def from_structure(cls, struct, term_decorate=True):
"""
Instantiates a ResidueTemplateContainer from a Structure instance filled
with residues
Parameters
----------
struct : :class:`parmed.structure.Structure`
The structure from which to generate the ResidueTemplateContainer
from
term_decorate : bool, optional
If True, terminal amino and nucleic acid residues will be adorned as
follows:
* N-prepended if it is an N-terminal amino acid
* C-prepended if it is a C-terminal amino acid
* 5-appended if it is a 5'-terminal nucleic acid
* 3-appended if it is a 3'-terminal nucleic acid
For example, an N-terminal GLY will become NGLY, while a 5'-terminal
DA will become DA5. Default is True
"""
inst = cls()
for res in struct.residues:
rt = ResidueTemplate.from_residue(res)
# See if we need to decorate the termini names
if rt.head is None and rt.tail is not None and term_decorate:
if AminoAcidResidue.has(rt.name):
if len(rt.name) != 4 or rt.name[0] != 'N':
rt.name = 'N%s' % rt.name
elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
if rt.name[-1] != '5':
rt.name = '%s5' % rt.name
elif rt.tail is None and rt.head is not None and term_decorate:
if AminoAcidResidue.has(rt.name):
if len(rt.name) != 4 or rt.name[0] != 'C':
rt.name = 'C%s' % rt.name
elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
if rt.name[-1] != '3':
rt.name = '%s3' % rt.name
inst.append(rt)
inst.box = struct.box
return inst
def from_structure(cls, struct, term_decorate=True):
"""
Instantiates a ResidueTemplateContainer from a Structure instance filled
with residues
Parameters
----------
struct : :class:`parmed.structure.Structure`
The structure from which to generate the ResidueTemplateContainer
from
term_decorate : bool, optional
If True, terminal amino and nucleic acid residues will be adorned as
follows:
* N-prepended if it is an N-terminal amino acid
* C-prepended if it is a C-terminal amino acid
* 5-appended if it is a 5'-terminal nucleic acid
* 3-appended if it is a 3'-terminal nucleic acid
For example, an N-terminal GLY will become NGLY, while a 5'-terminal
DA will become DA5. Default is True
"""
inst = cls()
for res in struct.residues:
rt = ResidueTemplate.from_residue(res)
# See if we need to decorate the termini names
if rt.head is None and rt.tail is not None and term_decorate:
if AminoAcidResidue.has(rt.name):
if len(rt.name) != 4 or rt.name[0] != 'N':
rt.name = 'N%s' % rt.name
elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
if rt.name[-1] != '5':
rt.name = '%s5' % rt.name
elif rt.tail is None and rt.head is not None and term_decorate:
if AminoAcidResidue.has(rt.name):
if len(rt.name) != 4 or rt.name[0] != 'C':
rt.name = 'C%s' % rt.name
elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
if rt.name[-1] != '3':
rt.name = '%s3' % rt.name
inst.append(rt)
inst.box = struct.box
return inst
def write(struct, dest, mol3=False, split=False):
""" Writes a mol2 file from a structure or residue template
Parameters
----------
struct : :class:`Structure` or :class:`ResidueTemplate` or
:class:`ResidueTemplateContainer`
The input structure to write the mol2 file from
dest : str or file-like obj
Name of the file to write or open file handle to write to
mol3 : bool, optional
If True and ``struct`` is a ResidueTemplate or container, write
HEAD/TAIL sections. Default is False
split : bool, optional
If True and ``struct`` is a ResidueTemplateContainer or a Structure
with multiple residues, each residue is printed in a separate
