write_ins.py

import randpts
from linalg import dot, mat_vec_3_product, vec_sum
from random import random

def write_ins(template, args, matrices, fileName):
    '''
    Takes a template, fills in coordinates for the dummy atoms, and writes
    an ins file ready for ShelXL refinement.
    '''
    with open(fileName+'_or.ins', 'w') as outFile:
        cartMat, invCartMat = matrices #transform to and from a Cartesian basis
        v1, v2 = randpts.makeVectors() #these are perp., cartesian, unit vectors
        shift_multiplier = random()
        shift_cart = [args.shift * shift_multiplier * x for x in randpts.makeRand()]
        shift = mat_vec_3_product(invCartMat, shift_cart)
        cent = vec_sum(args.cent, shift)
        pivt = vec_sum(cent, mat_vec_3_product(invCartMat, v1))
        perp = vec_sum(cent, mat_vec_3_product(invCartMat, v2))
        
        for line in template:
            if 'cent_xyz' in line:
                line = line.replace(
                        'cent_xyz', '{:.5f} {:.5f} {:.5f}'.format(*cent)) 
            if 'pivt_xyz' in line:
                line = line.replace(
                        'pivt_xyz', '{:.5f} {:.5f} {:.5f}'.format(*pivt)) 
            if 'perp_xyz' in line:
                line = line.replace(
                        'perp_xyz', '{:.5f} {:.5f} {:.5f}'.format(*perp)) 
            outFile.write(line)