def getQuote(path):
"""
Get a quote to display for the refresh page.
Uses fortune to generate a quote.
Parameters:
path: The path to the fortune script (str)
Returns:
quote: The quote to display (str)
"""
fortune = os.popen(path)
quote = fortune.read()
quote = string.replace(quote, "\n", "<BR>")
quote = string.replace(quote, "\t", " "*5)
quote = "%s<P>" % quote
return quote
def splitInput(filename):
"""
Split the parallel input file into multiple async file names
Parameters
filename: The path to the original parallel input
file (string)
"""
nproc = 0
file = open(filename)
text = ""
while 1:
line = file.readline()
if line == "": break
text += line
line = string.strip(line)
if line.startswith("pdime"): # Get # Procs
words = string.split(line)
nproc = int(words[1]) * int(words[2]) * int(words[3])
if nproc == 0:
sys.stderr.write("%s is not a valid APBS parallel input file!\n" % filename)
sys.stderr.write("The inputgen script was unable to asynchronize this file!\n")
sys.exit(2)
period = string.find(filename,".")
for i in range(nproc):
outname = filename[0:period] + "-PE%i.in" % i
outtext = string.replace(text, "mg-para\n","mg-para\n async %i\n" % i)
outfile = open(outname, "w")
outfile.write(outtext)
outfile.close()
def parseLines(self, lines):
""" Parse the lines """
for line in lines:
if string.find(line, "ATOM") == 0:
subline = string.replace(line[30:], "-", " -")
words = string.split(subline)
if len(words) < 4:
#sys.stderr.write("Can't parse following line:\n")
#sys.stderr.write("%s\n" % line)
#sys.exit(2)
continue
self.gotatom = self.gotatom + 1
self.q = self.q + float(words[3])
rad = float(words[4])
center = []
for word in words[0:3]:
center.append(float(word))
for i in range(3):
self.minlen[i] = min(center[i] - rad, self.minlen[i])
self.maxlen[i] = max(center[i] + rad, self.maxlen[i])
elif string.find(line, "HETATM") == 0:
self.gothet = self.gothet + 1
def getCharmmParams(self, residue, name):
"""
Get the forcefield definitions from the Charmm database
Parameters
residue: The residue (residue)
name: The atom name (string)
Returns
resname: The name of the Charmm residue
atomname: The name of the Charmm atom
"""
resname = residue.get("name")
atomname = name
# Nucleic Acid Substitutions
if residue.get("type") == 4:
resname = resname[0]
if resname == "A": resname = "ADE"
elif resname == "C": resname = "CYT"
elif resname == "G": resname = "GUA"
elif resname == "T":
resname = "THY"
if atomname == "C7": atomname = "C5M"
elif atomname == "H71": atomname = "H51"
elif atomname == "H72": atomname = "H52"
elif atomname == "H73": atomname = "H53"
elif resname == "U": resname = "URA"
if atomname == "H5'1": atomname = "H5'"
elif atomname == "H5'2": atomname = "H5''"
elif atomname == "H2'1": atomname = "H2'"
elif atomname in ["H2'2", "HO'2"]: atomname = "H2''"
if residue.getAtom("O2'") == None:
if atomname in ["C2'", "H2'", "H2''"]: resname = "DEO1"
if residue.getAtom("H5T") != None:
if atomname in ["H5T", "O5'", "C5'"]: resname = "5TER"
if residue.getAtom("H3T") != None:
if atomname in ["H3T", "O3'", "C3'"]: resname = "3TER"
# Terminal/Water Substitutions
if residue.get("isNterm"):
if resname == "GLY" and atomname in [
"N", "H", "H2", "H3", "CA", "HA2", "HA3"
]:
resname = "GLYP"
if atomname == "H": atomname = "HT1"
elif atomname == "H2": atomname = "HT2"
elif atomname == "H3": atomname = "HT3"
