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ConnGO_master.py
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ConnGO_master.py
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import os, sys, string
import linecache, math
import numpy as np
current_dir_path = os.getcwd()
user_file = sys.argv[1]
control_file = current_dir_path + "/control.inp"
job_file = current_dir_path + "/job.inp"
settings = ["load_SDF", "SDF_filename", "Forcefield", "Opt_setting", "Steps", "Convergence_setting", "tier2_mem", "tier2_nprocs","tier2_Functional", "tier2_Basis","tier2_gaussian_setting", "tier3_mem", "tier3_nprocs", "tier3_Functional", "tier3_Basis","tier3_gaussian_setting", "tier4_mem", "tier4_nprocs","tier4_Functional", "tier4_Basis","tier4_gaussian_setting", "charge", "multiplicity", "long_bond", "job_type"]
### READING CONTROL FILE
value = {}
with open(control_file, "r") as ctrl:
u = 0
while u < len((settings)):
for line in ctrl:
if settings[u] in line:
val_line = line.split(":")
if "#" in val_line[1]:
val_split = val_line[1].split("#")
value[settings[u]] = val_split[0].strip()
else:
value[settings[u]] = val_line[1].strip()
break
u = u +1
if value["load_SDF"] == "false":
initial_smi_path = current_dir_path + "/" + user_file
smi_fsplit = user_file.split(".")
smi_file = user_file
obmin_sdf = smi_fsplit[0] + "_tier1.sdf"
obmin_xyz = smi_fsplit[0] + "_tier1.xyz"
else:
initial_sdf_path = current_dir_path + "/" + user_file
obmin_sdf = user_file
sdf_fsplit = user_file.split(".")
obmin_xyz = sdf_fsplit[0] + ".xyz"
smi_file = sdf_fsplit[0] + ".xyz"
def count_pass(filen):
with open(filen,"r") as cf:
blc = cf.read()
if "PASS" in blc:
count = 1
else:
count = 0
return(count)
if sys.argv[1] == "analyse":
with open("title_list", "r") as tl:
total_mol = sum(1 for t_line in tl)
with open("title_list", "r") as tl:
tier2_p_count = 0
tier3_p_count = 0
tier4_p_count = 0
for le in tl:
os.chdir(le.strip())
t4_check = 0
if os.path.exists("compare_tier1_vs_tier2"):
tier2_p_count = tier2_p_count + count_pass("compare_tier1_vs_tier2")
if os.path.exists("compare_tier1_vs_tier3"):
tier3_p_count = tier3_p_count + count_pass("compare_tier1_vs_tier3")
if os.path.exists("compare_tier1_vs_tier4"):
tier4_p_count = tier4_p_count + count_pass("compare_tier1_vs_tier4")
t4_check = 1
if os.path.exists("compare_tier2_vs_tier4"):
tier4_p_count = tier4_p_count + count_pass("compare_tier2_vs_tier4")
t4_check = 1
if os.path.exists("compare_tier3_vs_tier4"):
tier4_p_count = tier4_p_count + count_pass("compare_tier3_vs_tier4")
t4_check = 1
if not (os.path.exists("compare_tier1_vs_tier4") or os.path.exists("compare_tier2_vs_tier4") or os.path.exists("compare_tier3_vs_tier4")):
with open("tier4.log","r") as logc:
t4out = logc.read()
if "Error termination" in t4out or "imaginary freq" in t4out or t4_check == 0:
temp11 = current_dir_path + "/tempfails"
with open(temp11, "a") as tmf:
tmf.write(le.strip())
tmf.write("\n")
for files in os.listdir(current_dir_path):
if files.endswith(".smi"):
smi_file = files
com1 = "python " + current_dir_path + "/ConnGO_check_smiles.py " + le.strip() + " " + smi_file + " " + current_dir_path
os.system(com1)
break
os.chdir("..")
if os.path.exists("temp11"):
with open("temp11", "r") as tempf:
count_ions = sum(1 for ee in tempf)
else:
count_ions = 0
with open("Results.dat", "w") as res:
res.write("Total number of molecules entering ConnGO = " + str(total_mol) + "\n\n")
res.write("TIER-2\n")
res.write("Number of molecules PASS = " + str(tier2_p_count) + "\n")
res.write("Number of molecules FAIL = " + str(total_mol-tier2_p_count) + "\n\n")
res.write("TIER-3\n")
res.write("Number of molecules PASS = " + str(tier3_p_count) + "\n")
res.write("Number of molecules FAIL = " + str(total_mol-tier2_p_count-tier3_p_count) + "\n\n")
res.write("TIER-4\n")
res.write("Number of molecules PASS = " + str(tier4_p_count) + "\n")
res.write("Number of molecules FAIL = " + str(total_mol-tier4_p_count) + "\n\n") ## WRONG
res.write("Number of zwitterions encountered that fail ConnGO = " + str(count_ions) + " (if greater than 0, see modified_smiles.smi)\n\n")
res.write("List of molecules failing ConnGO:\n")
n = 1
if os.path.exists("tempfails"):
for fail_l in open("tempfails", "r"):
res.write(str(n) + " " + fail_l )
n = n+1
os.system("rm -f temp* ")
sys.exit()
if sys.argv[1] == "launch":
if value["job_type"] == "submission":
#os.system("ls run*.sh > runlist")
with open("title_list", "r") as tl:
for linet in tl:
os.chdir(linet.strip())
pt1 = "launching " + linet.strip()
print(pt1)
os.system("qsub run.sh")
os.chdir("..")
