def create_subs_peptide_charmm(filename, atomtypes=["CA"], frequency=1):
"""Create subsystem selection for CHARMM peptides
Argument:
| filename -- the CHARMM coordinate file (typically extension .crd or
.cor)
Optional argument:
| atomtypes -- list of strings. Let only these atom types be part of
the subsystem.
| frequency -- let only one out of every *frequency* residues be part
of the subsystem.
"""
N, calpha, proline, carbon, oxygen, nitrogen = load_peptide_info_charmm(filename)
subs = []
if "C" in atomtypes:
subs.extend(carbon[::frequency])
if "O" in atomtypes:
subs.extend(oxygen[::frequency])
if "N" in atomtypes:
subs.extend(nitrogen[::frequency])
if "CA" in atomtypes:
subs.extend(calpha[::frequency])
if len(subs) == 0:
raise NotImplementedError("No matching atom types found.")
return subs
def create_subs_peptide_charmm(filename, atomtypes=["CA"], frequency=1):
"""Create subsystem selection for CHARMM peptides
Argument:
| filename -- the CHARMM coordinate file (typically extension .crd or
.cor)
Optional argument:
| atomtypes -- list of strings. Let only these atom types be part of
the subsystem.
| frequency -- let only one out of every *frequency* residues be part
of the subsystem.
"""
N, calpha, proline, carbon, oxygen, nitrogen = load_peptide_info_charmm(
filename)
subs = []
if "C" in atomtypes:
subs.extend(carbon[::frequency])
if "O" in atomtypes:
subs.extend(oxygen[::frequency])
if "N" in atomtypes:
subs.extend(nitrogen[::frequency])
if "CA" in atomtypes:
subs.extend(calpha[::frequency])
if len(subs) == 0:
raise NotImplementedError("No matching atom types found.")
return subs
def create_blocks_peptide_charmm(filename, label="normal", blocksize=1):
"""Create blocks list for CHARMM peptides
Argument:
| filename -- the CHARMM coordinate file (typically extension .crd or
.cor)
Optional argument:
| label -- type of MBH blocks: RTB, dihedral, RHbending, normal
[default=normal]
| blocksize -- when using the RTB scheme, blocksize defines the number
of residues in a block
TODO: referenties
"""
N, calpha, proline, carbon, oxygen, nitrogen = load_peptide_info_charmm(filename)
if label is "RTB":
return _calc_blocks_RTB(blocksize, N, calpha, proline, carbon, oxygen, nitrogen)
elif label is "dihedral":
return _calc_blocks_dihedral(N, calpha, proline, carbon, oxygen, nitrogen)
elif label is "RHbending":
return _calc_blocks_RHbending(N, calpha, proline, carbon, oxygen, nitrogen)
elif label is "normal":
return _calc_blocks_normal(N, calpha, proline, carbon, oxygen, nitrogen)
else:
raise NotImplementedError
def create_blocks_peptide_charmm(filename, label="normal", blocksize=1):
"""Create blocks list for CHARMM peptides
Argument:
| filename -- the CHARMM coordinate file (typically extension .crd or
.cor)
Optional argument:
| label -- type of MBH blocks: RTB, dihedral, RHbending, normal
[default=normal]
| blocksize -- when using the RTB scheme, blocksize defines the number
of residues in a block
TODO: referenties
"""
N, calpha, proline, carbon, oxygen, nitrogen = load_peptide_info_charmm(
filename)
if label is "RTB":
return _calc_blocks_RTB(blocksize, N, calpha, proline, carbon, oxygen,
nitrogen)
elif label is "dihedral":
return _calc_blocks_dihedral(N, calpha, proline, carbon, oxygen,
nitrogen)
elif label is "RHbending":
return _calc_blocks_RHbending(N, calpha, proline, carbon, oxygen,
nitrogen)
elif label is "normal":
return _calc_blocks_normal(N, calpha, proline, carbon, oxygen,
nitrogen)
else:
raise NotImplementedError