测量最小距离-pymol

脚本

"""
Created on Fri Dec 24 14:33:08 2021


@author: lywu
"""
from pymol import cmd
from math import sqrt
#import numpy as np
def mindist():
    atoms = {}
    atoms2 = {}
    list1=list(range(4,201,1)) #anti-residue-index
    list2=list(range(292,700,1)) #spike-no-NTD-residue-index
            
    for r in list1:
        command = "7ly2 and chain L and resi %s" % (r)
        coordinates = {'atoms': []}
        cmd.iterate_state(-1, command, 
                          'atoms.append([x, y, z, name])', space=coordinates)
        atoms[r] = coordinates['atoms']


    for i in list2:
        command = "7ly2 and chain B and resi %s" % (i)
        coordinates = {'atoms': []}
        cmd.iterate_state(-1, command, 
                          'atoms.append([x, y, z, name])', space=coordinates)
        atoms2[i] = coordinates['atoms']


    distances=[]
    for i in list2:
        min_dist= 10**3
        #min_dist_residue = 1000        
        for c in list1:
            for cc in atoms[c]:
                for ii in atoms2[i]:
                    dist = sqrt((cc[0] - ii[0])**2 + 
                                (cc[1] - ii[1])**2 + (cc[2] - ii[2])**2)
                    if dist < min_dist:
                        min_dist = dist
                        min_c = [c, cc[3]]
                        min_i = [i, ii[3]]
                        distances.append(min_dist)
       # cmd.distance('dist_%s_%s' % (min_c[0], min_i[0]), 
        #            'chain S and resi %s and name %s' % (min_c[0], min_c[1]), 
         #           'chain A and resi %s and name %s' % (min_i[0], min_i[1]))
    min_dist_final=min(distances)
    print(min_dist_final)
    #np.savetxt("mindist_7lab-1.txt",min_dist_final)
cmd.extend("mindist", mindist)
mindist()

使用方法

备注