@<MOLECULE> section that appear sequentially in the output file
"""
own_handle = False
if not hasattr(dest, 'write'):
own_handle = True
dest = genopen(dest, 'w')
if split:
# Write sequentially if it is a multi-residue container or Structure
if isinstance(struct, ResidueTemplateContainer):
for res in struct:
Mol2File.write(res, dest, mol3)
return
elif isinstance(struct, Structure) and len(struct.residues) > 1:
for res in ResidueTemplateContainer.from_structure(struct):
Mol2File.write(res, dest, mol3)
return
try:
if isinstance(struct, ResidueTemplateContainer):
natom = sum([len(c) for c in struct])
# To find the number of bonds, we need to total number of bonds
# + the number of bonds that would be formed by "stitching"
# together residues via their head and tail
bonds = []
charges = []
bases = [1 for res in struct]
for i, res in enumerate(struct):
if i < len(struct) - 1:
bases[i+1] = bases[i] + len(res)
for i, res in enumerate(struct):
for bond in res.bonds:
bonds.append((bond.atom1.idx+bases[i],
bond.atom2.idx+bases[i]))
if i < len(struct)-1 and (res.tail is not None and
struct[i+1].head is not None):
bonds.append((res.tail.idx+bases[i],
struct[i+1].head.idx+bases[i+1]))
charges.extend([a.charge for a in res])
residues = struct
if not struct.name:
name = struct[0].name
else:
name = struct.name
else:
natom = len(struct.atoms)
bonds = [(b.atom1.idx+1, b.atom2.idx+1) for b in struct.bonds]
if isinstance(struct, ResidueTemplate):
residues = [struct]
name = struct.name
else:
residues = struct.residues
name = struct.residues[0].name
charges = [a.charge for a in struct.atoms]
dest.write('@<TRIPOS>MOLECULE\n')
dest.write('%s' % name)
dest.write('\n')
dest.write('%d %d %d 0 1\n' % (natom, len(bonds), len(residues)))
if len(residues) == 1:
dest.write('SMALL\n')
else:
for residue in residues:
if AminoAcidResidue.has(residue.name):
dest.write('PROTEIN\n')
break
if (RNAResidue.has(residue.name) or
DNAResidue.has(residue.name)):
dest.write('NUCLEIC\n')
break
else:
dest.write('BIOPOLYMER\n')
if not any(charges):
dest.write('NO_CHARGES\n')
printchg = False
else:
dest.write('USER_CHARGES\n')
printchg = True
# Now do ATOM section
dest.write('@<TRIPOS>ATOM\n')
j = 1
for i, res in enumerate(residues):
for atom in res:
try:
x = atom.xx
except AttributeError:
x = 0
try:
y = atom.xy
except AttributeError:
y = 0
try:
z = atom.xz
except AttributeError:
z = 0
dest.write('%8d %-8s %10.4f %10.4f %10.4f %-8s %6d %-8s' % (
j, atom.name, x, y, z,
atom.type.strip() or atom.name, i+1, res.name))
if printchg:
dest.write(' %10.6f\n' % atom.charge)
else:
dest.write('\n')
j += 1
dest.write('@<TRIPOS>BOND\n')
for i, bond in enumerate(bonds):
dest.write('%8d %8d %8d 1\n' % (i+1, bond[0], bond[1]))
dest.write('@<TRIPOS>SUBSTRUCTURE\n')
first_atom = 0
for i, res in enumerate(residues):
if not hasattr(res, 'chain') or not res.chain:
chain = '****'
else:
chain = res.chain
intresbonds = 0
if isinstance(res, ResidueTemplate):
if i != len(residues)-1 and (res.tail is not None and
residues[i+1].head is not None):
intresbonds += 1
if i != 0 and (res.head is not None and residues[i-1].tail
is not None):
intresbonds += 1
else:
for atom in res:
for a2 in atom.bond_partners:
if a2.residue is not res:
intresbonds += 1
dest.write('%8d %-8s %8d RESIDUE %4d %-4s ROOT %6d\n' % (i+1,
res.name, first_atom+1, 0, chain[:4], intresbonds))
first_atom += len(res)
if mol3:
dest.write('@<TRIPOS>HEADTAIL\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
