def getPDBAtomName(self, name, element):
"""Figure out the real atom name as well as the atom element, if name
string is in pdb format"""
# To be DONE
## bad = 0
## for c in element:
## if c not in string.letters: bad = 1
if element == ' ' or element == '':# or bad:
## if name[0] != ' ':
## element = string.strip(name[0:1])
## # Won't work if the atomType is FE !!!!
## else:
element = string.strip(name[0:2])
else:
element = string.strip(element)
# should I still check that it really is an element ???
if name[1]=='H':
if name[0] in ('1','2','3'):
name = string.strip(name[1:])+name[0]
element = 'H'
if len(element)==2:
element = element[0]+string.lower(element[1])
elem = string.lower(element)
if elem =='lp' or elem =='ld':
element = 'Xx'
return string.strip(name), element
def clean_atom_type(self, type_name):
name = string.upper(type_name[0])
if len(type_name) > 1:
name = name + string.lower(type_name[1])
if name[1] not in string.letters:
return name[0]
return name
def get_atomic_number(self, name):
"""return the element number for a given name or raises a
ValueError exception if the element is not known"""
_name = string.upper(name[0])
if len(name) > 1:
if not name[1] in string.digits:
_name = _name + string.lower(name[1])
if _name in list(babel_elements.keys()):
return babel_elements[_name]['num']
else:
raise ValueError( "Could not find atomic number for %s %s"% \
(name,_name) )
def get_Attr(self, html, pattern, lc=0):
attrPat = re.compile(
('([%s]*=[%s]*' % (string.whitespace, string.whitespace)) +
r'(\'[^\']*\'|"[^"]*"|[-a-zA-Z0-9./:+*%?!\(\)_#=~]*))?')
found = pattern.search(html)
if found:
attrP = attrPat.search(html[found.end():])
if attrP:
attr = attrP.group()[1:]
if attr and attr[0] == '"' and attr[-1] == '"':
if len(attr) > 2:
attr = attr[1:-1]
if lc:
return string.lower(attr)
else:
return attr
else:
return None
def __init__(self,
url=None,
name=None,
method=None,
action=None,
enctype=None,
input=None,
radiobutton=None,
checkbutton=None,
select=None,
textarea=None,
arguments=None,
hiddenInput=None,
fieldOrder=None):
# note: something i don't understand: in the constructor, i cannot say
# radiobutton={} and then self.radiobutton = radiobutton
# because every new instance of this class would point to the
# dictionary of the first instance (tested with python1.5 to 2.2).
# Instead, i have to initialise radiobutton=None and do the test below
self.url = url # url: e.g. 'http://www.google.com'
self.name = name # name of this form object
if method is None: method = 'get'
assert string.lower(method) in ['post', 'get']
self.method = method # default cgi method, if not specified
self.action = action # the cgi action. In case of google: '/search'
self.enctype = enctype # enctype of CGI Form
if input is None: input = {}
self.input = input # dictionary with all the 'inputs' of this form
# note that input of type 'hidden' is not added
# to this dict, but to self.hiddenInput, input of
# type 'radio' and 'checkbox' are added to
# different dicts too as well as input of type
# 'select' and 'textarea'
if radiobutton is None: radiobutton = {}
self.radiobutton = radiobutton # dict holding the radiobuttons
if checkbutton is None: checkbutton = {}
self.checkbutton = checkbutton # dict holding the checkbox buttons
if select is None: select = {}
self.select = select # dictionary with all the 'selects' of this form
if textarea is None: textarea = {}
self.textarea = textarea # dictionary with all the 'textareas'
if arguments is None: arguments = {}
self.arguments = arguments # dict with the arguments that are used to
# generate the string to be sent to the
# server
if hiddenInput is None: hiddenInput = {}
self.hiddenInput = hiddenInput # dictionary with all the inputs of
# type 'hidden'
if fieldOrder is None: fieldOrder = []
self.fieldOrder = fieldOrder # stores tuples of (inputname, dictname)