def __init__(self, path, structureList=[]):
self.path = path
self.pathMap = {}
self.structure_paths = []
if os.path.isdir(path):
if structureList == []:
for filename in os.listdir(path):
if filename[0] == ".": continue # avoid dotfiles (eg .svn dirs)
fullpath = os.path.join(path, filename)
self.mapFilename(filename, fullpath)
self.structure_paths.append(fullpath)
else:
print(structureList)
filenamesInDir = os.listdir(path)
if filenamesInDir == []:
raise IOError, "WARNING : No files in directory %s" % path
for filename in structureList:
if filename in filenamesInDir:
fullpath = os.path.join(path, filename)
self.mapFilename(filename, fullpath)
self.structure_paths.append(fullpath)
else:
raise IOError, "WARNING : File %s is not in directory %s" % (filename, path)
elif os.path.isfile(path):
self.structure_paths = [path]
else:
raise IOError, "WARNING : The path %s is not a directory or a file - it may not exist!" % path
self.parser = PDBParser(StructureBuilder())
class PDBFileList(object):
def __init__(self, path, structureList=[]):
self.path = path
self.pathMap = {}
self.structure_paths = []
if os.path.isdir(path):
if structureList == []:
for filename in os.listdir(path):
if filename[0] == ".": continue # avoid dotfiles (eg .svn dirs)
fullpath = os.path.join(path, filename)
self.mapFilename(filename, fullpath)
self.structure_paths.append(fullpath)
else:
print(structureList)
filenamesInDir = os.listdir(path)
if filenamesInDir == []:
raise IOError, "WARNING : No files in directory %s" % path
for filename in structureList:
if filename in filenamesInDir:
fullpath = os.path.join(path, filename)
self.mapFilename(filename, fullpath)
self.structure_paths.append(fullpath)
else:
raise IOError, "WARNING : File %s is not in directory %s" % (filename, path)
elif os.path.isfile(path):
self.structure_paths = [path]
else:
raise IOError, "WARNING : The path %s is not a directory or a file - it may not exist!" % path
self.parser = PDBParser(StructureBuilder())
def mapFilename(self, filename, fullpath):
# XXX take the first four letters of a filename
id = filename[0:4]
self.pathMap[id] = fullpath
def __iter__(self):
try:
for i, path in enumerate(self.structure_paths):
yield self.parser.getStructure(path)
except IOError, ioe:
raise IOError, "I/O problem with path [%s] %s" % (path, ioe)
def structureFromFile(filepath):
parser = PDBParser(StructureBuilder())
return parser.getStructure(filepath)
