def SetupStream(strm, format):
format = format.strip('.')
ftype = oechem.OEGetFileType(format)
if ftype == oechem.OEFormat_UNDEFINED:
raise ValueError("Unsupported file format sent to server '%s'" %
format)
strm.SetFormat(ftype)
strm.Setgz(oechem.OEIsGZip(format))
return strm
def SetupInterface(argv, itf):
oechem.OEConfigure(itf, InterfaceData)
if oechem.OECheckHelp(itf, argv):
return False
if not oechem.OEParseCommandLine(itf, argv):
return False
if not oechem.OEIsReadable(
oechem.OEGetFileType(
oechem.OEGetFileExtension(itf.GetString("-in")))):
oechem.OEThrow.Warning("%s is not a readable input file" %
itf.GetString("-in"))
return False
if not oechem.OEIsWriteable(
oechem.OEGetFileType(
oechem.OEGetFileExtension(itf.GetString("-out")))):
oechem.OEThrow.Warning("%s is not a writable output file" %
itf.GetString("-out"))
return False
return True
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % argv[0])
# input - preserve rotor-offset-compression
ifs = oechem.oemolistream()
ihand = ifs.GetBinaryIOHandler()
ihand.Clear()
oechem.OEInitHandler(ihand, oechem.OEBRotCompressOpts(),
oechem.OEBRotCompressOpts())
ifname = argv[1]
if not ifs.open(ifname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
# output
ofname = argv[2]
oformt = oechem.OEGetFileType(oechem.OEGetFileExtension(ofname))
if oformt != oechem.OEFormat_OEB:
oechem.OEThrow.Fatal("Output file format much be OEB")
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open %s for writing" % ofname)
iss = oechem.oeisstream(COLOR_FORCE_FIELD)
cff = oeshape.OEColorForceField()
if not cff.Init(iss):
oechem.OEThrow.Fatal("Unable to initialize OEColorForceField")
dots = oechem.OEDots(10000, 200, "molecules")
for mol in ifs.GetOEMols():
oefastrocs.OEPrepareFastROCSMol(mol, cff)
oechem.OEWriteMolecule(ofs, mol)
dots.Update()
dots.Total()
ofs.close()
print("Indexing %s" % ofname)
if not oechem.OECreateMolDatabaseIdx(ofname):
oechem.OEThrow.Fatal("Failed to index %s" % argv[2])
return 0
def __init__(self, ipf, keepAlts=F, verbose=T):
self.ipf = ipf
self.keepAlts = keepAlts
self.verbose = verbose
flavor = oechem.OEIFlavor_PDB_Default
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, flavor)
if not ims.open(self.ipf):
oechem.OEThrow.Fatal("Unable to open %s for reading." % self.ipf)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % self.ipf)
iftp = oechem.OEGetFileType(oechem.OEGetFileExtension(self.ipf))
if (iftp == oechem.OEFormat_PDB) and not self.keepAlts:
oechem.OEThrow.Verbose(
"Default processing of alt locations (keep just 'A' and ' ').")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Unable to read %s." % self.ipf)
ims.close()
if (inmol.NumAtoms() == 0):
oechem.OEThrow.Fatal("Input molecule %s contains no atoms." %
self.ipf)
if inmol.GetTitle() == "":
inmol.SetTitle(ipf[:-4])
oechem.OEThrow.Verbose("Processing %s." % inmol.GetTitle())
if not oechem.OEHasResidues(inmol):
oechem.OEPerceiveResidues(inmol, oechem.OEPreserveResInfo_All)
self.inmol = inmol
self.mol = inmol.CreateCopy()
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from openeye import oechem
import sys
if len(sys.argv) != 4:
oechem.OEThrow.Usage("%s <input> <output> <title>" % sys.argv[0])
moldb = oechem.OEMolDatabase()
if not moldb.Open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])
if moldb.GetFormat() != oechem.OEGetFileType(
oechem.OEGetFileExtension(sys.argv[2])):
oechem.OEThrow.Fatal(
"Output format does not match input format: %s != %s" %
(oechem.OEGetFileExtension(
sys.argv[1]), oechem.OEGetFileExtension(sys.argv[2])))
ofs = oechem.oemolostream()
if not ofs.open(sys.argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % sys.argv[2])
title = sys.argv[3]
for idx in range(moldb.GetMaxMolIdx()):
if moldb.GetTitle(idx) == title:
moldb.WriteMolecule(ofs, idx)
# @ </SNIPPET>