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result2pdb.py
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result2pdb.py
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import voxel2pdb
import pdb2voxel
from scitbx.array_family import flex
import align
import os
import numpy as np
from sastbx.zernike_model import pdb2zernike
import zalign
import map2iq
def write2pdb(group,rmax,output_folder,iq_file=None,target_pdb=None):
if iq_file is not None:
tar_iq_curve=np.loadtxt(iq_file,usecols=(0))
tar_iq_curve=tar_iq_curve.reshape(-1,1)
num=len(group)
os.system('mkdir %s/sub2'%output_folder)
os.system('mkdir %s/sub3'%output_folder)
for ii in range(num):
voxel2pdb.write_pdb(group[ii],'%s/sub2/%d.pdb'%(output_folder,ii),rmax)
fix='%s/sub2/0.pdb'%output_folder
data=[]
for ii in range(num):
mov='%s/sub2/%d.pdb'%(output_folder,ii)
align.run(fix,mov,'%s/sub3/%d.pdb'%(output_folder,ii))
voxel=pdb2voxel.run(['pdbfile=%s/sub3/%d.pdb'%(output_folder,ii)])
data.append(voxel)
data=np.array(data)
data=np.mean(data,axis=0)
ccp4data=np.copy(data)
data=np.greater(data,0.3).astype(int)
if iq_file is not None:
iq_curve,exp_data=map2iq.run_get_voxel_iq(data,iq_file,rmax)
iq_curve=np.array(iq_curve)
#iq_curve=iq_curve/iq_curve[0]
newiq_curve=np.concatenate((tar_iq_curve,iq_curve.reshape((-1,1))),axis=1)
np.savetxt('%s/final_saxs.txt'%output_folder,newiq_curve)
voxel2pdb.write_pdb(data,'%s/out.pdb'%output_folder,rmax)
'''
if iq_file is not None:
out_voxel=pdb2voxel.run(['pdbfile=%s/out.pdb'%output_folder])
out_curve,exp_data=map2iq.run_get_voxel_iq(out_voxel,iq_file,rmax)
out_curve=np.array(out_curve)
out_curve=out_curve/out_curve[0]
newout_curve=np.concatenate((tar_iq_curve,out_curve.reshape((-1,1))),axis=1)
np.savetxt('%s/final_pdb_saxs.txt'%output_folder,newout_curve)
'''
ccp4data=flex.double(ccp4data)
pdb2zernike.ccp4_map_type(ccp4data, 15, rmax/0.9,file_name='%s/out.ccp4'%output_folder)
shiftrmax=rmax/0.9
args=['fix=%s/out.ccp4'%output_folder,'typef=ccp4','mov=%s/out.pdb'%output_folder,'rmax=%f'%shiftrmax]
zalign.run(args,output_folder)
os.system('rm -r %s/sub2'%output_folder)
os.system('rm -r %s/sub3'%output_folder)
if target_pdb is not None:
args=['fix=%s/out.ccp4'%output_folder,'typef=ccp4','mov=%s'%target_pdb,'rmax=%f'%shiftrmax]
zalign.run(args,output_folder)
if 'sample.pdb' in os.listdir(output_folder):
args=['fix=%s/out.ccp4'%output_folder,'typef=ccp4','mov=%s/sample.pdb'%output_folder,'rmax=%f'%shiftrmax]
zalign.run(args,output_folder)
def write_single_pdb(group,rmax,output_folder,target_pdb=None):
ccp4data=np.copy(group.astype(float))
voxel2pdb.write_pdb(group,'%s/out.pdb'%output_folder,rmax)
ccp4data=flex.double(ccp4data)
pdb2zernike.ccp4_map_type(ccp4data, 15, rmax/0.9,file_name='%s/out.ccp4'%output_folder)
shiftrmax=rmax/0.9
args=['fix=%s/out.ccp4'%output_folder,'typef=ccp4','mov=%s/out.pdb'%output_folder,'rmax=%f'%shiftrmax]
zalign.run(args,output_folder)
