def run(
self,
chain=None,
chargeType="bcc",
chargeVal=None,
guessCharge=False,
multiplicity="1",
atomType="gaff",
force=False,
basename=None,
debug=False,
outTopol="all",
engine="tleap",
allhdg=False,
timeTol=36000,
qprog="sqm",
ekFlag=None,
outType="mol2",
):
ccpnProject = self.project
if chain:
other = [chain]
else:
other = self.getHeteroMols()
if not other:
print("WARN: no molecules entitled for ACPYPE")
return None
acpypeDict = {}
for chain in other:
if chargeVal is None and not guessCharge:
chargeVal = chain.molecule.formalCharge
# pdbCode = ccpnProject.name
res = chain.findFirstResidue()
resName = res.ccpCode.upper()
if chargeVal is None:
print("Running ACPYPE for '%s : %s' and trying to guess net charge" % (resName, chain.molecule.name))
else:
print("Running ACPYPE for '%s : %s' with charge '%s'" % (resName, chain.molecule.name, chargeVal))
random.seed()
d = [random.choice(letters) for x in range(10)]
randString = "".join(d)
randString = "test"
dirTemp = "/tmp/ccpn2acpype_%s" % randString
if not os.path.exists(dirTemp):
os.mkdir(dirTemp)
if outType == "mol2":
resTempFile = os.path.join(dirTemp, "%s.mol2" % resName)
else:
resTempFile = os.path.join(dirTemp, "%s.pdb" % resName)
entry = ccpnProject.currentNmrEntryStore.findFirstEntry()
strucGen = entry.findFirstStructureGeneration()
refStructure = strucGen.structureEnsemble.sortedModels()[0]
if outType == "mol2":
mol2Format = Mol2Format.Mol2Format(ccpnProject)
mol2Format.writeChemComp(
resTempFile,
chemCompVar=chain.findFirstResidue().chemCompVar,
coordSystem="pdb",
minimalPrompts=True,
forceNamingSystemName="XPLOR",
)
else:
pdbFormat = PdbFormat.PdbFormat(ccpnProject)
pdbFormat.writeCoordinates(
resTempFile,
exportChains=[chain],
structures=[refStructure],
minimalPrompts=True,
forceNamingSystemName="XPLOR",
)
origCwd = os.getcwd()
os.chdir(dirTemp)
t0 = time.time()
print(header)
try:
molecule = ACTopol(
resTempFile,
chargeType=chargeType,
chargeVal=chargeVal,
debug=debug,
multiplicity=multiplicity,
atomType=atomType,
force=force,
outTopol=outTopol,
engine=engine,
allhdg=allhdg,
basename=basename,
timeTol=timeTol,
qprog=qprog,
ekFlag='''"%s"''' % ekFlag,
)
if not molecule.acExe:
molecule.printError("no 'antechamber' executable... aborting!")
hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
hint2 = (
"HINT2: is 'antechamber' in your $PATH?"
+ " What 'which antechamber' in your terminal says?"
+ " 'alias' doesn't work for ACPYPE."
)
molecule.printMess(hint1)
molecule.printMess(hint2)
sys.exit(1)
molecule.createACTopol()
molecule.createMolTopol()
acpypeFailed = False
except:
raise
_exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
print("ACPYPE FAILED: %s" % exceptionValue)
if debug:
traceback.print_tb(exceptionTraceback, file=sys.stdout)
acpypeFailed = True
execTime = int(round(time.time() - t0))
if execTime == 0:
msg = "less than a second"
else:
msg = elapsedTime(execTime)
try:
rmtree(molecule.tmpDir)
except:
raise
print("Total time of execution: %s" % msg)
if not acpypeFailed:
acpypeDict[resName] = [x for x in dirWalk(os.path.join(dirTemp, "%s.acpype" % resName))]
else:
acpypeDict[resName] = []
# sys.exit(1)
os.chdir(origCwd)
self.acpypeDictFiles = acpypeDict
def run(self, chain = None, chargeType = 'bcc', chargeVal = None, guessCharge = False,
multiplicity = '1', atomType = 'gaff', force = False, basename = None,
debug = False, outTopol = 'all', engine = 'tleap', allhdg = False,
timeTol = 36000, qprog = 'sqm', ekFlag = None, outType='mol2'):
ccpnProject = self.project
if chain:
other = [chain]
else:
other = self.getHeteroMols()
if not other:
print("WARN: no molecules entitled for ACPYPE")
return None
acpypeDict = {}
for chain in other:
if chargeVal == None and not guessCharge:
chargeVal = chain.molecule.formalCharge
# pdbCode = ccpnProject.name
res = chain.findFirstResidue()
resName = res.ccpCode.upper()
if chargeVal == None:
print("Running ACPYPE for '%s : %s' and trying to guess net charge" % (resName, chain.molecule.name))
else:
print("Running ACPYPE for '%s : %s' with charge '%s'" % (resName, chain.molecule.name, chargeVal))
random.seed()
d = [random.choice(string.letters) for x in xrange(10)]
randString = "".join(d)
randString = 'test'
dirTemp = '/tmp/ccpn2acpype_%s' % randString
if not os.path.exists(dirTemp):
os.mkdir(dirTemp)
if outType == 'mol2':
resTempFile = os.path.join(dirTemp, '%s.mol2' % resName)
else:
resTempFile = os.path.join(dirTemp, '%s.pdb' % resName)
entry = ccpnProject.currentNmrEntryStore.findFirstEntry()
strucGen = entry.findFirstStructureGeneration()
refStructure = strucGen.structureEnsemble.sortedModels()[0]
if outType == 'mol2':
mol2Format = Mol2Format.Mol2Format(ccpnProject)
mol2Format.writeChemComp(resTempFile, chemCompVar=chain.findFirstResidue().chemCompVar,coordSystem='pdb', minimalPrompts = True, forceNamingSystemName = 'XPLOR')
else:
pdbFormat = PdbFormat.PdbFormat(ccpnProject)
pdbFormat.writeCoordinates(resTempFile, exportChains = [chain], structures = [refStructure], minimalPrompts = True, forceNamingSystemName = 'XPLOR')
origCwd = os.getcwd()
os.chdir(dirTemp)
t0 = time.time()
print(header)
try:
molecule = ACTopol(resTempFile, chargeType = chargeType,
chargeVal = chargeVal, debug = debug, multiplicity = multiplicity,
atomType = atomType, force = force, outTopol = outTopol,
engine = engine, allhdg = allhdg, basename = basename,
timeTol = timeTol, qprog = qprog, ekFlag = '''"%s"''' % ekFlag)
if not molecule.acExe:
molecule.printError("no 'antechamber' executable... aborting!")
hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
hint2 = "HINT2: is 'antechamber' in your $PATH?\n What 'which antechamber' in your terminal says?\n 'alias' doesn't work for ACPYPE."
molecule.printMess(hint1)
molecule.printMess(hint2)
sys.exit(1)
molecule.createACTopol()
molecule.createMolTopol()
acpypeFailed = False
except:
raise
_exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
print("ACPYPE FAILED: %s" % exceptionValue)
if debug:
traceback.print_tb(exceptionTraceback, file = sys.stdout)
acpypeFailed = True
execTime = int(round(time.time() - t0))
if execTime == 0:
msg = "less than a second"
else:
msg = elapsedTime(execTime)
try: rmtree(molecule.tmpDir)
except: raise
print("Total time of execution: %s" % msg)
if not acpypeFailed:
acpypeDict[resName] = [x for x in dirWalk(os.path.join(dirTemp, '%s.acpype' % resName))]
else:
acpypeDict[resName] = []
# sys.exit(1)
os.chdir(origCwd)
self.acpypeDictFiles = acpypeDict
# from ogpdb to amber pdb and top
agpdb = 'ag%s.pdb' % res # output name
agtop = 'ag%s.top' % res
cmd = ' %s -f %s -o %s -p %s -ff amber99sb %s' % (pdb2gmx, apdb, agpdb, agtop, water)
pdebug(cmd)
out = _getoutput(cmd)
#print(out)
#parseOut(out)
# acpype on agpdb file
fixRes4Acpype(agpdb)
cv = None
#cmd = "%s -dfi %s -c %s -a %s" % (acpypeExe, agpdb, cType, ffType)
if res in ['JJJ', 'RRR'] and cType == 'bcc': cv = 3 #cmd += ' -n 3' # acpype failed to get correct charge
mol = ACTopol(agpdb, chargeType = cType, atomType = ffType, chargeVal = cv,
debug = False, verbose = debug, gmx45 = True)
mol.createACTopol()
mol.createMolTopol()
#out = commands.getstatusoutput(cmd)
#parseOut(out[1])
print("Compare ACPYPE x GMX AMBER99SB topol & param")
checkTopAcpype(res)
# calc Pot Energy
print("Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)")
# calc gmx amber energies
dihAmb, dihAcp = calcGmxPotEnerDiff(res)
# calc gmx acpype energies
os.system('rm -f %s/\#* posre.itp tempScript.py' % tmpDir)
os.system("find . -name 'ag*GMX*.itp' | xargs grep -v 'created by acpype on' > standard_ag_itp.txt")
cType = 'gas' #'gas'
debug = False
water = ' -water none'
print('usePymol: %s, ffType: %s, cType: %s' % (usePymol, ffType, cType))
tmpDir = '/tmp/testAcpype'
delList = ['topol.top', 'posre.itp']
#create Dummy PDB
tpdb = '/tmp/tmp.pdb'
dummyLine = 'ATOM 1 N ALA A 1 -1.188 -0.094 0.463 1.00 0.00 N\n'
open(tpdb, 'w').writelines(dummyLine)
tempObj = ACTopol(tpdb, chargeVal=0, verbose=False)
# Binaries for ambertools
acExe = tempObj.acExe
tleapExe = tempObj.tleapExe
sanderExe = os.path.join(os.path.dirname(acExe), 'sander')
ambpdbExe = os.path.join(os.path.dirname(acExe), 'ambpdb')
exePymol = '/sw/bin/pymol'
# Binaries for gromacs
gpath = '/sw/'
gmxTopDir = gpath + "share"
pdb2gmx = gpath + 'bin/pdb2gmx'
grompp = gpath + 'bin/grompp'
mdrun = gpath + 'bin/mdrun'