elif resname == "PRO" and atomname in [
"N", "HN1", "HN2", "CD", "CA", "HD1", "HD2", "HA", "H2",
"H3"
]:
resname = "PROP"
if atomname == "H2": atomname = "HN1"
elif atomname == "H3": atomname = "HN2"
elif resname == "ACE":
if atomname == "CH3": atomname = "CAY"
elif atomname == "HH31": atomname = "HY1"
elif atomname == "HH32": atomname = "HY2"
elif atomname == "HH33": atomname = "HY3"
elif atomname == "C": atomname = "CY"
elif atomname == "O": atomname = "OY"
else:
if atomname in ["N", "H", "H2", "H3", "CA", "HA"]:
resname = "NTER"
if atomname == "H": atomname = "HT1"
elif atomname == "H2": atomname = "HT2"
elif atomname == "H3": atomname = "HT3"
elif residue.get("isCterm"):
if atomname in ["O", "OXT", "C"]:
resname = "CTER"
if atomname == "O":
atomname = "OT1"
elif atomname == "OXT":
atomname = "OT2"
elif residue.get("type") == 3:
resname = "TP3M"
if atomname == "O": atomname = "OH2"
# Residue substitutions
if resname == "ILE":
if atomname == "CD1": atomname = "CD"
elif atomname == "HD11": atomname = "HD1"
elif atomname == "HD12": atomname = "HD2"
elif atomname == "HD13": atomname = "HD3"
elif atomname == "HG12": atomname = "HG11"
elif atomname == "HG13": atomname = "HG12"
elif resname == "CYS" and "HG" not in residue.get("map"):
if atomname == "CB":
resname = "DISU"
atomname = "1CB"
elif atomname == "SG":
resname = "DISU"
atomname = "1SG"
elif resname == "HIS":
if "HD1" in residue.get("map") and "HE2" in residue.get("map"):
resname = "HSP"
elif "HD1" in residue.get("map"):
resname = "HSD"
elif "HE2" in residue.get("map"):
resname = "HSE"
elif resname == "GLU" or resname == "GLH":
if "HE1" in residue.get("map"):
if atomname == "HE1": atomname = "HE2"
elif atomname == "OE1": atomname = "OE2"
elif atomname == "OE2": atomname = "OE1"
if atomname in [
"CG", "HG3", "HG1", "HG2", "CD", "OE1", "OE2", "HE2"
]:
resname = "GLUP"
else:
resname == "GLU"
elif "HE2" in residue.get("map"):
if atomname in [
"CG", "HG3", "HG1", "HG2", "CD", "OE1", "OE2", "HE2"
]:
resname = "GLUP"
else:
resname == "GLU"
elif resname == "ASP" or resname == "ASH":
if "HD1" in residue.get("map"):
if atomname == "HD1": atomname = "HD2"
elif atomname == "OD1": atomname = "OD2"
elif atomname == "OD2": atomname = "OD1"
if atomname in [
"CB", "HB3", "HB1", "HB2", "CG", "OD1", "OD2", "HD2"
]:
resname = "ASPP"
else:
resname == "ASP"
elif "HD2" in residue.get("map"):
if atomname in [
"CB", "HB3", "HB1", "HB2", "CG", "OD1", "OD2", "HD2"
]:
resname = "ASPP"
else:
resname == "ASP"
# HETATM Substitutions
if resname == "ACE":
if atomname == "CH3": atomname = "CAY"
elif atomname == "HH31": atomname = "HY1"
elif atomname == "HH32": atomname = "HY2"
elif atomname == "HH33": atomname = "HY3"
elif atomname == "C": atomname = "CY"
elif atomname == "O": atomname = "OY"
elif resname == "ADP":
atomname = string.replace(atomname, "*", "\'")
# Hydrogen Substitutions
if atomname == "H": atomname = "HN"
elif atomname == "HA2": atomname = "HA1"
elif atomname == "HA3": atomname = "HA2"
elif atomname == "HB2" and resname not in ["ALA"]: atomname = "HB1"
elif atomname == "HB3" and resname not in ["ALA"]: atomname = "HB2"
elif atomname == "HD2" and resname not in [
"HSP", "HSE", "HSD", "ASPP"
]:
atomname = "HD1"
elif atomname == "HD3" and resname not in ["HIS", "HSE", "HSD"]:
atomname = "HD2"
elif atomname == "HE2" and resname not in [
"TRP", "HSP", "HSE", "HSD", "GLUP"
]:
atomname = "HE1"
elif atomname == "HE3" and resname not in ["TRP", "HSP", "HSE", "HSD"]:
atomname = "HE2"
elif atomname == "HG2":
atomname = "HG1"
elif atomname == "HG3":
atomname = "HG2"
elif atomname == "HG" and resname in ["SER", "CYS"]:
atomname = "HG1"
return resname, atomname
def createResults(header, input, name, time, missedligands=[]):
"""
Create the results web page for CGI-based runs
Parameters
header: The header of the PQR file (string)
input: A flag whether an input file has been created (int)
tmpdir: The resulting file directory (string)
name: The result file root name, based on local time (string)
time: The time taken to run the script (float)
missedligands: A list of ligand names whose parameters could
not be assigned. Optional. (list)
"""
newheader = string.replace(header, "\n", "<BR>")
newheader = string.replace(newheader," "," ")
filename = "%s%s%s.html" % (LOCALPATH, TMPDIR, name)
file = open(filename, "w")
file.write("<html>\n")
file.write("<head>\n")
file.write("<title>PDB2PQR Results</title>\n")
file.write("<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET)
file.write("</head>\n")
file.write("<body>\n")
file.write("<h2>PDB2PQR Results</h2>\n")
file.write("<P>\n")
file.write("Here are the results from PDB2PQR. The files will be available on the ")
file.write("server for a short period of time if you need to re-access the results.<P>\n")
file.write("<a href=\"%s%s%s.pqr\">%s.pqr</a><BR>\n" % (WEBSITE, TMPDIR, name, name))
if input:
file.write("<a href=\"%s%s%s.in\">%s.in</a><BR>\n" % (WEBSITE, TMPDIR, name, name))
pkaname = "%s%s%s.propka" % (LOCALPATH, TMPDIR, name)
if os.path.isfile(pkaname):
file.write("<a href=\"%s%s%s.propka\">%s.propka</a><BR>\n" % (WEBSITE, TMPDIR, name, name))
typename = "%s%s%s-typemap.html" % (LOCALPATH, TMPDIR, name)
if os.path.isfile(typename):
file.write("<a href=\"%s%s%s-typemap.html\">%s-typemap.html</a><BR>\n" % (WEBSITE, TMPDIR, name, name))
file.write("<P>The header for your PQR file, including any warnings generated, is:<P>\n")
file.write("<blockquote><code>\n")
file.write("%s<P>\n" % newheader)
file.write("</code></blockquote>\n")
if missedligands != []:
file.write("The forcefield that you have selected does not have ")
file.write("parameters for the following ligands in your PDB file. Please visit ")
file.write("<a href=\"http://davapc1.bioch.dundee.ac.uk/programs/prodrg/\">PRODRG</a> ")
file.write("to convert these ligands into MOL2 format. This ligand can the be ")
file.write("parameterized in your PDB2PQR calculation using the PEOE_PB methodology via ")
file.write("the 'Assign charges to the ligand specified in a MOL2 file' checkbox:<P>\n")
file.write("<blockquote><code>\n")
for item in missedligands:
file.write("%s<BR>\n" % item)
file.write("<P></code></blockquote>\n")
file.write("If you would like to run PDB2PQR again, please click <a href=\"%s%s\">\n" % (WEBSITE, WEBNAME))
file.write("here</a>.<P>\n")
file.write("<P>Thank you for using the PDB2PQR server!<P>\n")
file.write("<font size=\"-1\"><P>Total time on server: %.2f seconds</font><P>\n" % time)
file.write("<font size=\"-1\"><CENTER><I>Last Updated %s</I></CENTER></font>\n" % __date__)
file.write("</body>\n")
file.write("</html>\n")
def read4(self, filename):
"""Read from and set the current state according to the AutoGrid4 file.
