parm = amberParm(prmtop) if len(mdcrds) == 0: # if no mdcrd supplied, give default mdcrds.append('mdcrd') ptraj = utilities.which('cpptraj') # look for ptraj if ptraj is None: print 'Error: cpptraj needed for FindSaltbridge.py!' sys.exit() # quit if not found if not parm.valid: printusage() for x in range(len(mdcrds)): # check for mdcrd existences if utilities.fileexists(mdcrds[x]) == -1: printusage() residues = parm.parm_data['RESIDUE_LABEL'] for x in range(len(residues)): # build acceptor list and donor list try: tmp = acceptorlist[residues[x]] acceptor_inds.append(x + 1) except KeyError: pass try: tmp = donorlist[residues[x]] donor_inds.append(x + 1) except KeyError:
parm = amberParm(prmtop) if len(mdcrds) == 0: # if no mdcrd supplied, give default mdcrds.append('mdcrd') ptraj = utilities.which('cpptraj') # look for ptraj if ptraj is None: print 'Error: cpptraj needed for FindSaltbridge.py!' sys.exit() # quit if not found if not parm.valid: printusage() for x in range(len(mdcrds)): # check for mdcrd existences if utilities.fileexists(mdcrds[x]) == -1: printusage() residues = parm.parm_data['RESIDUE_LABEL'] for x in range(len(residues)): # build acceptor list and donor list try: tmp = acceptorlist[residues[x]] acceptor_inds.append(x+1) except KeyError: pass try: tmp = donorlist[residues[x]] donor_inds.append(x+1) except KeyError:
for z in range(int(lims[0].strip()),int(lims[1].strip()) + 1): residues.append(z) else: residues.append(int(ress[y].strip())) elif 'bin' in words[0].lower(): bins = words[1].lower().split('x') if len(bins) != 2: print 'Error: Invalid input file!' sys.exit() bins[0] = int(bins[0].strip()) bins[1] = int(bins[1].strip()) except ValueError: print 'Error: Invalid input file!' sys.exit() if utilities.fileexists(topname) == -1: sys.exit() residue_names = utilities.getallresinfo(topname,'RESIDUE_LABEL') if len(mdcrds) == 0: mdcrds.append('mdcrd') residue_number = utilities.resnum(topname) if residue_number == -1: print 'Error: Invalid topology file ' + topname + '!' sys.exit() for x in range(len(residues)): if residues[x] < 1: print 'Error: You chose a nonsensical residue (residue 0 or less)'
print >> sys.stderr, "Error: Command line error!" sys.exit() except ValueError: print >> sys.stderr, "Error: Command line error!" sys.exit() print "Removing py_leap.in" os.system("rm -f py_leap.in") leapfile = open("py_leap.in", "w") leapfile.write("source " + frc_fld + "\n") #### BEGIN INPUT FILE TYPES #### if pdb != "": if utilities.fileexists(pdb) == -1: leapfile.close() os.system("rm -f py_leap.in") 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")
for z in range(int(lims[0].strip()), int(lims[1].strip()) + 1): residues.append(z) else: residues.append(int(ress[y].strip())) elif "bin" in words[0].lower(): bins = words[1].lower().split("x") if len(bins) != 2: print "Error: Invalid input file!" sys.exit() bins[0] = int(bins[0].strip()) bins[1] = int(bins[1].strip()) except ValueError: print "Error: Invalid input file!" sys.exit() if utilities.fileexists(topname) == -1: sys.exit() residue_names = utilities.getallresinfo(topname, "RESIDUE_LABEL") if len(mdcrds) == 0: mdcrds.append("mdcrd") residue_number = utilities.resnum(topname) if residue_number == -1: print "Error: Invalid topology file " + topname + "!" sys.exit() for x in range(len(residues)): if residues[x] < 1: print "Error: You chose a nonsensical residue (residue 0 or less)"
sys.exit() except ValueError: print >> sys.stderr, "Error: Command line error!" sys.exit() print "Removing py_leap.in" os.system("rm -f py_leap.in") leapfile = open("py_leap.in", "w") leapfile.write("source " + frc_fld + "\n") #### BEGIN INPUT FILE TYPES #### if pdb != "": if utilities.fileexists(pdb) == -1: leapfile.close() os.system("rm -f py_leap.in") 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: