本文整理汇总了Python中simtk.openmm.app.Topology.bonds方法的典型用法代码示例。如果您正苦于以下问题：Python Topology.bonds方法的具体用法？Python Topology.bonds怎么用？Python Topology.bonds使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类simtk.openmm.app.Topology的用法示例。
在下文中一共展示了Topology.bonds方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import bonds [as 别名]
#.........这里部分代码省略.........
resNumCol = atomData.getAttributeIndex('auth_seq_id')
resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
chainIdCol = atomData.getAttributeIndex('auth_asym_id')
elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id')
modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
xCol = atomData.getAttributeIndex('Cartn_x')
yCol = atomData.getAttributeIndex('Cartn_y')
zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None
lastResId = None
atomTable = {}
atomsInResidue = set()
models = []
for row in atomData.getRowList():
atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol])
if model not in models:
models.append(model)
self._positions.append([])
modelIndex = models.index(model)
if row[altIdCol] != '.' and atomKey in atomTable and len(self._positions[modelIndex]) > atomTable[atomKey].index:
# This row is an alternate position for an existing atom, so ignore it.
continue
if modelIndex == 0:
# This row defines a new atom.
if lastChainId != row[chainIdCol]:
# The start of a new chain.
chain = top.addChain(row[chainIdCol])
lastChainId = row[chainIdCol]
lastResId = None
if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
# The start of a new residue.
resId = (None if resNumCol == -1 else row[resNumCol])
resIC = ('' if resInsertionCol == -1 else row[resInsertionCol])
res = top.addResidue(row[resNameCol], chain, resId, resIC)
lastResId = row[resNumCol]
atomsInResidue.clear()
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atom = top.addAtom(row[atomNameCol], element, res, row[atomIdCol])
atomTable[atomKey] = atom
atomsInResidue.add(row[atomNameCol])
else:
# This row defines coordinates for an existing atom in one of the later models.
try:
atom = atomTable[atomKey]
except KeyError:
raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resNumCol], model))
if atom.index != len(self._positions[modelIndex]):
raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0]))
self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
for i in range(len(self._positions)):
self._positions[i] = self._positions[i]*nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None
# Record unit cell information, if present.
cell = block.getObj('cell')
if cell is not None and cell.getRowCount() > 0:
row = cell.getRow(0)
(a, b, c) = [float(row[cell.getAttributeIndex(attribute)])*0.1 for attribute in ('length_a', 'length_b', 'length_c')]
(alpha, beta, gamma) = [float(row[cell.getAttributeIndex(attribute)])*math.pi/180.0 for attribute in ('angle_alpha', 'angle_beta', 'angle_gamma')]
self.topology.setPeriodicBoxVectors(computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))
# Add bonds based on struct_conn records.
connectData = block.getObj('struct_conn')
if connectData is not None:
res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
typeCol = connectData.getAttributeIndex('conn_type_id')
connectBonds = []
for row in connectData.getRowList():
type = row[typeCol][:6]
if type in ('covale', 'disulf', 'modres'):
key1 = (row[res1Col], row[asym1Col], row[atom1Col])
key2 = (row[res2Col], row[asym2Col], row[atom2Col])
if key1 in atomTable and key2 in atomTable:
connectBonds.append((atomTable[key1], atomTable[key2]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)示例2: __init__
# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import bonds [as 别名]
#.........这里部分代码省略.........
inputfile = file
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile, load_all_models=True, extraParticleIdentifier=extraParticleIdentifier)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
for atom in residue.atoms:
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element == 'EP':
element = None
elif element is None:
# Try to guess the element.
upper = atomName.upper()
while len(upper) > 1 and upper[0].isdigit():
upper = upper[1:]
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('BE'):
element = elem.beryllium
elif upper.startswith('LI'):
element = elem.lithium
elif upper.startswith('K'):
element = elem.potassium
elif upper.startswith('ZN'):
element = elem.zinc
elif( len( residue ) == 1 and upper.startswith('CA') ):
element = elem.calcium
else:
try:
element = elem.get_by_symbol(upper[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r, str(atom.serial_number))
atomByNumber[atom.serial_number] = newAtom
self._positions = []
for model in pdb.iter_models(True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.atoms:
pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords*nanometers)
## The atom positions read from the PDB file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.
connectBonds = []
for connect in pdb.models[-1].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
if atomByNumber[i].element is not None and atomByNumber[j].element is not None:
if atomByNumber[i].element.symbol not in metalElements and atomByNumber[j].element.symbol not in metalElements:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
elif atomByNumber[i].element.symbol in metalElements and atomByNumber[j].residue.name not in PDBFile._standardResidues:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
elif atomByNumber[j].element.symbol in metalElements and atomByNumber[i].residue.name not in PDBFile._standardResidues:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
else:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)示例3: __init__
# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import bonds [as 别名]
#.........这里部分代码省略.........
file : string
the name of the file to load
"""
top = Topology()
## The Topology read from the PDB file
self.topology = top
# Load the PDB file
if isinstance(file, PdbStructure):
pdb = file
else:
inputfile = file
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile, load_all_models=True)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
for atom in residue.atoms:
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element is None:
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('BE'):
element = elem.beryllium
elif upper.startswith('LI'):
element = elem.lithium
elif upper.startswith('K'):
element = elem.potassium
elif upper.startswith('ZN'):
element = elem.zinc
elif( len( residue ) == 1 and upper.startswith('CA') ):
element = elem.calcium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r, str(atom.serial_number))
atomByNumber[atom.serial_number] = newAtom
self._positions = []
for model in pdb.iter_models(True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.atoms:
pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords*nanometers)
## The atom positions read from the PDB file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records.
connectBonds = []
for connect in pdb.models[0].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)