/usr/share/pyshared/MMTK/Biopolymers.py is in python-mmtk 2.7.9-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 | # This module implements the base classes for proteins and
# nucleic acid chains.
#
# Written by Konrad Hinsen
#
"""
Base classes for proteins and nucleic acids
"""
from MMTK import Bonds, ChemicalObjects, Collections, Database, PDB
import Scientific.IO.PDB
class Residue(ChemicalObjects.Group):
"""
Base class for aminoacid and nucleic acid residues
"""
def __setstate__(self, state):
self.__dict__.update(state)
try:
self.model = self.hydrogens
except AttributeError:
pass
self._init()
def _init(self):
# construct PDB map and alternative names
type = self.type
if not hasattr(type, 'pdbmap'):
pdb_dict = {}
type.pdbmap = [(type.symbol, pdb_dict)]
offset = 0
for g in type.groups:
for name, atom in g.pdbmap[0][1].items():
pdb_dict[name] = Database.AtomReference(atom.number + \
offset)
offset = offset + len(g.atoms)
if not hasattr(type, 'pdb_alternative'):
alt_dict = {}
for g in type.groups:
if hasattr(g, 'pdb_alternative'):
for key, value in g.pdb_alternative.items():
alt_dict[key] = value
setattr(type, 'pdb_alternative', alt_dict)
def _residueThroughLinkAtom(self, link_atom):
if link_atom is None:
return None
levels = 0
obj = link_atom
while obj is not None and obj != self:
obj = obj.parent
levels += 1
for atom in link_atom.bondedTo():
if atom.parent is not link_atom.parent:
obj = atom
while levels > 0:
obj = obj.parent
levels -= 1
return obj
return None
def precedingResidue(self):
"""
:returns the preceding residue in the chain
"""
return self._residueThroughLinkAtom(self.chain_links[0])
def nextResidue(self):
"""
:returns the next residue in the chain
"""
return self._residueThroughLinkAtom(self.chain_links[1])
class ResidueChain(ChemicalObjects.Molecule):
"""
Chain of residues
Base class for peptide chains and nucleotide chains
"""
is_chain = 1
def _setupChain(self, circular, properties, conf):
self.atoms = []
self.bonds = []
for g in self.groups:
self.atoms.extend(g.atoms)
self.bonds.extend(g.bonds)
for i in range(len(self.groups)-1):
link1 = self.groups[i].chain_links[1]
link2 = self.groups[i+1].chain_links[0]
self.bonds.append(Bonds.Bond((link1, link2)))
if circular:
link1 = self.groups[-1].chain_links[1]
link2 = self.groups[0].chain_links[0]
self.bonds.append(Bonds.Bond((link1, link2)))
self.bonds = Bonds.BondList(self.bonds)
self.parent = None
self.type = None
self.configurations = {}
try:
self.name = properties['name']
del properties['name']
except KeyError:
self.name = ''
if conf:
conf.applyTo(self)
try:
self.translateTo(properties['position'])
del properties['position']
except KeyError:
pass
self.addProperties(properties)
def __len__(self):
return len(self.groups)
def __getitem__(self, item):
return self.groups[item]
def __setitem__(self, item, value):
self.replaceResidue(self.groups[item], value)
def residuesOfType(self, *types):
"""
:param types: residue type codes
:type types: str
:returns: a collection that contains all residues whose type
(residue code) is contained in types
:rtype: :class:`~MMTK.Collections.Collection`
"""
types = [t.lower() for t in types]
rlist = [r for r in self.groups if r.type.symbol.lower() in types]
return Collections.Collection(rlist)
def residues(self):
"""
:returns: a collection containing all residues
:rtype: :class:`~MMTK.Collections.Collection`
"""
return Collections.Collection(self.groups)
def sequence(self):
"""
:returns: the residue sequence as a list of residue codes
:rtype: list of str
"""
return [r.type.symbol.lower() for r in self.groups]
#
# Find the full name of a residue
#
def _fullName(residue):
residue = residue.lower()
try:
return _aa_residue_names[residue]
except KeyError:
return _na_residue_names[residue]
_aa_residue_names = {'ala': 'alanine', 'a': 'alanine',
