def ConstructSegmentForAnalysis(raw_chain):
"""Returns a list of Segment instance from the
Chain instance which is properly modified for use in
the this application.
"""
## Sets that atm.include attribute for each atom in the chains
## being analyzed by tlsmd
for atm in raw_chain.iter_all_atoms():
atm.include = atom_selection.calc_include_atom(atm)
## ok, use the chain but use a segment and cut off
## any leading and trailing non-amino acid residues
## do not include a fragment with no included atoms
naa = raw_chain.count_amino_acids()
nna = raw_chain.count_nucleic_acids()
if naa > nna:
iter_residues = raw_chain.iter_amino_acids()
elif nna > naa:
iter_residues = raw_chain.iter_nucleic_acids()
segment = Structure.Segment(chain_id = raw_chain.chain_id)
for frag in iter_residues:
for atm in frag.iter_all_atoms():
if atm.include:
segment.add_fragment(frag)
break
## apply data smooth if desired
if conf.globalconf.adp_smoothing > 0:
adp_smoothing.IsotropicADPDataSmoother(segment, conf.globalconf.adp_smoothing)
## this is useful: for each fragment in the minimization
## set a attribute for its index position
for i, frag in enumerate(segment.iter_fragments()):
frag.ifrag = i
## create a TLSModelAnalyzer instance for the chain, and
## attach the instance to the chain for use by the rest of the
## program
segment.tls_analyzer = tlsmdmodule.TLSModelAnalyzer()
xlist = atom_selection.chain_to_xmlrpc_list(segment.iter_all_atoms())
segment.tls_analyzer.set_xmlrpc_chain(xlist)
return segment
def ConstructSegmentForAnalysis(raw_chain):
"""Returns a list of Segment instance from the Chain instance which is
properly modified for use in the this application.
"""
console.debug_stdoutln(">tlsmd_analysis->ConstructSegmentForAnalysis(chain %s)" % (
raw_chain.chain_id))
## NOTE: raw_chain = "Chain(1:A, Res(MET,1,A)...Res(VAL,50,A))"
## Sets that atm.include attribute for each atom in the chains
## being analyzed by tlsmd
for atm in raw_chain.iter_all_atoms():
#atm.include = atom_selection.calc_include_atom(atm)
atm.include = atom_selection.calc_include_atom(atm, reject_messages = True)
## ok, use the chain but use a segment and cut off
## any leading and trailing non-amino acid residues
## do not include a fragment with no included atoms
naa = nna = ota = 0
naa = raw_chain.count_amino_acids()
nna = raw_chain.count_nucleic_acids()
ota = raw_chain.count_fragments()
if naa > nna:
## Probably a protein with (possibly) some nucleic acids.
iter_residues = raw_chain.iter_amino_acids()
elif nna > naa:
## Probably a nucleic acid with (possibly) some amino acids.
iter_residues = raw_chain.iter_nucleic_acids()
if naa == 0 and nna == 0 and ota > 0:
## This chain does not have any amino or nucleic acids, so skip.
return ""
segment = Structure.Segment(chain_id = raw_chain.chain_id)
for frag in iter_residues:
for atm in frag.iter_all_atoms():
if atm.include:
segment.add_fragment(frag)
break
## apply data smooth if desired (default is "0")
if conf.globalconf.adp_smoothing > 0:
adp_smoothing.IsotropicADPDataSmoother(segment,
conf.globalconf.adp_smoothing)
## this is useful: for each fragment in the minimization
## set an attribute for its index position
for i, frag in enumerate(segment.iter_fragments()):
## NOTE (by Christoph):
## Example output:
## 0 : Res(MET,1,A)
## 1 : Res(ILE,2,A)
## ...
frag.ifrag = i
## create a TLSModelAnalyzer instance for the chain, and attach the
## instance to the chain for use by the rest of the program
segment.tls_analyzer = tlsmdmodule.TLSModelAnalyzer()
xlist = atom_selection.chain_to_xmlrpc_list(segment.iter_all_atoms())
segment.tls_analyzer.set_xmlrpc_chain(xlist)
## INPUT : raw_chain = "Chain(1:A, Res(MET,1,A)...Res(VAL,50,A))"
## OUTPUT: segment = "Segment(1:A, Res(MET,1,A)...Res(VAL,50,A))"
return segment