) >= 0) and (densMap.z_size() > (pos[2]+z) >= 0)):
+                            densMap.fullMap[pos[2]+z][pos[1]+y][pos[0]+x] += 1
+                elif atom.atom_name[:1] == 'O':
+                    for (x,y,z) in sphere['OH']:
+                        if((densMap.x_size() > (pos[0]+x) >= 0) and (densMap.y_size() > (pos[1]+y) >= 0) and (densMap.z_size() > (pos[2]+z) >= 0)):
+                            densMap.fullMap[pos[2]+z][pos[1]+y][pos[0]+x] += 1
+                elif atom.atom_name[:1] == 'N':
+                    for (x,y,z) in sphere['N']:
+                        if((densMap.x_size() > (pos[0]+x) >= 0) and (densMap.y_size() > (pos[1]+y) >= 0) and (densMap.z_size() > (pos[2]+z) >= 0)):
+                            densMap.fullMap[pos[2]+z][pos[1]+y][pos[0]+x] += 1
+                elif atom.atom_name[:1] == 'S':
+                    for (x,y,z) in sphere['S']:
+                        if((densMap.x_size() > (pos[0]+x) >= 0) and (densMap.y_size() > (pos[1]+y) >= 0) and (densMap.z_size() > (pos[2]+z) >= 0)):
+                            densMap.fullMap[pos[2]+z][pos[1]+y][pos[0]+x] += 1
+                            
+    return densMap
+        
+def find_empty_space(res,sphere,densMap,CA):
+    
+    """
+    
+    Returns list of empty voxels in voxel sphere shell
+    
+    Arguments:
+    
+       *res*
+           residue where search is happening around
+       *sphere*
+           voxel sphere shell to be expanded around CA voxel
+        *densMap*
+           Solvent accessible surface (masked array)
+        *CA*
+           Calpha voxels
+           
+    """ 
+    
+    starters = []
+    (x,y,z) = CA[res]
+    for (x_s,y_s,z_s) in sphere:
+        if((densMap.x_size() > (x+x_s) >= 0) and (densMap.y_size() > (y+y_s) >= 0) and (densMap.z_size() > (z+z_s) >= 0)):
+            if densMap.fullMap[z_s+z][y_s+y][x_s+x] <= 0:
+                starters.append([x_s+x,y_s+y,z_s+z])
+    return starters
+    
+def find_surface_voxels(aa1_CA, densMap, xl_list = []):
+        
+    """
+    
+    Returns ordered dictionaries containing all possible staring voxels for each Calpha of
+    interest. If Calpha is not solvent accessible then no starting voxels are returned.
+    
+    If xl_list flag True, then list of entries to be removed is also returned. empty list 
+    otherwise.
+    
+    Arguments:
+    
+       *aa1_CA*
+           Calpha voxels for amino acid type 1
+       *densMap*
+           Solvent accessible surface (masked array)
+           
+    """    
+    
+    # generate voxel spheres shells to progressively extend search for starting voxels
+    # this is to keep starting voxels as close to CA as possible.    
+    
+    sphere1 = []
+    sphere2 = []
+    sphere3 = []
+    sphere4 = []
+    sphere5 = []
+    sphere6 = []
+    
+    C = 1.68
+    
+    radius = 1.73 + C
+    
+    radius4 = int(round(radius/densMap.apix))+1 # radius rounded up = 4 with apix = 1
+    radius3 = radius4 -1
+    radius2 = radius3 -1
+    radius1 = radius2 -1
+    radius5 = radius4 + 1
+    radius6 = radius5 + 1
+    
+    for x in range(-radius1,radius1+1):
+        for y in range(-radius1,radius1+1):
+            for z in range(-radius1,radius1+1):
+                if (x**2 + y**2 + z**2) <= (radius1**2):
+                    sphere1.append([x,y,z])
+    sphere1_set = {(v[0],v[1],v[2]) for v in sphere1}
+                    
+    for x in range(-radius2,radius2+1):
+        for y in range(-radius2,radius2+1):
+            for z in range(-radius2,radius2+1):
+                if (x**2 + y**2 + z**2) <= (radius2**2):
+                    if (x,y,z) not in sphere1_set:
+                        sphere2.append([x,y,z])
+    sphere2_set = {(v[0],v[1],v[2]) for v in sphere2}
+                    
+    for x in range(-radius3,radius3+1):
+        for y in range(-radius3,radius3+1):
