lib.structure.represent.cone

1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2015 Edward d'Auvergne # 4 # # 5 # This file is part of the program relax (http://www.nmr-relax.com). # 6 # # 7 # This program is free software: you can redistribute it and/or modify # 8 # it under the terms of the GNU General Public License as published by # 9 # the Free Software Foundation, either version 3 of the License, or # 10 # (at your option) any later version. # 11 # # 12 # This program is distributed in the hope that it will be useful, # 13 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 15 # GNU General Public License for more details. # 16 # # 17 # You should have received a copy of the GNU General Public License # 18 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 19 # # 20 ############################################################################### 21 22 # Python module imports. 23 from math import cos, sin 24 from numpy import array, dot, eye, float64, zeros 25 26 # relax module imports. 27 from lib.geometry.rotations import two_vect_to_R 28 from lib.structure.angles import angles_regular, angles_uniform 29 from lib.structure.conversion import get_proton_name 30 from lib.structure.geometric import generate_vector_dist 31 32

33 -def cone_edge(mol=None, cone_obj=None, res_name='CON', res_num=None, chain_id='', apex=None, axis=None, R=None, scale=None, inc=None, distribution='uniform'):

34 """Add a residue to the atomic data representing a cone of the given angle. 35 36 A series of vectors totalling the number of increments and starting at the origin are equally spaced around the cone axis. The atoms representing neighbouring vectors will be directly bonded together. This will generate an object representing the outer edge of a cone. 37 38 39 @keyword mol: The molecule container. 40 @type mol: MolContainer instance 41 @keyword cone_obj: The cone object. This should provide the limit_check() method with determines the limits of the distribution accepting two arguments, the polar angle phi and the azimuthal angle theta, and return True if the point is in the limits or False if outside. It should also provide the phi_max() method for returning the phi value for the given theta. 42 @type cone_obj: class instance 43 @keyword res_name: The residue name. 44 @type res_name: str 45 @keyword res_num: The residue number. 46 @type res_num: int 47 @keyword chain_id: The chain identifier. 48 @type chain_id: str 49 @keyword apex: The apex of the cone. 50 @type apex: numpy array, len 3 51 @keyword axis: The central axis of the cone. If supplied, then this arg will be used to construct the rotation matrix. 52 @type axis: numpy array, len 3 53 @keyword R: A 3x3 rotation matrix. If the axis arg supplied, then this matrix will be ignored. 54 @type R: 3x3 numpy array 55 @keyword scale: The scaling factor to stretch all points by. 56 @type scale: float 57 @keyword inc: The number of increments or number of vectors used to generate the outer edge of the cone. 58 @type inc: int 59 @keyword distribution: The type of point distribution to use. This can be 'uniform' or 'regular'. 60 @type distribution: str 61 """ 62 63 # The atom numbers (and indices). 64 atom_num = 1 65 if len(mol.atom_num): 66 atom_num = mol.atom_num[-1]+1 67 68 # Add an atom for the cone apex. 69 mol.atom_add(pdb_record='HETATM', atom_num=atom_num, atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, segment_id=None, element='H') 70 origin_atom = atom_num 71 72 # Get the polar and azimuthal angles for the distribution. 73 if distribution == 'uniform': 74 phi, theta = angles_uniform(inc) 75 else: 76 phi, theta = angles_regular(inc) 77 78 # Initialise the rotation matrix. 79 if R is None: 80 R = eye(3) 81 82 # Get the rotation matrix. 83 if axis != None: 84 two_vect_to_R(array([0, 0, 1], float64), axis, R) 85 86 # Determine the maximum phi values of the point just above the edge. 87 phi_max = zeros(len(theta), float64) 88 for i in range(len(theta)): 89 phi_max[i] = cone_obj.phi_max(theta[i]) 90 91 # Move around the azimuth. 92 atom_num = atom_num + 1 93 for i in range(len(theta)): 94 # The vector in the unrotated frame. 95 x = cos(theta[i]) * sin(phi_max[i]) 96 y = sin(theta[i])* sin(phi_max[i]) 97 z = cos(phi_max[i]) 98 vector = array([x, y, z], float64) 99 100 # Rotate the vector. 101 vector = dot(R, vector) 102 103 # The atom id. 104 atom_id = 'T' + repr(i) 105 106 # The atom position. 107 pos = apex+vector*scale 108 109 # Add the vector as a H atom of the cone residue. 110 mol.atom_add(pdb_record='HETATM', atom_num=atom_num, atom_name=get_proton_name(atom_num), res_name=res_name, res_num=res_num, pos=pos, segment_id=None, element='H') 111 112 # Join the longitude atom to the cone apex. 113 mol.atom_connect(index1=origin_atom-1, index2=atom_num-1) 114 115 # Increment the atom number. 116 atom_num = atom_num + 1 117 118 # Build the cone edge. 119 for i in range(origin_atom, atom_num-2): 120 mol.atom_connect(index1=i, index2=i+1) 121 122 # Connect the last radial array to the first (to zip up the circle). 123 mol.atom_connect(index1=atom_num-2, index2=origin_atom)

