def sequence(self, xtable=MU.xxDic):
"""
Amino acid sequence in one letter code.
@param xtable: dict {str:str}, additional residue:single_letter mapping
for non-standard residues (default molUtils.xxDic)
@type xtable: dict
@return: 1-letter-code AA sequence (based on first atom of each res).
@rtype: str
"""
l = self.residues['name']
return ''.join(MU.singleAA(l, xtable))
def createResidue( self, res, atoms ):
"""
"""
r = AmberResidueType( **res )
r.letter = M.singleAA( [r.code] )[0]
r.xyz = atoms['xyz']
n = len(r.xyz)
for key in B.PDBModel.PDB_KEYS:
r[key] = n * ['']
r['type'] = ['ATOM'] * n
r['residue_name'] = [r.code] * n
r['residue_number'] = [1] * n
r['occupancy'] = [1.0] * n
r['after_ter'] = [0] * n
r['temperature_factor'] = [0] * n
del atoms['xyz']
for key, profile in atoms.items():
r.atoms[key] = profile
return r
def createResidue(self, res, atoms):
"""
"""
r = AmberResidueType(**res)
r.letter = M.singleAA([r.code])[0]
r.xyz = atoms['xyz']
n = len(r.xyz)
for key in B.PDBModel.PDB_KEYS:
r[key] = n * ['']
r['type'] = ['ATOM'] * n
r['residue_name'] = [r.code] * n
r['residue_number'] = [1] * n
r['occupancy'] = [1.0] * n
r['after_ter'] = [0] * n
r['temperature_factor'] = [0] * n
del atoms['xyz']
for key, profile in atoms.items():
r.atoms[key] = profile
return r
def __fromPDB( self ):
self.code = self.atoms['name'][0]
self.letter = M.singleAA( [ self.code ] )
def parse_lines(self, lines):
## Collect secondary structure data. Note that:
##
## 1. If Dssp detects a chain break or a residue with an
## incomplete backbone it inserts a line with an
## exclamation mark "!" in the residue column.
##
## Example: 496 524 C V <
## 497 525 C P
## 498 !
## 499 539 C F
## 500 540 C N > -
##
## 2. A termini (a switch of chain identifier) is marked
## by a asterisk "*" in the column next to the "!"
##
## Example: 721 789 C Q T <
## 722 790 C A <
## 723 !*
## 724 33 Z E >
## 725 34 Z K T 4 +
## 726 35 Z L T >> S+
##
## 3. If DSSP detects an incomplete residue in the terminus
## we only get a single line with a "!" and "*" not a
## for the incomplete residue and one for the terminus
## as woulld be expected!
##
## Example: 84 101 A A
## 85 102 A E
## 86 !* <-- residue 103 skipped!
## 87 16 B S
## 88 17 B G E
## skip header (may be interesting to get total area and bonds though)
while lines and not lines[0][:12]==' # RESIDUE':
lines.pop(0)
lines.pop(0)
table = ParseDSSPTable()
r = [ table.parse_line(l) for l in lines ]
r = [ res for res in r if res ] ## filter out TER and invalid records
m = self.model
len_res = m.lenResidues()
m.residues.set('dssp', ['.']*len_res ,default='.')
m.residues.set('dssp_acc', N.zeros(len_res), default=0.0)
m.residues.set('dssp_phi', N.ones(len_res)*360.0, default=360.0 )
m.residues.set('dssp_psi', N.ones(len_res)*360.0, default=360.0 )
m.residues['residue'] = MU.singleAA( m.atom2resProfile('residue_name'),
unknown='X')
m.residues['insertion_code'] = m.atom2resProfile('insertion_code')
m.residues['chain'] = m.atom2resProfile('chain_id')
i = 0
for res in r:
while i < (len_res-1) and \
not ( m.residues['residue'][i] == res['residue'] and\
m.residues['chain'][i] == res['chain'] and\
m.residues['insertion_code'][i] == res['insertion_code'] ):
i += 1
m.residues['dssp'][i] = res['ss'] if res['ss'] else '.'
m.residues['dssp_acc'][i] = res['acc']
m.residues['dssp_phi'][i] = res['phi']
m.residues['dssp_psi'][i] = res['psi']
i += 1
def __fromPDB(self):
self.code = self.atoms['name'][0]
self.letter = M.singleAA([self.code])