if value["job_type"] == "interactive":
with open("title_list", "r") as tl:
for linet in tl:
os.chdir(linet.strip())
pt1 = "launching " + linet.strip()
print(pt1)
os.system("bash run.sh &")
os.chdir("..")
sys.exit()
if value["load_SDF"] == "false":
#obmin
to_genxyz = "obabel -oxyz " + smi_file + " > " + smi_fsplit[0] + "_initial.xyz --gen3d"
#to_obmin = "obminimize -osdf -ff MMFF94 -sd -n 100000 -c 1e-8 " + smi_fsplit[0] + "_initial.xyz > " + OMST_sdf
to_obmin = "obminimize -osdf -ff " + value["Forcefield"] + " -" + value["Opt_setting"] + " -n " + value["Steps"] + " -c " + value["Convergence_setting"] +" " + smi_fsplit[0] + "_initial.xyz > " + obmin_sdf
omst_xyzgen = "obabel -oxyz " + obmin_sdf + " > " + obmin_xyz
print("generating initial xyz from smi")
os.system(to_genxyz)
print("OMST in progess")
os.system(to_obmin)
print("OMST done, sdf created")
os.system(omst_xyzgen)
print("OMST xyz created")
def launch_test(title_name, sdf_file,xyz_file, tier_level):
fl1 = tier_level+"_Functional"
bl1 = tier_level+"_Basis"
st1 = tier_level+"_gaussian_setting"
tt1 = tier_level+"_mem"
tt2 = tier_level+"_nprocs"
#current_launch_com = current_title + "_" + tier_level + ".com"
current_launch_com = tier_level + ".com"
create_comfile = "python " + current_dir_path +"/ConnGO_xyz2sdf.py " + sdf_file + " " + xyz_file + " 1.7 discard.sdf " + current_launch_com + " discard_rmsd " + value["charge"].strip() +" "+ value["multiplicity"].strip() +" "+ value[tt1].strip() +" " + value[tt2].strip() + " \n\n"
#method_insert_hf = "sed -i \"s/METHOD/HF\\\/sto-3G SCF(maxcycles=100) Opt(calcall,cartesian,tight,maxcyc=100) Int(Grid=Ultrafine) freq /\" " + current_launch_com + " \n\n"
#method_insert_hf = "sed -i \"s/METHOD/" + func + "\\\/" + basis1 + " SCF(maxcycles=100) Opt(calcall,cartesian,tight,maxcyc=100) Int(Grid=Ultrafine) freq /\" " + current_launch_com + " \n\n"
method_insert_hf = "sed -i \"s/METHOD/" + value[fl1] + "\\\/" + value[bl1] + " " + value[st1] +" /\" " + current_launch_com + " \n\n"
launch_gaussian = "g16 " + current_launch_com + "\n\n"
run_file.write(create_comfile)
run_file.write(method_insert_hf)
run_file.write(launch_gaussian)
def hf_fail(title_name):
launch_test(current_title,current_sdf, current_xyz , "tier3" )
check_ET_321log = "if grep -q \"Error termination\" " + current_321g_log + " ; then\n"
run_file.write(check_ET_321log)
launch_test(current_title, current_sdf,current_xyz, "tier4")
check_2dfp_status(title_name, current_sdf, "tier1")
check_IF_321log = "elif grep -q \"imaginary freq\" " + current_321g_log + " ; then\n"
run_file.write(check_IF_321log)
launch_test(current_title, current_sdf,current_xyz, "tier4")
check_2dfp_status(title_name, current_sdf, "tier1")
run_file.write("else\n")
opt_321g_xyz = "for f in " + current_321g_log+ "; do NATOMS=$(grep -m1 NAtom $f | awk \'{print $2}\'); echo $NATOMS; echo ${f%.*}; grep -i -A $(( $NATOMS + 4 )) \'Standard Orientation\' $f| tail -$NATOMS | awk \'{printf \"%3g\" \"%15.8f\" \"%15.8f\" \"%15.8f\", $2, $4, $5, $6}{printf \"\\n\"}\' ; done > " +current_321g_xyz+ " \n\n"
