#######################################################################
# #
# This utility prints the amino acid decomposition for a given prmtop #
# #
# Written by Jason Swails, 04/26/2010 #
# #
#######################################################################
import sys, utilities
if len(sys.argv) != 2 or '-help' in sys.argv[1]:
print 'AA_decomp.py <prmtop> || <pdb>'
sys.exit()
if sys.argv[1].lower().endswith("pdb"):
residue_decomp = utilities.getresdecmp_pdb(sys.argv[1])
else:
residue_decomp = utilities.getresdecmp_prmtop(sys.argv[1])
# residue indices are : ALA, ARG, ASN, ASP, CYS, GLU, GLN, GLY
# HIS, ILE, LEU, LYS, MET, PHE, PRO, SER
# THR, TRP, VAL, WAT, UNK
print 'ALA: ' + str(residue_decomp[0])
print 'ARG: ' + str(residue_decomp[1])
print 'ASN: ' + str(residue_decomp[2])
print 'ASP: ' + str(residue_decomp[3])
print 'CYS: ' + str(residue_decomp[4])
print 'GLU: ' + str(residue_decomp[5])
print 'GLN: ' + str(residue_decomp[6])
print 'GLY: ' + str(residue_decomp[7])
print 'HIS: ' + str(residue_decomp[8])
# #
# This utility prints the amino acid decomposition for a given prmtop #
# #
# Written by Jason Swails, 04/26/2010 #
# #
#######################################################################
import sys, utilities
if len(sys.argv) != 2 or '-help' in sys.argv[1]:
print 'AA_decomp.py <prmtop> || <pdb>'
sys.exit()
if sys.argv[1].lower().endswith("pdb"):
residue_decomp = utilities.getresdecmp_pdb(sys.argv[1])
else:
residue_decomp = utilities.getresdecmp_prmtop(sys.argv[1])
# residue indices are : ALA, ARG, ASN, ASP, CYS, GLU, GLN, GLY
# HIS, ILE, LEU, LYS, MET, PHE, PRO, SER
# THR, TRP, VAL, WAT, UNK
print 'ALA: ' + str(residue_decomp[0])
print 'ARG: ' + str(residue_decomp[1])
print 'ASN: ' + str(residue_decomp[2])
print 'ASP: ' + str(residue_decomp[3])
print 'CYS: ' + str(residue_decomp[4])
print 'GLU: ' + str(residue_decomp[5])
print 'GLN: ' + str(residue_decomp[6])
print 'GLY: ' + str(residue_decomp[7])
print 'HIS: ' + str(residue_decomp[8])
sys.exit()
leapfile.write("l = loadpdb " + pdb + "\n")
infiles = True
#### END INPUT FILE TYPES ####
if not infiles:
print "Error: You have not specified any structures!"
leapfile.close()
os.system("rm -f py_leap.in")
sys.exit()
if ci == 1:
leapfile.write("addIons l Na+\n")
elif ci == 2:
if pdb != "":
residue_decmp = utilities.getresdecmp_pdb(pdb)
if len(residue_decmp) == 0:
print "Not ready yet..."
leapfile.close()
os.system("rm -f py_leap.in")
sys.exit()
leapfile.write("addIons l Na+ " + str(residue_decmp[21]) + \
" Cl- " + str(residue_decmp[20]) + "\n")
if sol > 0:
leapfile.write("solvateOct l TIP3PBOX " + str(sol) + "\n")
if radii != "" and cph == "no":
leapfile.write("set default PBRadii " + radii + "\n")
leapfile.write("l = loadpdb " + pdb + "\n")
infiles = True
#### END INPUT FILE TYPES ####
if not infiles:
print "Error: You have not specified any structures!"
leapfile.close()
os.system("rm -f py_leap.in")
sys.exit()
if ci == 1:
leapfile.write("addIons l Na+\n")
elif ci == 2:
if pdb != "":
residue_decmp = utilities.getresdecmp_pdb(pdb)
if len(residue_decmp) == 0:
print "Not ready yet..."
leapfile.close()
os.system("rm -f py_leap.in")
sys.exit()
leapfile.write("addIons l Na+ " + str(residue_decmp[21]) + " Cl- " + str(residue_decmp[20]) + "\n")
if sol > 0:
leapfile.write("solvateOct l TIP3PBOX " + str(sol) + "\n")
if radii != "" and cph == "no":
leapfile.write("set default PBRadii " + radii + "\n")