124 125

126 -def cone(mol=None, cone_obj=None, start_res=1, apex=None, axis=None, R=None, inc=None, scale=30.0, distribution='regular', axis_flag=True):

127 """Create a structural representation of the given cone object. 128 129 @keyword mol: The molecule container. 130 @type mol: MolContainer instance 131 @keyword cone_obj: The cone object. This should provide the limit_check() method with determines the limits of the distribution accepting two arguments, the polar angle phi and the azimuthal angle theta, and return True if the point is in the limits or False if outside. It should also provide the theta_max() method for returning the theta value for the given phi, the phi_max() method for returning the phi value for the given theta. 132 @type cone_obj: class instance 133 @keyword start_res: The starting residue number. 134 @type start_res: str 135 @keyword apex: The apex of the cone. 136 @type apex: rank-1, 3D numpy array 137 @keyword axis: The central axis of the cone. If not supplied, the z-axis will be used. 138 @type axis: rank-1, 3D numpy array 139 @keyword R: The rotation matrix. 140 @type R: rank-2, 3D numpy array 141 @keyword inc: The increment number used to determine the number of latitude and longitude lines. 142 @type inc: int 143 @keyword scale: The scaling factor to stretch the unit cone by. 144 @type scale: float 145 @keyword distribution: The type of point distribution to use. This can be 'uniform' or 'regular'. 146 @type distribution: str 147 @keyword axis_flag: A flag which if True will create the cone's axis. 148 @type axis_flag: bool 149 """ 150 151 # The cone axis default of the z-axis. 152 if not axis: 153 axis = array([0, 0, 1], float64) 154 155 # No rotation. 156 if R is None: 157 R = eye(3) 158 159 # The first atom number. 160 start_atom = 1 161 if hasattr(mol, 'atom_num') and len(mol.atom_num): 162 start_atom = mol.atom_num[-1]+1 163 164 # The axis. 165 if axis_flag: 166 # Add the apex (or centre point). 167 mol.atom_add(pdb_record='HETATM', atom_num=start_atom, atom_name='R', res_name='CNC', res_num=start_res, pos=apex, element='C') 168 169 # Generate the axis vectors. 170 print("\nGenerating the axis vectors.") 171 res_num = generate_vector_residues(mol=mol, vector=dot(R, axis), atom_name='Axis', res_name_vect='CNX', res_num=start_res+1, origin=apex, scale=scale) 172 173 # Generate the cone outer edge. 174 print("\nGenerating the cone outer edge.") 175 edge_start_atom = 1 176 if hasattr(mol, 'atom_num') and len(mol.atom_num): 177 edge_start_atom = mol.atom_num[-1]+1 178 cone_edge(mol=mol, cone_obj=cone_obj, res_name='CNE', res_num=start_res+2, apex=apex, R=R, scale=scale, inc=inc, distribution=distribution) 179 180 # Generate the cone cap, and stitch it to the cone edge. 181 print("\nGenerating the cone cap.") 182 cone_start_atom = mol.atom_num[-1]+1 183 generate_vector_dist(mol=mol, res_name='CON', res_num=start_res+3, centre=apex, R=R, phi_max_fn=cone_obj.phi_max, scale=scale, inc=inc, distribution=distribution)

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Source Code for Module lib.structure.represent.cone