Module | Bio::PDB::Utils
In: | lib/bio/db/pdb/utils.rb

Utility methods for PDB data. The methods in this mixin should be applicalbe to all PDB objects.

Bio::PDB::Utils is included by Bio::PDB, Bio::PDB::Model, Bio::PDB::Chain, Bio::PDB::Residue, and Bio::PDB::Heterogen classes.

### Methods

acos calculatePlane centreOfGravity convert_to_xyz dihedral_angle distance finder geometricCentre rad2deg to_xyz

### Constants

ElementMass | = | { 'H' => 1, 'C' => 12, 'N' => 14, 'O' => 16, 'S' => 32, 'P' => 31 |  | Returns the coords of the centre of gravity for any AtomFinder implementing object Blleurgh! - working out what element it is from the atom name is tricky - this‘ll work in most cases but not metals etc… a proper element field is included in some PDB files but not all.

### Public Class methods

to_xyz(obj)

(Deprecated) alias of convert_to_xyz(obj)

[Source]

         # File lib/bio/db/pdb/utils.rb, line 150
    150:     def self.to_xyz(obj)
    151:       convert_to_xyz(obj)
    152:     end

### Public Instance methods

acos(x)

acos

[Source]

         # File lib/bio/db/pdb/utils.rb, line 166
    166:     def acos(x)
    167:       Math.atan2(Math.sqrt(1 - x**2),x)
    168:     end

calculatePlane(coord1, coord2, coord3)

calculates plane

[Source]

         # File lib/bio/db/pdb/utils.rb, line 172
    172:     def calculatePlane(coord1, coord2, coord3)
    173:       a = coord1.y * (coord2.z - coord3.z) +
    174:           coord2.y * (coord3.z - coord1.z) +
    175:           coord3.y * (coord1.z - coord2.z)
    176:       b = coord1.z * (coord2.x - coord3.x) +
    177:           coord2.z * (coord3.x - coord1.x) +
    178:           coord3.z * (coord1.x - coord2.x)
    179:       c = coord1.x * (coord2.y - coord3.y) +
    180:           coord2.x * (coord3.y - coord1.y) +
    181:           coord3.x * (coord1.y - coord2.y)
    182:       d = -1 *
    183:           (
    184:            (coord1.x * (coord2.y * coord3.z - coord3.y * coord2.z)) +
    185:            (coord2.x * (coord3.y * coord1.z - coord1.y * coord3.z)) +
    186:            (coord3.x * (coord1.y * coord2.z - coord2.y * coord1.z))
    187:            )
    188:
    189:       return [a,b,c,d]
    190:     end

centreOfGravity()

calculates centre of gravitiy

[Source]

         # File lib/bio/db/pdb/utils.rb, line 89
     89:     def centreOfGravity()
     90:       x = y = z = total = 0
     91:
     92:       self.each_atom{ |atom|
     93:         element = atom.element[0,1]
     94:         mass    = ElementMass[element]
     95:         total += mass
     96:         x += atom.x * mass
     97:         y += atom.y * mass
     98:         z += atom.z * mass
     99:       }
    100:
    101:       x = x / total
    102:       y = y / total
    103:       z = z / total
    104:
    105:       Coordinate[x,y,z]
    106:     end

convert_to_xyz(obj)

Implicit conversion into Vector or Bio::PDB::Coordinate

[Source]

         # File lib/bio/db/pdb/utils.rb, line 137
    137:     def convert_to_xyz(obj)
    138:       unless obj.is_a?(Vector)
    139:         begin
    140:           obj = obj.xyz
    141:         rescue NameError
    142:           obj = Vector.elements(obj.to_a)
    143:         end
    144:       end
    145:       obj
    146:     end

dihedral_angle(coord1, coord2, coord3, coord4)

Calculates dihedral angle.

[Source]

         # File lib/bio/db/pdb/utils.rb, line 122
    122:     def dihedral_angle(coord1, coord2, coord3, coord4)
    123:       (a1,b1,c1,d) = calculatePlane(coord1,coord2,coord3)
    124:       (a2,b2,c2)   = calculatePlane(coord2,coord3,coord4)
    125:
    126:       torsion = acos((a1*a2 + b1*b2 + c1*c2)/(Math.sqrt(a1**2 + b1**2 + c1**2) * Math.sqrt(a2**2 + b2**2 + c2**2)))
    127:
    128:       if ((a1*coord4.x + b1*coord4.y + c1*coord4.z + d) < 0)
    129:         -torsion
    130:       else
    131:         torsion
    132:       end
    133:     end

distance(coord1, coord2)

Calculates distance between _coord1_ and _coord2_.

[Source]

         # File lib/bio/db/pdb/utils.rb, line 114
    114:     def distance(coord1, coord2)
    115:       coord1 = convert_to_xyz(coord1)
    116:       coord2 = convert_to_xyz(coord2)
    117:       (coord1 - coord2).r
    118:     end

finder(findtype) {|obj| ...}

Every class in the heirarchy implements finder, this takes a class which determines which type of object to find, the associated block is then run in classic .find style.

The method might be deprecated. You‘d better using find_XXX directly.

[Source]

         # File lib/bio/db/pdb/utils.rb, line 199
    199:     def finder(findtype, &block) #:yields: obj
    200:       if findtype == Bio::PDB::Atom
    201:         return self.find_atom(&block)
    202:       elsif findtype == Bio::PDB::Residue
    203:         return self.find_residue(&block)
    204:       elsif findtype == Bio::PDB::Chain
    205:         return self.find_chain(&block)
    206:       elsif findtype == Bio::PDB::Model
    207:         return self.find_model(&block)
    208:       else
    209:         raise TypeError, "You can't find a #{findtype}"
    210:       end
    211:     end

geometricCentre(method = :each_atom)

Returns the coordinates of the geometric centre (average co-ord) of any AtomFinder (or .atoms) implementing object

If you want to get the geometric centre of hetatms, call geometricCentre(:each_hetatm).

[Source]

        # File lib/bio/db/pdb/utils.rb, line 57
    57:     def geometricCentre(method = :each_atom)
    58:       x = y = z = count = 0
    59:
    60:       self.__send__(method) do |atom|
    61:         x += atom.x
    62:         y += atom.y
    63:         z += atom.z
    64:         count += 1
    65:       end
    66:
    67:       x = (x / count)
    68:       y = (y / count)
    69:       z = (z / count)
    70:
    71:       Coordinate[x,y,z]
    72:     end

rad2deg(r)

radian to degree

[Source]

         # File lib/bio/db/pdb/utils.rb, line 160
    160:     def rad2deg(r)
    161:       (r/Math::PI)*180
    162:     end

[Validate]