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 152 152: def self.to_xyz(obj) 153: convert_to_xyz(obj) 154: end
calculates plane
# File lib/bio/db/pdb/utils.rb, line 174 174: def calculatePlane(coord1, coord2, coord3) 175: a = coord1.y * (coord2.z - coord3.z) + 176: coord2.y * (coord3.z - coord1.z) + 177: coord3.y * (coord1.z - coord2.z) 178: b = coord1.z * (coord2.x - coord3.x) + 179: coord2.z * (coord3.x - coord1.x) + 180: coord3.z * (coord1.x - coord2.x) 181: c = coord1.x * (coord2.y - coord3.y) + 182: coord2.x * (coord3.y - coord1.y) + 183: coord3.x * (coord1.y - coord2.y) 184: d = -1 * 185: ( 186: (coord1.x * (coord2.y * coord3.z - coord3.y * coord2.z)) + 187: (coord2.x * (coord3.y * coord1.z - coord1.y * coord3.z)) + 188: (coord3.x * (coord1.y * coord2.z - coord2.y * coord1.z)) 189: ) 190: 191: return [a,b,c,d] 192: end
calculates centre of gravitiy
# File lib/bio/db/pdb/utils.rb, line 91 91: def centreOfGravity() 92: x = y = z = total = 0 93: 94: self.each_atom{ |atom| 95: element = atom.element[0,1] 96: mass = ElementMass[element] 97: total += mass 98: x += atom.x * mass 99: y += atom.y * mass 100: z += atom.z * mass 101: } 102: 103: x = x / total 104: y = y / total 105: z = z / total 106: 107: Coordinate[x,y,z] 108: end
Implicit conversion into Vector or Bio::PDB::Coordinate
# File lib/bio/db/pdb/utils.rb, line 139 139: def convert_to_xyz(obj) 140: unless obj.is_a?(Vector) 141: begin 142: obj = obj.xyz 143: rescue NameError 144: obj = Vector.elements(obj.to_a) 145: end 146: end 147: obj 148: end
Calculates dihedral angle.
# File lib/bio/db/pdb/utils.rb, line 124 124: def dihedral_angle(coord1, coord2, coord3, coord4) 125: (a1,b1,c1,d) = calculatePlane(coord1,coord2,coord3) 126: (a2,b2,c2) = calculatePlane(coord2,coord3,coord4) 127: 128: torsion = acos((a1*a2 + b1*b2 + c1*c2)/(Math.sqrt(a1**2 + b1**2 + c1**2) * Math.sqrt(a2**2 + b2**2 + c2**2))) 129: 130: if ((a1*coord4.x + b1*coord4.y + c1*coord4.z + d) < 0) 131: -torsion 132: else 133: torsion 134: end 135: 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 201 201: def finder(findtype, &block) #:yields: obj 202: if findtype == Bio::PDB::Atom 203: return self.find_atom(&block) 204: elsif findtype == Bio::PDB::Residue 205: return self.find_residue(&block) 206: elsif findtype == Bio::PDB::Chain 207: return self.find_chain(&block) 208: elsif findtype == Bio::PDB::Model 209: return self.find_model(&block) 210: else 211: raise TypeError, "You can't find a #{findtype}" 212: end 213: 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 59 59: def geometricCentre(method = :each_atom) 60: x = y = z = count = 0 61: 62: self.__send__(method) do |atom| 63: x += atom.x 64: y += atom.y 65: z += atom.z 66: count += 1 67: end 68: 69: x = (x / count) 70: y = (y / count) 71: z = (z / count) 72: 73: Coordinate[x,y,z] 74: end