lib.structure.represent.cone

1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2010,2012-2014 Edward d'Auvergne # 4 # Copyright (C) 2008 Sebastien Morin # 5 # # 6 # This file is part of the program relax (http://www.nmr-relax.com). # 7 # # 8 # This program is free software: you can redistribute it and/or modify # 9 # it under the terms of the GNU General Public License as published by # 10 # the Free Software Foundation, either version 3 of the License, or # 11 # (at your option) any later version. # 12 # # 13 # This program is distributed in the hope that it will be useful, # 14 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 16 # GNU General Public License for more details. # 17 # # 18 # You should have received a copy of the GNU General Public License # 19 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 20 # # 21 ############################################################################### 22 23 # Python module imports. 24 from math import cos, sin 25 from numpy import array, dot, eye, float64, zeros 26 27 # relax module imports. 28 from lib.geometry.rotations import two_vect_to_R 29 from lib.structure.angles import angles_regular, angles_uniform 30 from lib.structure.conversion import get_proton_name 31 from lib.structure.geometric import generate_vector_dist 32 33

34 -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'):

35 """Add a residue to the atomic data representing a cone of the given angle. 36 37 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. 38 39 40 @keyword mol: The molecule container. 41 @type mol: MolContainer instance 42 @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. 43 @type cone_obj: class instance 44 @keyword res_name: The residue name. 45 @type res_name: str 46 @keyword res_num: The residue number. 47 @type res_num: int 48 @keyword chain_id: The chain identifier. 49 @type chain_id: str 50 @keyword apex: The apex of the cone. 51 @type apex: numpy array, len 3 52 @keyword axis: The central axis of the cone. If supplied, then this arg will be used to construct the rotation matrix. 53 @type axis: numpy array, len 3 54 @keyword R: A 3x3 rotation matrix. If the axis arg supplied, then this matrix will be ignored. 55 @type R: 3x3 numpy array 56 @keyword scale: The scaling factor to stretch all points by. 57 @type scale: float 58 @keyword inc: The number of increments or number of vectors used to generate the outer edge of the cone. 59 @type inc: int 60 @keyword distribution: The type of point distribution to use. This can be 'uniform' or 'regular'. 61 @type distribution: str 62 """ 63 64 # The atom numbers (and indices). 65 atom_num = 1 66 if len(mol.atom_num): 67 atom_num = mol.atom_num[-1]+1 68 69 # Add an atom for the cone apex. 70 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') 71 origin_atom = atom_num 72 73 # Get the polar and azimuthal angles for the distribution. 74 if distribution == 'uniform': 75 phi, theta = angles_uniform(inc) 76 else: 77 phi, theta = angles_regular(inc) 78 79 # Initialise the rotation matrix. 80 if R is None: 81 R = eye(3) 82 83 # Get the rotation matrix. 84 if axis != None: 85 two_vect_to_R(array([0, 0, 1], float64), axis, R) 86 87 # Determine the maximum phi values of the point just above the edge. 88 phi_max = zeros(len(theta), float64) 89 for i in range(len(theta)): 90 phi_max[i] = cone_obj.phi_max(theta[i]) 91 92 # Move around the azimuth. 93 atom_num = atom_num + 1 94 for i in range(len(theta)): 95 # The vector in the unrotated frame. 96 x = cos(theta[i]) * sin(phi_max[i]) 97 y = sin(theta[i])* sin(phi_max[i]) 98 z = cos(phi_max[i]) 99 vector = array([x, y, z], float64) 100 101 # Rotate the vector. 102 vector = dot(R, vector) 103 104 # The atom id. 105 atom_id = 'T' + repr(i) 106 107 # The atom position. 108 pos = apex+vector*scale 109 110 # Add the vector as a H atom of the cone residue. 111 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') 112 113 # Join the longitude atom to the cone apex. 114 mol.atom_connect(index1=origin_atom-1, index2=atom_num-1) 115 116 # Increment the atom number. 117 atom_num = atom_num + 1 118 119 # Build the cone edge. 120 for i in range(origin_atom, atom_num-2): 121 mol.atom_connect(index1=i, index2=i+1) 122 123 # Connect the last radial array to the first (to zip up the circle). 124 mol.atom_connect(index1=atom_num-2, index2=origin_atom)

125 126

127 -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):

128 """Create a structural representation of the given cone object. 129 130 @keyword mol: The molecule container. 131 @type mol: MolContainer instance 132 @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. 133 @type cone_obj: class instance 134 @keyword start_res: The starting residue number. 135 @type start_res: str 136 @keyword apex: The apex of the cone. 137 @type apex: rank-1, 3D numpy array 138 @keyword axis: The central axis of the cone. If not supplied, the z-axis will be used. 139 @type axis: rank-1, 3D numpy array 140 @keyword R: The rotation matrix. 141 @type R: rank-2, 3D numpy array 142 @keyword inc: The increment number used to determine the number of latitude and longitude lines. 143 @type inc: int 144 @keyword scale: The scaling factor to stretch the unit cone by. 145 @type scale: float 146 @keyword distribution: The type of point distribution to use. This can be 'uniform' or 'regular'. 147 @type distribution: str 148 @keyword axis_flag: A flag which if True will create the cone's axis. 149 @type axis_flag: bool 150 """ 151 152 # The cone axis default of the z-axis. 153 if not axis: 154 axis = array([0, 0, 1], float64) 155 156 # No rotation. 157 if R is None: 158 R = eye(3) 159 160 # The first atom number. 161 start_atom = 1 162 if hasattr(mol, 'atom_num') and len(mol.atom_num): 163 start_atom = mol.atom_num[-1]+1 164 165 # The axis. 166 if axis_flag: 167 # Add the apex (or centre point). 168 mol.atom_add(pdb_record='HETATM', atom_num=start_atom, atom_name='R', res_name='CNC', res_num=start_res, pos=apex, element='C') 169 170 # Generate the axis vectors. 171 print("\nGenerating the axis vectors.") 172 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) 173 174 # Generate the cone outer edge. 175 print("\nGenerating the cone outer edge.") 176 edge_start_atom = 1 177 if hasattr(mol, 'atom_num') and len(mol.atom_num): 178 edge_start_atom = mol.atom_num[-1]+1 179 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) 180 181 # Generate the cone cap, and stitch it to the cone edge. 182 print("\nGenerating the cone cap.") 183 cone_start_atom = mol.atom_num[-1]+1 184 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