if target_pdb is not None:
args=['fix=%s/out.ccp4'%output_folder,'typef=ccp4','mov=%s'%target_pdb,'rmax=%f'%shiftrmax]
zalign.run(args,output_folder)
def cal_cc(voxel_group,rmax,output_folder,target_pdb):
os.system('mkdir %s/temp'%output_folder)
num=voxel_group.shape[0]
cc_mat=np.zeros(shape=(num,20))
for ii in range(num):
for jj in range(20):
voxel2pdb.write_pdb(voxel_group[ii,jj],'%s/temp/%d_%d.pdb'%(output_folder,ii,jj),rmax)
cc=align.run(fix=target_pdb,mov='%s/temp/%d_%d.pdb'%(output_folder,ii,jj))
cc_mat[ii,jj]=cc
print ii,jj,'%.3f'%cc
#np.save('%s/cc_mat.npy'%output_folder,cc_mat)
np.savetxt('%s/cc_mat.txt'%output_folder,cc_mat,fmt='%.3f')
os.system('rm -rf %s/temp'%output_folder)
'''
def cal_cc(voxel_group,rmax,output_folder,target_pdb,iq_file=None):
os.system('mkdir %s/temp'%output_folder)
os.system('mkdir %s/temp1'%output_folder)
os.system('mkdir %s/temp2'%output_folder)
if iq_file is not None:
os.system('mkdir %s/saxs_fit_data'%output_folder)
tar_iq_curve=np.loadtxt(iq_file,usecols=(0))
tar_iq_curve=tar_iq_curve.reshape(-1,1)
num=voxel_group.shape[0]
cc_mat=np.zeros(shape=(num,20))
cc_mat_aver=np.zeros(shape=(num))
for ii in range(num):
for jj in range(20):
voxel2pdb.write_pdb(voxel_group[ii,jj],'%s/temp/%d_%d.pdb'%(output_folder,ii,jj),rmax)
if iq_file is not None and jj==0:
iq_curve,exp_data=map2iq.run_get_voxel_iq(voxel_group[ii,jj],iq_file,rmax)
iq_curve=np.array(iq_curve)
iq_curve=iq_curve/iq_curve[0]
newiq_curve=np.concatenate((tar_iq_curve,iq_curve.reshape((-1,1))),axis=1)
np.savetxt('%s/saxs_fit_data/%d_generation_voxelsaxs.txt'%(output_folder,ii),newiq_curve)
cc=align.run(fix=target_pdb,mov='%s/temp/%d_%d.pdb'%(output_folder,ii,jj))
cc_mat[ii,jj]=cc
print ii,jj,'%.3f'%cc
fix='%s/temp/%d_0.pdb'%(output_folder,ii)
if iq_file is not None:
out_voxel=pdb2voxel.run(['pdbfile=%s'%fix])
out_curve,exp_data=map2iq.run_get_voxel_iq(out_voxel,iq_file,rmax)
out_curve=np.array(out_curve)
out_curve=out_curve/out_curve[0]
newout_curve=np.concatenate((tar_iq_curve,out_curve.reshape((-1,1))),axis=1)
np.savetxt('%s/saxs_fit_data/%d_generation_pdbsaxs.txt'%(output_folder,ii),newout_curve)
data=[]
for jj in range(20):
mov='%s/temp/%d_%d.pdb'%(output_folder,ii,jj)
align.run(fix,mov,'%s/temp1/%d_%d.pdb'%(output_folder,ii,jj))
voxel=pdb2voxel.run(['pdbfile=%s/temp1/%d_%d.pdb'%(output_folder,ii,jj)])
data.append(voxel)
data=np.array(data)
data=np.mean(data,axis=0)
data=np.greater(data,0.3).astype(int)
voxel2pdb.write_pdb(data,'%s/temp2/%d.pdb'%(output_folder,ii),rmax)
cc_aver=align.run(fix=target_pdb,mov='%s/temp2/%d.pdb'%(output_folder,ii))
cc_mat_aver[ii]=cc_aver
print ii,'%.3f'%cc_aver
np.savetxt('%s/cc_mat.txt'%output_folder,cc_mat,fmt='%.3f')
np.savetxt('%s/cc_mat_aver.txt'%output_folder,cc_mat_aver,fmt='%.3f')
os.system('rm -rf %s/temp'%output_folder)
os.system('rm -rf %s/temp1'%output_folder)
os.system('rm -rf %s/temp2'%output_folder)
'''