'arg': 'arginine', 'r': 'arginine',
'asn': 'asparagine', 'n': 'asparagine',
'asp': 'aspartic_acid', 'd': 'aspartic_acid',
'cys': 'cysteine', 'c': 'cysteine',
'gln': 'glutamine', 'q': 'glutamine',
'glu': 'glutamic_acid', 'e': 'glutamic_acid',
'gly': 'glycine', 'g': 'glycine',
'his': 'histidine', 'h': 'histidine',
'ile': 'isoleucine', 'i': 'isoleucine',
'leu': 'leucine', 'l': 'leucine',
'lys': 'lysine', 'k': 'lysine',
'met': 'methionine', 'm': 'methionine',
'phe': 'phenylalanine', 'f': 'phenylalanine',
'pro': 'proline', 'p': 'proline',
'ser': 'serine', 's': 'serine',
'thr': 'threonine', 't': 'threonine',
'trp': 'tryptophan', 'w': 'tryptophan',
'tyr': 'tyrosine', 'y': 'tyrosine',
'val': 'valine', 'v': 'valine',
'cyx': 'cystine_ss',
'cym': 'cysteine_with_negative_charge',
'app': 'aspartic_acid_neutral',
'glp': 'glutamic_acid_neutral',
'hsd': 'histidine_deltah', 'hse': 'histidine_epsilonh',
'hsp': 'histidine_plus',
'hid': 'histidine_deltah', 'hie': 'histidine_epsilonh',
'hip': 'histidine_plus',
'lyp': 'lysine_neutral',
'ace': 'ace_beginning', 'nme': 'nmethyl',
'nhe': 'amide',
}
_na_residue_names = {'da': 'd-adenosine',
'da5': 'd-adenosine_5ter',
'da3': 'd-adenosine_3ter',
'dan': 'd-adenosine_5ter_3ter',
'dc': 'd-cytosine',
'dc5': 'd-cytosine_5ter',
'dc3': 'd-cytosine_3ter',
'dcn': 'd-cytosine_5ter_3ter',
'dg': 'd-guanosine',
'dg5': 'd-guanosine_5ter',
'dg3': 'd-guanosine_3ter',
'dgn': 'd-guanosine_5ter_3ter',
'dt': 'd-thymine',
'dt5': 'd-thymine_5ter',
'dt3': 'd-thymine_3ter',
'dtn': 'd-thymine_5ter_3ter',
'ra': 'r-adenosine',
'ra5': 'r-adenosine_5ter',
'ra3': 'r-adenosine_3ter',
'ran': 'r-adenosine_5ter_3ter',
'rc': 'r-cytosine',
'rc5': 'r-cytosine_5ter',
'rc3': 'r-cytosine_3ter',
'rcn': 'r-cytosine_5ter_3ter',
'rg': 'r-guanosine',
'rg5': 'r-guanosine_5ter',
'rg3': 'r-guanosine_3ter',
'rgn': 'r-guanosine_5ter_3ter',
'ru': 'r-uracil',
'ru5': 'r-uracil_5ter',
'ru3': 'r-uracil_3ter',
'run': 'r-uracil_5ter_3ter',
}
for code in _aa_residue_names:
if len(code) == 3:
Scientific.IO.PDB.defineAminoAcidResidue(code)
for code in _na_residue_names:
Scientific.IO.PDB.defineNucleicAcidResidue(code)
#
# Add a residue to the residue list
#
def defineAminoAcidResidue(full_name, code3, code1 = None):
"""
Add a non-standard amino acid residue to the internal residue table.
Once added to the residue table, the new residue can be used
like any of the standard residues in the creation of peptide chains.
:param full_name: the name of the group definition in the chemical database
:type full_name: str
:param code3: the three-letter residue code
:type code3: str
:param code1: an optionel one-letter residue code
:type code1: str
"""
code3 = code3.lower()
if code1 is not None:
code1 = code1.lower()
if _aa_residue_names.has_key(code3) or _na_residue_names.has_key(code3):
raise ValueError("residue name " + code3 + " already used")
if _aa_residue_names.has_key(code1):
raise ValueError("residue name " + code1 + " already used")
_aa_residue_names[code3] = full_name
if code1 is not None:
_aa_residue_names[code1] = full_name
Scientific.IO.PDB.defineAminoAcidResidue(code3)
def defineNucleicAcidResidue(full_name, code):
"""
Add a non-standard nucleic acid residue to the internal residue table.
Once added to the residue table, the new residue can be used
like any of the standard residues in the creation of nucleotide chains.
:param full_name: the name of the group definition in the chemical database
:type full_name: str
:param code: the residue code
:type code3: str
"""
code = code.lower()
if _aa_residue_names.has_key(code) or _na_residue_names.has_key(code):
raise ValueError("residue name " + code + " already used")
_na_residue_names[code] = full_name
Scientific.IO.PDB.defineNucleicAcidResidue(code)
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