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.
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. |
(Deprecated) alias of convert_to_xyz(obj)
# File lib/bio/db/pdb/utils.rb, line 150 150: def self.to_xyz(obj) 151: convert_to_xyz(obj) 152: end
calculates plane
# 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
calculates centre of gravitiy
# 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
Implicit conversion into Vector or Bio::PDB::Coordinate
# 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
Calculates dihedral angle.
# 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
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.
# 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
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).
# 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