+            for z in range(-radius3,radius3+1):
+                if (x**2 + y**2 + z**2) <= (radius3**2):
+                    if (x,y,z) not in sphere1_set and (x,y,z) not in sphere2_set:
+                        sphere3.append([x,y,z])
+    sphere3_set = {(v[0],v[1],v[2]) for v in sphere3}
+                                    
+    for x in range(-radius4,radius4+1):
+        for y in range(-radius4,radius4+1):
+            for z in range(-radius4,radius4+1):
+                if (x**2 + y**2 + z**2) <= (radius4**2):
+                    if (x,y,z) not in sphere1_set and (x,y,z) not in sphere2_set and (
+                    x,y,z) not in sphere3_set:
+                        sphere4.append([x,y,z])
+    sphere4_set = {(v[0],v[1],v[2]) for v in sphere4}
+    
+    for x in range(-radius5,radius5+1):
+        for y in range(-radius5,radius5+1):
+            for z in range(-radius5,radius5+1):
+                if (x**2 + y**2 + z**2) <= (radius5**2):
+                    if (x,y,z) not in sphere1_set and (x,y,z) not in sphere2_set and (
+                    x,y,z) not in sphere3_set and (x,y,z) not in sphere4_set:
+                        sphere5.append([x,y,z])
+    sphere5_set = {(v[0],v[1],v[2]) for v in sphere5}
+                        
+    for x in range(-radius6,radius6+1):
+        for y in range(-radius6,radius6+1):
+            for z in range(-radius6,radius6+1):
+                if (x**2 + y**2 + z**2) <= (radius6**2):
+                    if (x,y,z) not in sphere1_set and (x,y,z) not in sphere2_set and (
+                    x,y,z) not in sphere3_set and (x,y,z) not in sphere4_set and (x,y,z) not in sphere5_set:
+                        sphere6.append([x,y,z])
+    
+    # iterate through sphere shells and append starting voxels to dictionary
+                    
+    aa_1_start_voxels = OrderedDict()   
+    buried = []
+    k_count = 0
+    k_buried = 0
+    
+    for k in aa1_CA:
+        k_count +=1
+        aa_1_start_voxels[k] = find_empty_space(k,sphere1,densMap,aa1_CA)
+        if aa_1_start_voxels[k] == []:
+            aa_1_start_voxels[k] = find_empty_space(k,sphere2,densMap,aa1_CA)
+        if aa_1_start_voxels[k] == []:
+            aa_1_start_voxels[k] = find_empty_space(k,sphere3,densMap,aa1_CA)
+        if aa_1_start_voxels[k] == []:
+            aa_1_start_voxels[k] = find_empty_space(k,sphere4,densMap,aa1_CA)   
+        if aa_1_start_voxels[k] == []:
+            aa_1_start_voxels[k] = find_empty_space(k,sphere5,densMap,aa1_CA)
+        if aa_1_start_voxels[k] == []:
+            aa_1_start_voxels[k] = find_empty_space(k,sphere6,densMap,aa1_CA)
+        
+    rem_x = []
+    
+    if len(buried) > 0 and len(xl_list) > 0:
+        print("ERROR - {} buried residue(s) in xl_list:".format(k_buried))
+        for t in buried:
+            print("{} - {} - {}".format(str(t[0]), str(t[1]), str(t[2])))
+            rem_x.append([t[0],t[1]])
+        #sys.exit(2)
+    
+    return aa_1_start_voxels, rem_x
+        
+def remove_duplicates(sasds):
+    
+    """
+    
+    Returns sasds with duplicates removed.
+    
+    Arguments:
+    
+       *sasds*
+           dictionary of sasds
+           
+    """ 
+    
+    keep = {}
+    keep_keys = []
+    keep_sasds = {}
+    
+    for (start, end, distance) in sasds:
+        
+        # check if there is a duplicate
+        if (start, end) not in keep:
+            keep[start, end] = distance
+            
+        # if there is a duplicate check which has the shortest distance and keep   
+        elif (start, end) in keep:
+            if (distance < keep[start, end]):
+                keep[start, end] = distance
+    
+    # reform the dictionary key
+    for (j,k) in keep:
+        keep_keys.append((j,k,keep[j,k])) 
+    
+    # filter out original dictionary
+    for k in keep_keys:
+        keep_sasds[k] = sasds[k]
+
+    return keep_sasds