def save_all_files(info, pdb1, ch1, pdb2, ch2, sol_num=5, dock_pool='.'):
from use_dock import UseZDOCK
dock = UseZDOCK(pool_path=dock_pool)
area_file = dock_area(dock, info, pdb1, ch1, pdb2, ch2, sol_num, skip=False)[0][0]
rcf_file = zdock_rcf(info, pdb1, ch1, pdb2, ch2, sol_num, dock_pool)[0][0]
f1 = feature_rcf(info, area_file, rcf_file)
f2 = feature_area(info, area_file, sol_num)
f3 = feature_residue(info, area_file)
if f1 == [] or f2 == [] or f3 == []:
dock.clean_temp_path()
return []
dock.prepare_data(pdb1, ch1, pdb2, ch2)
if not os.path.exists('zdock_pool'):
os.mkdir('zdock_pool')
if not os.path.exists('zdock_pdbs'):
os.mkdir('zdock_pdbs')
if not os.path.exists('zdock_pool/'+dock.solution.split('/')[-1]): ## check one
sfiles = dock.generate_complex(sol_num)
from shutil import copy
copy(dock.solution, 'zdock_pool/'+dock.solution.split('/')[-1])
copy(area_file, 'zdock_pool/'+area_file.split('/')[-1])
copy(rcf_file, 'zdock_pool/'+rcf_file.split('/')[-1])
for i in xrange(sol_num):
copy(sfiles[i], 'zdock_pdbs/%s-%s-%s-%s-ZDOCK-%d.pdb'%(pdb1,ch1,pdb2,ch2,i+1))
# break ## save only one for now
dock.clean_temp_path()
return [a1+a2[1:]+a3[1:] for a1,a2,a3 in zip(f1,f2,f3)]
def main(para):
known = []
known += get_dock_list('set1_all.txt')
known += get_dock_list('set2_all.txt')
known += get_dock_list('set3_top3.txt')
gs_set = []
with open('../data/GSset_docking.txt', 'r') as infile:
for line in infile:
p1, p2 = line.strip().split()
show(p1)
show(p2)
for P1, P2, PDB1, CH1, PDB2, CH2, Mark in known:
if p1 == P1 and p2 == P2:
gs_set.append((P1, P2, PDB1, CH1, PDB2, CH2))
show([PDB1, CH1, PDB2, CH2])
break
elif p1 == P2 and p2 == P1:
gs_set.append((P2, P1, PDB2, CH2, PDB1, CH1))
show([PDB2, CH2, PDB1, CH1])
break
show()
show('We have\t%s\tknown docking pairs.\n' % len(gs_set))
if not os.path.exists('GSset'):
os.mkdir('GSset')
from use_dock import UseZDOCK
for p1, p2, pdb1, ch1, pdb2, ch2 in gs_set:
dock1 = UseZDOCK(temp_path='GSset/%s_%s' % (p1, p2),
pool_path='../data/dock_pool')
dock1.prepare_data(pdb1, ch1, pdb2, ch2)
dock1.dock_them(10)
dock1.generate_complex(10)
def zdock_rcf(info, pdb1, ch1, pdb2, ch2, sol_num=None, pool='.'):
from use_dock import UseZDOCK
dock = UseZDOCK(pool_path=pool)
outfile = '/rcf_%s_%s%s%s%s.txt'%(dock.TOOL.lower(),pdb1,ch1,pdb2,ch2)
outfile = dock.POOL_PATH + outfile.replace(' ', '-')
if os.path.exists(outfile) and len([l for l in open(outfile,'r')]) > 1:
return [[outfile, 'Precomputed']]
pdb1, ch1, pdb2, ch2 = dock.prepare_data(pdb1, ch1, pdb2, ch2)
rcf_path = os.path.abspath(dock.TOOL_PATH + '/../proteins_journal')
old_path = os.path.abspath('.')
try:
os.chdir(dock.TOOL_PATH)
os.system('./mark_sur %s %s_m.pdb'%(dock._receptor, dock._receptor[:-4]))
os.system('./mark_sur %s %s_m.pdb'%(dock._ligand, dock._ligand[:-4]))
os.chdir(dock.TEMP_PATH)
chain1 = os.path.basename(dock._receptor[:-4]+'_m.pdb')
chain2 = os.path.basename(dock._ligand[:-4]+'_m.pdb')
os.system("cp %s zout"%dock.solution)
os.system('%s/source/reformat zout %s/source/euler.15 3.0'%(rcf_path, rcf_path))
os.system('%s/source/contact_frequency -i zout.hout -o CG'%rcf_path)
os.system('perl %s/source/Cal_RCF.pl %s.CG'%(rcf_path, chain1))
os.system('perl %s/source/Cal_RCF.pl %s.CG'%(rcf_path, chain2))
os.system('cat %s.CG.RCF %s.CG.RCF > %s_old'%(chain1, chain2, outfile))
except Exception as e:
print 'Failed to run RCF due to', e
return [[outfile, 'Failed']]
finally:
dock.clean_temp_path()
os.chdir(old_path)
## reformat file
file1 = open(outfile + '_old', 'r')
file2 = open(outfile, 'w')
for line in file1:
if line[0] in '-0123456789':
ele = line.split('\t')
pos, res, cha, val = ele[:4]
val = float(val)
if cha in dock.chain1_id:
file2.write('%s\t%s\n'%(pdb1+':'+ch1.strip()+':'+pos, val))
elif cha in dock.chain2_id:
file2.write('%s\t%s\n'%(pdb2+':'+ch2.strip()+':'+pos, val))
else:
pass ## skip
file1.close()
file2.close()
return [[outfile, 'New']]
def main(para):
known = []
known += get_dock_list("set1_all.txt")
known += get_dock_list("set2_all.txt")
known += get_dock_list("set3_top3.txt")
gs_set = []
with open("../data/GSset_docking.txt", "r") as infile:
for line in infile:
p1, p2 = line.strip().split()
show(p1)
show(p2)
for P1, P2, PDB1, CH1, PDB2, CH2, Mark in known:
if p1 == P1 and p2 == P2:
gs_set.append((P1, P2, PDB1, CH1, PDB2, CH2))
show([PDB1, CH1, PDB2, CH2])
break
elif p1 == P2 and p2 == P1:
gs_set.append((P2, P1, PDB2, CH2, PDB1, CH1))
show([PDB2, CH2, PDB1, CH1])
break
show()
show("We have\t%s\tknown docking pairs.\n" % len(gs_set))
if not os.path.exists("GSset"):
os.mkdir("GSset")
from use_dock import UseZDOCK
for p1, p2, pdb1, ch1, pdb2, ch2 in gs_set:
dock1 = UseZDOCK(temp_path="GSset/%s_%s" % (p1, p2), pool_path="../data/dock_pool")
dock1.prepare_data(pdb1, ch1, pdb2, ch2)
dock1.dock_them(10)
dock1.generate_complex(10)
def zdock_clean(info, pdb1, ch1, pdb2, ch2, sol_num=5, pool='.'):
from use_dock import UseZDOCK
dock = UseZDOCK(pool_path=pool)
infilename, linenum = dock_area(dock, info, pdb1, ch1, pdb2, ch2, sol_num, skip=True)[0]
if linenum < sol_num:
os.remove(infilename)
dock.prepare_data(pdb1, ch1, pdb2, ch2)
if os.path.exists(dock.solution) and dock.solution_number() < sol_num:
os.remove(dock.solution)
print 'Delete', dock.solution
dock.clean_temp_path()
show('The clean function has deleted %s'%infilename)
return [[infilename, 'Deleted', linenum]]
else:
return []