if res.head is not None:
dest.write('%s %d\n' % (res.head.name, i+1))
else:
dest.write('0 0\n')
if res.tail is not None:
dest.write('%s %d\n' % (res.tail.name, i+1))
else:
dest.write('0 0\n')
else:
head = tail = None
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
head = atom
if a2.residue.idx == res.idx + 1:
tail = atom
if head is not None:
dest.write('%s %d\n' % (head.name, i+1))
else:
dest.write('0 0\n')
if tail is not None:
dest.write('%s %d\n' % (tail.name, i+1))
else:
dest.write('0 0\n')
dest.write('@<TRIPOS>RESIDUECONNECT\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
con = [res.head, res.tail, None, None, None, None]
for i, a in enumerate(res.connections):
con[i+2] = a
else:
con = [None, None, None, None, None, None]
ncon = 2
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
con[0] = atom
elif a2.residue.idx == res.idx + 1:
con[1] = atom
elif a2.residue.idx != res.idx:
con[ncon] = atom
ncon += 1
dest.write('%d' % (i+1))
for a in con:
if a is not None:
dest.write(' %s' % a.name)
else:
dest.write(' 0')
dest.write('\n')
finally:
if own_handle: dest.close()
def write(struct, dest, mol3=False, split=False):
""" Writes a mol2 file from a structure or residue template
Parameters
----------
struct : :class:`Structure` or :class:`ResidueTemplate` or
:class:`ResidueTemplateContainer`
The input structure to write the mol2 file from
dest : str or file-like obj
Name of the file to write or open file handle to write to
mol3 : bool, optional
If True and ``struct`` is a ResidueTemplate or container, write
HEAD/TAIL sections. Default is False
split : bool, optional
If True and ``struct`` is a ResidueTemplateContainer or a Structure
with multiple residues, each residue is printed in a separate
@<MOLECULE> section that appear sequentially in the output file
"""
own_handle = False
if not hasattr(dest, 'write'):
own_handle = True
dest = genopen(dest, 'w')
if split:
# Write sequentially if it is a multi-residue container or Structure
if isinstance(struct, ResidueTemplateContainer):
try:
for res in struct:
Mol2File.write(res, dest, mol3)
finally:
if own_handle: dest.close()
return
elif isinstance(struct, Structure) and len(struct.residues) > 1:
try:
for res in ResidueTemplateContainer.from_structure(struct):
Mol2File.write(res, dest, mol3)
finally:
if own_handle: dest.close()
return
try:
if isinstance(struct, ResidueTemplateContainer):
natom = sum([len(c) for c in struct])
# To find the number of bonds, we need to total number of bonds
# + the number of bonds that would be formed by "stitching"
# together residues via their head and tail
bonds = []
charges = []
bases = [1 for res in struct]
for i, res in enumerate(struct):
if i < len(struct) - 1:
bases[i+1] = bases[i] + len(res)
for i, res in enumerate(struct):
for bond in res.bonds:
bonds.append((bond.atom1.idx+bases[i],
bond.atom2.idx+bases[i]))
if i < len(struct)-1 and (res.tail is not None and
struct[i+1].head is not None):
bonds.append((res.tail.idx+bases[i],
struct[i+1].head.idx+bases[i+1]))
charges.extend([a.charge for a in res])
residues = struct
name = struct.name or struct[0].name
else:
natom = len(struct.atoms)
bonds = [(b.atom1.idx+1, b.atom2.idx+1) for b in struct.bonds]
if isinstance(struct, ResidueTemplate):
residues = [struct]
name = struct.name
else:
residues = struct.residues
name = struct.residues[0].name
charges = [a.charge for a in struct.atoms]
dest.write('@<TRIPOS>MOLECULE\n')
dest.write('%s\n' % name)