"""
self.gpf_filename = filename
gpf_ptr = open(filename)
lines = gpf_ptr.readlines()
gpf_ptr.close()
keys = list(self.keys())
self.file_params = []
for line in lines:
#print "reading ", line
words = string.split(string.replace(line, '\t', ' '))
#print "words=", words
if words != [] and words[0][0] != '#':
p = words[0]
if p not in keys:
print("WARNING: unrecognized parameter in ", filename,
":\n", p)
continue
#print "p=", p
# maintain a list of the parameters read from the file
if self.file_params == [] or p != self.file_params[-1]:
self.file_params.append(p)
# parse the line
l = len(words)
for i in range(l):
if words[i][0] == '#':
l = i
break
values = words[1:l]
if p == 'parameter_file':
self['custom_parameter_file']['value'] = 1
self['parameter_file']['value'] = values[0]
elif ((len(values) == 1)
and (type(self[p]['default']) != list)):
self[p]['value'] = self._get_val(values[0])
#print " value=", self[p]['value']
#if words[0]=='types':
# #in this case have to set flags for possible new type
# extraLigandTypes = self.checkLigTypes(values[0])
#setting dielectric from a gpf is no longer supported
#instead must be set in a parameter library file
#elif p=='dielectric':
# self['dielectric4']['value'] = self._get_val(values[0])
elif p == 'ligand_types':
self['ligand_types']['value'] = string.join(words[1:l])
elif p == 'receptor_types':
self['receptor_types']['value'] = string.join(words[1:l])
elif words[0] == 'covalentmap':
#in this case set:
#covalent_ coords,constant,energy_barrier,half_width
self['covalentmap']['value'] = 1
self['covalent_half_width']['value'] = float(values[1])
self['covalent_energy_barrier']['value'] = float(values[2])
self['covalent_coords']['value'] = [float(values[3]),\
float(values[4]), float(values[5])]
self[p]['value'] = []
elif words[0] == 'gridcenter' and l > 1:
#need to convert to float
newvalue = [
float(values[0]),
float(values[1]),
float(values[2])
]
self['gridcenterAuto']['value'] = 0
self[p]['value'] = newvalue
else:
#print "in else for ", p
self[p]['value'] = []
for v in values:
self[p]['value'].append(self._get_val(v))
def read(self, filename):
"""Read from and set the current state according to the file.
"""
self.gpf_filename = filename
gpf_ptr = open(filename)
lines = gpf_ptr.readlines()
gpf_ptr.close()
self.file_params = []
checkedTypes = []
extraLigandTypes = []
keys = list(self.keys())
for line in lines:
words = string.split(string.replace(line, '\t', ' '))
if words != [] and words[0][0] != '#':
p = words[0]
if p not in keys:
print("WARNING: unrecognized parameter in ", filename,
":\n", p)
continue
# maintain a list of the parameters read from the file
if self.file_params == [] or p != self.file_params[-1]:
self.file_params.append(p)
# parse the line
l = len(words)
for i in range(l):
if words[i][0] == '#':
l = i
break
values = words[1:l]
if ((len(values) == 1) and (type(self[p]['default']) != list)):
self[p]['value'] = self._get_val(values[0])
if words[0] == 'types':
#in this case have to set flags for possible new type
extraLigandTypes = self.checkLigTypes(values[0])
elif words[0] == 'ligand_types':
self[p]['value'] = string.join(words[1:l])
elif words[0] == 'receptor_types':
self[p]['value'] = string.join(words[1:l])
elif words[0] == 'covalentmap':
#in this case set:
#covalent_ coords,constant,energy_barrier,half_width
self['covalentmap']['value'] = 1
self['covalent_half_width']['value'] = float(values[0])
self['covalent_energy_barrier']['value'] = float(values[1])
self['covalent_coords']['value'] = [float(values[2]),\
float(values[3]), float(values[4])]
self[p]['value'] = []
elif words[0] == 'nbp_r_eps':
#in this case have to check for nhb,ohb,shb +mset
#in this case have to check for new type constants
ptype = words[-1]
if len(words[l]) == 1: keyWord = words[l + 1]
else:
keyWord = words[l][1:]
mtype = string.split(keyWord, '-')[0]
ntype = string.split(keyWord, '-')[1]
if mtype in checkedTypes:
continue
if mtype in ['N', 'O', 'S'] and ntype == 'H':
#check for 12 6 vs 12 10 here
ind = mtype + 'HB'
if values[3] == '10':
self[ind]['value'] = 1
else:
self[ind]['value'] = 0
checkedTypes.append(mtype)
if mtype in extraLigandTypes:
i = ptype + mtype + ntype
Rij[i] = float(words[1])
epsij[i] = float(words[2])
elif words[0] == 'sol_par':
if len(words[l]) == 1: mtype = words[l + 1]
else: mtype = words[l][1]
if mtype in extraLigandTypes:
SolVol[mtype] = float(values[0])
SolPar[mtype] = float(values[1])
elif words[0] == 'constant':
if len(words[l]) == 1: mtype = words[l + 1]
else: mtype = words[l][1]
SolCon[mtype] = float(values[0])
elif words[0] == 'gridcenter' and l > 1:
#need to convert to float
newvalue = [
float(values[0]),
float(values[1]),
float(values[2])
]
self['gridcenterAuto']['value'] = 0
self[p]['value'] = newvalue
else:
self[p]['value'] = []
for v in values:
self[p]['value'].append(self._get_val(v))