#create_321g_rmsd = "/apps/moldis_utils/sdf2sdf/xyz2sdf_v1.exe " + current_sdf +" " + current_321g_xyz + " 321g.sdf 1.7 " + " temp1.com 2 > rmsd_mmff_dp_" + current_title + "\n\n"
create_321g_rmsd = "python " + current_dir_path + "/ConnGO_xyz2sdf.py " + current_sdf + " " + current_321g_xyz + " 1.7 " + current_321g_sdf + " temp.com compare_tier1_vs_tier3 " + value["charge"].strip() +" "+ value["multiplicity"].strip() + " 8 2 \n\n"
check_FAIL_321g = "if grep -q \"FAIL\" compare_tier1_vs_tier3 ; then\n"
run_file.write(opt_321g_xyz)
run_file.write(create_321g_rmsd)
run_file.write(check_FAIL_321g)
launch_test(current_title,current_sdf, current_xyz , "tier4")
check_2dfp_status(title_name, current_sdf, "tier1")
run_file.write("else\n")
launch_test(current_title, current_321g_sdf,current_321g_xyz, "tier4")
check_2dfp_status(title_name,current_321g_sdf, "tier3")
run_file.write(" \n fi \n fi \n")
def check_2dfp_status(title_name, previous_tier_sdf, tier):
check_normalterm = "if grep -q \"Normal termination\" " + current_2dfp_log + " ; then\n\n"
opt_2dfp_xyz = "for f in " + current_2dfp_log + "; do NATOMS=$(grep -m1 NAtom $f | awk \'{print $2}\'); echo $NATOMS; echo ${f%.*}; grep -i -A $(( $NATOMS + 4 )) \'Standard Orientation\' $f| tail -$NATOMS | awk \'{printf \"%3g\" \"%15.8f\" \"%15.8f\" \"%15.8f\", $2, $4, $5, $6}{printf \"\\n\"}\' ; done > " + current_2dfp_xyz + " \n\n"
#create_2dfp_rmsd = "/apps/moldis_utils/sdf2sdf/xyz2sdf_v1.exe " + previous_tier_sdf + " " +current_2dfp_xyz + " 2dfp.sdf 1.7 " + "temp1.com 2 > rmsd_"+ tier+"_2dfp_" + current_title + "\n\n"
create_2dfp_rmsd = "python " + current_dir_path + "/ConnGO_xyz2sdf.py " + previous_tier_sdf + " " + current_2dfp_xyz + " 1.7 " + current_2dfp_sdf + " temp.com compare_" + tier + "_vs_tier4 " + value["charge"].strip() +" "+ value["multiplicity"].strip() +" 8 2 \n\n"
run_file.write(check_normalterm)
run_file.write(opt_2dfp_xyz)
run_file.write(create_2dfp_rmsd)
copy_files(title_name)
run_file.write("\nfi\n")
def copy_files(title_name):
if value["job_type"] == "submission":
copy_back = "cp *com *log compare* *xyz *sdf " + current_dir_path + "/"+title_name+"/ \n"
run_file.write(copy_back)
run_file.write("rm -rf $WORKDIR\n\n")
run_file.write("exit\n\n")
else:
run_file.write("exit\n\n")
######## Create seperate sdf files from OMST sdf
ln_sdf = 1
with open(obmin_sdf, "r") as initial_sdf:
num_lines_sdf = sum(1 for line_par in initial_sdf)
while ln_sdf <= num_lines_sdf:
P = linecache.getline(obmin_sdf, ln_sdf+3)
P_lsp = P.split()
num_atoms_sdf = int(P_lsp[0])
count_ext_sdf = int(P_lsp[1])
next_ln_sdf = ln_sdf + num_atoms_sdf + count_ext_sdf + 6
if IndexError:
print("extra lines in sdf file, check if there are additional lines like CHG, RAD. If yes, remove them")
sys.exit()
P1 = linecache.getline(obmin_sdf, ln_sdf).strip()
fname_sdf = P1 + "_tier1.sdf"
with open("title_list", "a") as dl1:
dl1.write(P1.strip())
dl1.write("\n")
os.mkdir(P1)
os.chdir(P1)
for line_sdf in range(ln_sdf, next_ln_sdf):
with open("tier1.sdf","a") as new_f_sdf:
pline_sdf = linecache.getline(obmin_sdf, line_sdf)
new_f_sdf.write(pline_sdf)
os.chdir("..")
