def _torpn(self, infix, prnlev):
""" Converts the infix to an RPN array """
postfix = ''
stack = ['_'] # use a list as a stack. Then pop() works as expected
flag = 0
i = 0
while i < len(infix):
p = infix[i]
if p == '[':
postfix += p
flag = 1
elif p == ']':
postfix += p
flag = 0
elif flag:
postfix += p
elif p == '(':
stack.append(p)
elif p == ')':
pp = stack.pop()
while pp != '(':
if pp == '_':
raise MaskError('Unbalanced parentheses in Mask.')
postfix += pp
pp = stack.pop()
# At this point both ()s are discarded
elif p == '_':
pp = stack.pop()
while pp != '_':
if pp == '(':
raise MaskError('Unbalanced parentheses in Mask.')
postfix += pp
pp = stack.pop()
elif self._isOperator(p):
P1 = self._priority(p)
P2 = self._priority(stack[len(stack) - 1])
if P1 > P2:
stack.append(p)
else:
while P1 <= P2:
pp = stack.pop()
postfix += pp
P1 = self._priority(p)
P2 = self._priority(stack[len(stack) - 1])
stack.append(p)
else:
raise MaskError('Unknown symbol %s' %
p) # should not reach here
i += 1
# end while i < len(infix):
return postfix
def Or(self, other):
if self.natom != other.natom:
raise MaskError('_mask: or() requires another mask of equal size!')
new_mask = _mask(self.natom)
for i in range(len(self)):
new_mask[i] = int(self[i] or other[i])
return new_mask
def And(self, other):
if self.natom != other.natom:
raise MaskError("_mask: and() requires another mask of equal size!")
new_mask = _mask(self.natom)
for i in range(len(self)):
new_mask[i] = int(self[i] and other[i])
return new_mask
def _binop(self, op, pmask1, pmask2):
""" Does a binary operation on a pair of masks """
if op == '&':
return pmask1.And(pmask2)
if op == '|':
return pmask1.Or(pmask2)
raise MaskError('Unknown operator [%s]' % op)
def _residue_numlist(self, instring, mask):
""" Fills a _mask based on residue numbers """
buffer = ''
pos = 0
at1 = at2 = dash = 0
while pos < len(instring):
p = instring[pos]
if p.isdigit():
buffer += p
if p == ',' or pos == len(instring) - 1:
if dash == 0:
at1 = int(buffer)
self._resnum_select(at1, at1, mask)
else:
try:
at2 = int(buffer)
except ValueError:
raise MaskError('Bad mask: error in integer conversion')
self._resnum_select(at1, at2, mask)
dash = 0
buffer = ''
elif p == '-':
at1 = int(buffer)
dash = 1
buffer = ''
pos += 1
def _atom_numlist(self, instring, mask):
""" Fills a _mask based on atom numbers """
buffer = ''
pos = 0
at1 = at2 = dash = 0
while pos < len(instring):
p = instring[pos]
if p.isdigit():
buffer += p
if p == ',' or pos == len(instring) - 1:
if dash == 0:
at1 = int(buffer)
self._atnum_select(at1, at1, mask)
else:
at2 = int(buffer)
self._atnum_select(at1, at2, mask)
dash = 0
buffer = ''
elif p == '-':
at1 = int(buffer)
dash = 1
buffer = ''
if not (p.isdigit() or p in [',','-']):
raise MaskError('Unknown symbol in atom number parsing [%s]'%p)
pos += 1
def _selectDistd(self, pmask1, pmask2):
""" Selects atoms based on a distance criteria """
# pmask1 is either @<number> or :<number>, and represents the distance
# criteria. pmask2 is the selection of atoms from which the distance is
# evaluated.
pmask = _mask(len(self.parm.atoms))
# Determine if we want > or <
if pmask1[0] == '<':
cmp = lambda x, y: x < y
elif pmask1[0] == '>':
cmp = lambda x, y: x > y
else: # Should never execute this
raise MaskError(
'Unknown comparison criteria for distance mask: %s' %
pmask1[0])
pmask1 = pmask1[1:]
if pmask1[0] not in ':@': # Should never execute this
raise MaskError('Bad distance criteria for mask: %s' % pmask1)
try:
distance = float(pmask1[1:])
except (TypeError, ValueError):
raise MaskError('Distance must be a number: %s' % pmask1[1:])
distance *= distance # Faster to compare square of distance
# First select all atoms that satisfy the distance. If we ended up
# choosing residues, then we will go back through afterwards and select
# entire residues when one of the atoms in that residue is selected.
idxlist = [i for i, val in enumerate(pmask2) if val == 1]
for i, atomi in enumerate(self.parm.atoms):
for j in idxlist:
atomj = self.parm.atoms[j]
dx = atomi.xx - atomj.xx
dy = atomi.xy - atomj.xy
dz = atomi.xz - atomj.xz
d2 = dx * dx + dy * dy + dz * dz
if cmp(d2, distance):
pmask[i] = 1
break
# Now see if we have to select all atoms in residues with any selected
# atoms
if pmask1[0] == ':':
for res in self.parm.residues:
for atom in res.atoms:
if pmask[atom.idx] == 1:
for atom in res.atoms:
pmask[atom.idx] = 1
break
return pmask
def _priority(self, op):
if op in ['>','<']: return 6
if op in ['!']: return 5
if op in ['&']: return 4
if op in ['|']: return 3
if op in ['(']: return 2
if op in ['_']: return 1
raise MaskError('Unknown operator [%s] in Mask ==%s==' %
(op, self.mask))
def _atname_select(self, atname, mask, key='name'):
""" Fills a _mask array with all atom names of a given name """
if atname.isdigit():
atname = int(atname) - 1
for i, atom in enumerate(self.parm.atoms):
mask[i] = mask[i] | int(atname == i)
elif key == 'element':
try:
for i, atom in enumerate(self.parm.atoms):
mask[i] = mask[i] | int(AtomicNum[atname] ==
atom.atomic_number)
except KeyError:
raise MaskError('Unknown element %s' % atname)
else:
for i, atom in enumerate(self.parm.atoms):
mask[i] = mask[i] | int(_nameMatch(atname, getattr(atom, key)))
def _residue_namelist(self, instring, mask):
""" Fills a _mask based on residue names """
buffer = ''
pos = 0
while pos < len(instring):
p = instring[pos]
if p.isalnum() or p in ['*','?','+',"'",'-']:
buffer += p
if p == ',' or pos == len(instring) - 1:
if '-' in buffer and buffer[0].isdigit():
self._residue_numlist(buffer, mask)
else:
self._resname_select(buffer, mask)
buffer = ''
if not (p.isalnum() or p in ",?*'+-"):
raise MaskError('Unknown symbol in residue name '
'parsing [%s]' % p)
pos += 1
def _atom_namelist(self, instring, mask, key='name'):
""" Fills a _mask based on atom names/types """
buffer = ''
pos = 0
while pos < len(instring):
p = instring[pos]
if p.isalnum() or p in "\\*?+'-":
buffer += p
if p == ',' or pos == len(instring) - 1:
if '-' in buffer and buffer[0].isdigit():
self._atom_numlist(buffer, mask)
else:
self._atname_select(buffer, mask, key)
buffer = ''
if not (p.isalnum() or p in "\\,?*'+-"):
raise MaskError('Unrecognized symbol in atom name '
'parsing [%s]' % p)
pos += 1
def remove(self, *args, **kwargs):
raise MaskError('_mask is a fixed-length array!')
def extend(self, *args, **kwargs):
raise MaskError('_mask is a fixed-length array!')
def _selectElemMask(self, ptoken):
""" Selects an element mask """
# some constants
ALL = 0
NUMLIST = 1
NAMELIST = 2
TYPELIST = 3
ELEMLIST = 4
# define the mask object and empty buffer
pmask = _mask(len(self.parm.atoms))
buffer = ''
buffer_p = 0
# This is a residue NUMber LIST
if ptoken.startswith(':'):
reslist = NUMLIST
pos = 1
while pos < len(ptoken):
p = ptoken[pos]
buffer += p
buffer_p += 1
if p == '*' and ptoken[pos-1] != '\\':
if buffer_p == 1 and (pos == len(ptoken) - 1 or
ptoken[pos+1] == ','):
reslist = ALL
elif reslist == NUMLIST:
reslist = NAMELIST
elif p.isalpha() or p in '?*':
reslist = NAMELIST
if pos == len(ptoken) - 1:
buffer_p = 0
if len(buffer) != 0 and buffer_p == 0:
if reslist == ALL:
pmask.select_all()
elif reslist == NUMLIST:
self._residue_numlist(buffer, pmask)
elif reslist == NAMELIST:
self._residue_namelist(buffer, pmask)
reslist = NUMLIST
pos += 1
elif ptoken.startswith('@'):
atomlist = NUMLIST
pos = 1
while pos < len(ptoken):
p = ptoken[pos]
buffer += p
buffer_p += 1
if p == '*' and ptoken[pos-1] != "\\":
if atomlist == NUMLIST:
atomlist = NAMELIST
elif p.isalpha() or p in '?*':
if atomlist == NUMLIST:
atomlist = NAMELIST
elif p == '%':
atomlist = TYPELIST
elif p == '/':
atomlist = ELEMLIST
if pos == len(ptoken) - 1:
buffer_p = 0
if len(buffer) != 0 and buffer_p == 0:
if atomlist == ALL:
pmask.select_all()
elif atomlist == NUMLIST:
self._atom_numlist(buffer, pmask)
elif atomlist == NAMELIST:
self._atom_namelist(buffer, pmask)
elif atomlist == TYPELIST:
self._atom_typelist(buffer[1:], pmask)
elif atomlist == ELEMLIST:
self._atom_elemlist(buffer[1:], pmask)
pos += 1
elif ptoken.strip() == '*':
pmask.select_all()
elif ptoken[0] in ['<','>']:
return ptoken
else: # Should never reach here
raise MaskError('Mask is missing : and @')
# end if ':' in ptoken:
return pmask
def _evaluate(self, postfix, prnlev):
""" Evaluates a postfix in RPN format and returns a selection array """
from sys import stderr
buffer = ''
stack = []
pos = 0 # position in postfix
while pos < len(postfix):
p = postfix[pos]
if p == '[': buffer = ''
elif p == ']': # end of the token
ptoken = buffer
pmask = self._selectElemMask(ptoken)
stack.append(pmask)
elif self._isOperand(p) or p in [':','@']:
buffer += p
elif p in ['&','|']:
pmask1 = None
pmask2 = None
try:
pmask1 = stack.pop()
pmask2 = stack.pop()
pmask = self._binop(p, pmask1, pmask2)
except IndexError:
raise MaskError('Illegal binary operation')
stack.append(pmask)
elif p in ['<','>']:
if pos < len(postfix)-1 and postfix[pos+1] in [':','@']:
buffer += p
else:
try:
pmask1 = stack.pop() # distance criteria
pmask2 = stack.pop()
pmask = self._selectDistd(pmask1, pmask2)
except IndexError:
return [0 for a in self.parm.atoms]
stack.append(pmask)
elif p == '!':
try:
pmask1 = stack.pop()
except IndexError:
raise MaskError('Illegal ! operation')
pmask = self._neg(pmask1)
stack.append(pmask)
else:
raise MaskError('Unknown symbol evaluating RPN: %s' % p)
pos += 1
# end while i < len(postfix)
try:
pmask = stack.pop()
except IndexError:
raise MaskError('Empty stack -- no available operands')
if stack:
raise MaskError('There may be missing operands in the mask')
if prnlev > 7:
stderr.write('%d atoms selected by %s' % (sum(pmask), self.mask))
return pmask
def _tokenize(self, prnlev):
""" Tokenizes the mask string into individual selections:
1. remove spaces
2. isolate 'operands' into brackets [...]
3. split expressions of the type :1-10@CA,CB into 2 parts;
the 2 parts are joned with & operator and (for the sake
of preserving precedence of other operators) enclosed by
(...); i.e. :1-10@CA,CB is split into (:1-10 & @CA,CB)
4. do basic error checking
"""
buffer = '' # keeping track of a single operand
infix = '' # value that is returned at the end
# flag == 0: means new operand or operand was completed & ended with ]
# flag == 1: means operand with ":" read
# flag == 2: means operand with "@" read
# flag == 3: means '<' or '>' read, waiting for numbers
flag = 0
i = 0
while i < len(self.mask):
p = self.mask[i]
# skip whitespace
if p.isspace():
i += 1
continue
# If p is an operator, is the last character, or is a ()...
elif (self._isOperator(p) or
i == len(self.mask) - 1 or p in ['(',')']):
# Deal with the last character being a wildcard that we have to
# convert
if p == '=' and i == len(self.mask) - 1: # wildcard
if flag > 0:
p = '*'
else:
raise MaskError("AmberMask: '=' not in name "
"list syntax")
# If this is the end of an operand, terminate the buffer, flush
# it to infix, and reset flag to 0 and empty the buffer
if flag > 0:
if i == len(self.mask) - 1 and p != ')': buffer += p
buffer += '])'
flag = 0
infix += buffer
buffer = ''
if i != len(self.mask) - 1 or p == ')': infix += p
# else if p is >,<
if p in ['<','>']:
buffer = '([%s' % p
i += 1
try:
p = self.mask[i]
except IndexError:
raise MaskError('Bad distance syntax [%s]' % self.mask)
buffer += p
flag = 3
if self.parm.coordinates is None:
raise MaskError('<,> operators require coordinates')
if not p in [':','@']:
raise MaskError('Bad syntax [%s]' % self.mask)
elif self._isOperand(p):
if flag == 0:
buffer = '(['
flag = 1
if p != '*':
raise MaskError('Bad syntax [%s]' % self.mask)
if p == '=': # wildcard
if flag > 0:
p = '*'
else:
raise MaskError("'=' not in name list syntax")
buffer += p
elif p == ':':
if flag == 0:
buffer = '([:'
flag = 1
else:
buffer += '])|([:'
flag = 1
elif p == '@':
if flag == 0:
buffer = '([@'
flag = 2
elif flag == 1:
buffer += ']&[@'
flag = 2
elif flag == 2:
buffer += '])|([@'
flag = 2
else:
raise MaskError('Unknown symbol (%s) expression' % p)
i += 1
# end while i < len(self.mask):
# Check that each operand has at least 4 characters: [:1] and [@C], etc.
i = 0
n = 1 # number of characters in current operand
flag = 0
while i < len(infix):
p = infix[i]
if p == '[':
n += 1
flag = 1
elif p == ']':
if n < 4 and infix[i-1] != '*':
raise MaskError('empty token in infix')
n = 1
else:
if flag == 1:
n += 1
i += 1
return infix + '_' # terminating _ for next step