dest.write('%d %d %d 0 1\n' % (natom, len(bonds), len(residues)))
if len(residues) == 1:
dest.write('SMALL\n')
else:
for residue in residues:
if AminoAcidResidue.has(residue.name):
dest.write('PROTEIN\n')
break
if (RNAResidue.has(residue.name) or
DNAResidue.has(residue.name)):
dest.write('NUCLEIC\n')
break
else:
dest.write('BIOPOLYMER\n')
if not any(charges):
dest.write('NO_CHARGES\n')
printchg = False
else:
dest.write('USER_CHARGES\n')
printchg = True
# See if we want to print box info
if hasattr(struct, 'box') and struct.box is not None:
box = struct.box
dest.write('@<TRIPOS>CRYSIN\n')
dest.write('%10.4f %10.4f %10.4f %10.4f %10.4f %10.4f 1 1\n' %
(box[0], box[1], box[2], box[3], box[4], box[5]))
# Now do ATOM section
dest.write('@<TRIPOS>ATOM\n')
j = 1
for i, res in enumerate(residues):
for atom in res:
try:
x = atom.xx
except AttributeError:
x = 0
try:
y = atom.xy
except AttributeError:
y = 0
try:
z = atom.xz
except AttributeError:
z = 0
dest.write('%8d %-8s %10.4f %10.4f %10.4f %-8s %6d %-8s' % (
j, atom.name, x, y, z,
atom.type.strip() or atom.name, i+1, res.name))
if printchg:
dest.write(' %10.6f\n' % atom.charge)
else:
dest.write('\n')
j += 1
dest.write('@<TRIPOS>BOND\n')
for i, bond in enumerate(bonds):
dest.write('%8d %8d %8d 1\n' % (i+1, bond[0], bond[1]))
dest.write('@<TRIPOS>SUBSTRUCTURE\n')
first_atom = 0
for i, res in enumerate(residues):
if not hasattr(res, 'chain') or not res.chain:
chain = '****'
else:
chain = res.chain
intresbonds = 0
if isinstance(res, ResidueTemplate):
if i != len(residues)-1 and (res.tail is not None and
residues[i+1].head is not None):
intresbonds += 1
if i != 0 and (res.head is not None and residues[i-1].tail
is not None):
intresbonds += 1
else:
for atom in res:
for a2 in atom.bond_partners:
if a2.residue is not res:
intresbonds += 1
dest.write('%8d %-8s %8d RESIDUE %4d %-4s ROOT %6d\n' % (i+1,
res.name, first_atom+1, 0, chain[:4], intresbonds))
first_atom += len(res)
if mol3:
dest.write('@<TRIPOS>HEADTAIL\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
if res.head is not None:
dest.write('%s %d\n' % (res.head.name, i+1))
else:
dest.write('0 0\n')
if res.tail is not None:
dest.write('%s %d\n' % (res.tail.name, i+1))
else:
dest.write('0 0\n')
else:
head = tail = None
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
head = atom
if a2.residue.idx == res.idx + 1:
tail = atom
if head is not None:
dest.write('%s %d\n' % (head.name, i+1))
else:
dest.write('0 0\n')
if tail is not None:
dest.write('%s %d\n' % (tail.name, i+1))
else:
dest.write('0 0\n')
dest.write('@<TRIPOS>RESIDUECONNECT\n')
for i, res in enumerate(residues):
if isinstance(res, ResidueTemplate):
con = [res.head, res.tail, None, None, None, None]
for i, a in enumerate(res.connections):
con[i+2] = a
else:
con = [None, None, None, None, None, None]
ncon = 2
for atom in res:
for a2 in atom.bond_partners:
if a2.residue.idx == res.idx - 1:
con[0] = atom
elif a2.residue.idx == res.idx + 1:
con[1] = atom
elif a2.residue.idx != res.idx:
con[ncon] = atom
ncon += 1
dest.write('%d' % (i+1))
for a in con:
if a is not None:
dest.write(' %s' % a.name)
else:
dest.write(' 0')
dest.write('\n')
finally:
if own_handle: dest.close()
def count_nures(parm):
nnuc = 0
for res in parm.residues:
if RNAResidue.has(res.name) or DNAResidue.has(res.name):
nnuc += 1
return nnuc
def count_nures(parm):
nnuc = 0
for res in parm.residues:
if RNAResidue.has(res.name) or DNAResidue.has(res.name):
nnuc += 1
return nnuc