ln_sdf = next_ln_sdf
print("seperate OMST sdfs created")
######## Create seperate xyz files from OMST xyz
ln_mxyz = 1
with open(obmin_xyz, "r") as ini_xyz:
num_lines_mxyz = sum(1 for line_mxyz in ini_xyz)
countd = 1
while ln_mxyz <= num_lines_mxyz:
num_atoms_mxyz = linecache.getline(obmin_xyz, ln_mxyz)
next_ln_mxyz = ln_mxyz + int(num_atoms_mxyz) + 2
with open("title_list", "r") as dr:
dname = linecache.getline("title_list", countd).strip()
os.chdir(dname)
with open("tier1.xyz", "w") as new_f_mxyz:
new_f_mxyz.write(num_atoms_mxyz)
new_f_mxyz.write(dname)
new_f_mxyz.write("\n")
for ln_mxyz in range(ln_mxyz + 2, next_ln_mxyz):
ln_mxyz = linecache.getline(obmin_xyz, ln_mxyz)
new_f_mxyz.write(ln_mxyz)
os.chdir("..")
countd = countd + 1
ln_mxyz = next_ln_mxyz
print("seperate OMST xyzs created")
####### Begining of FLOW 3
for line_title in open("title_list","r"):
current_title = line_title.strip()
#run_script = "run_" + current_title + ".sh"
run_script = "run.sh"
os.chdir(current_title)
with open(run_script, "a") as run_file:
if value["job_type"] == "submission":
with open(job_file, "r") as job_block:
j = job_block.read()
run_file.write(j)
run_file.write("\n")
current_sdf = "tier1.sdf"
current_xyz = "tier1.xyz"
current_hf_log = "tier2.log"
current_hf_sdf = "tier2.sdf"
current_hf_xyz = "tier2.xyz"
current_321g_log = "tier3.log"
current_321g_sdf = "tier3.sdf"
current_321g_xyz = "tier3.xyz"
current_2dfp_log = "tier4.log"
current_2dfp_sdf = "tier4.sdf"
current_2dfp_xyz = "tier4.xyz"
if value["job_type"] == "submission":
#copy_smi = "cp " + current_dir_path+ "/" + smi_file + " . \n"
new_path = os.getcwd()
copy_sdf = "cp " + new_path+ "/" + current_sdf + " . \n"
copy_xyz = "cp " + new_path+ "/" + current_xyz + " .\n\n"
copy_ctrl = "cp " + current_dir_path+ "/control.inp .\n\n"
#run_file.write(copy_smi)
run_file.write(copy_sdf)
run_file.write(copy_xyz)
run_file.write(copy_ctrl)
launch_test(current_title, current_sdf, current_xyz , "tier2")
check_ET_HFlog = "if grep -q \"Error termination\" " + current_hf_log + " ; then\n"
run_file.write(check_ET_HFlog)
hf_fail(current_title)
check_IF_HFlog = "elif grep -q \"imaginary freq\" " + current_hf_log + " ; then\n"
run_file.write(check_IF_HFlog)
hf_fail(current_title)
run_file.write("\nelse\n")
opt_hf_xyz = " for f in " + current_hf_log+ "; do NATOMS=$(grep -m1 NAtom $f | awk \'{print $2}\'); echo $NATOMS; echo ${f%.*}; grep -i -A $(( $NATOMS + 4 )) \'Standard Orientation\' $f| tail -$NATOMS | awk \'{printf \"%3g\" \"%15.8f\" \"%15.8f\" \"%15.8f\", $2, $4, $5, $6}{printf \"\\n\"}\' ; done > " +current_hf_xyz+ " \n\n"
#create_hf_rmsd = "/apps/moldis_utils/sdf2sdf/xyz2sdf_v1.exe " + current_sdf + " "+ current_hf_xyz + " hf.sdf 1.7 " + "temp1.com 2 > rmsd_mmff_hf_" + current_title + "\n\n"
create_hf_rmsd = "python " + current_dir_path + "/ConnGO_xyz2sdf.py " + current_sdf + " " + current_hf_xyz + " 1.7 " + current_hf_sdf +" temp.com compare_tier1_vs_tier2 " + value["charge"].strip() +" "+ value["multiplicity"].strip() +" 8 2\n\n"
check_FAIL_hf = "if grep -q \"FAIL\" compare_tier1_vs_tier2 ; then\n"
run_file.write(opt_hf_xyz)
run_file.write(create_hf_rmsd)
run_file.write(check_FAIL_hf)
hf_fail(current_title)
run_file.write("else\n")
launch_test(current_title, current_hf_sdf, current_hf_xyz, "tier4")
check_2dfp_status(current_title, current_hf_sdf, "tier2")
run_file.write("\n fi \n fi\n")
print("created "+ run_script)
os.chdir("..")