def _newResidue(model, name):
# find an number unused in both the 'het' and 'water' chains...
pos = 1
while model.findResidue(chimera.MolResId('het', pos)) \
or model.findResidue(chimera.MolResId('water', pos)):
pos += 1
return model.newResidue(name, 'het', pos, ' ')
def create_box(self):
m = chimera.Molecule()
m.name = 'Subregion Selection Box'
chimera.openModels.add([m], noprefs=True)
chimera.addModelClosedCallback(m, self.model_closed_cb)
rid = chimera.MolResId(1)
r = m.newResidue('markers', rid)
corners = []
for name in ('a000', 'a001', 'a010', 'a011', 'a100', 'a101', 'a110',
'a111'):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
corners.append(a)
green = chimera.MaterialColor(0, 1, 0, 1)
for a1, a2 in ((0, 1), (2, 3), (4, 5), (6, 7), (0, 2), (1, 3), (4, 6),
(5, 7), (0, 4), (1, 5), (2, 6), (3, 7)):
b = m.newBond(corners[a1], corners[a2])
b.halfbond = 0
b.drawMode = chimera.Bond.Wire
b.color = green
return corners
def make_model(self, length, thickness, rgb, label, xy_offset, label_rgb,
model_id):
m = chimera.Molecule()
m.name = 'scale bar'
#
# Need to create a residue because atom without residue causes
# unknown C++ exceptions.
#
rid = chimera.MolResId(1)
r = m.newResidue('sb', rid)
atoms = []
for name, pos in (('1', (-length / 2.0, 0, 0)), ('2', (length / 2.0, 0,
0)),
('label', (xy_offset[0],
xy_offset[1] + thickness / 2.0, 0))):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
c = chimera.Coord()
c.x, c.y, c.z = pos
a.setCoord(c) # a.coord = c does not work
a.display = 0
atoms.append(a)
m.atom1, m.atom2, m.label_atom = atoms
m.label_atom.color = background_color()
m.label_atom.display = 1
b = m.newBond(m.atom1, m.atom2)
b.display = b.Always
b.drawMode = b.Stick
b.radius = thickness / 2.0
b.color = chimera_color(rgb)
b.halfbond = 0
m.label_atom.label = label
m.label_atom.labelColor = chimera_color(label_rgb)
self.model = m
if model_id == None:
id, subid = (self.model_id(), chimera.openModels.Default)
else:
id, subid = model_id
chimera.openModels.add([m], baseId=id, subid=subid)
chimera.addModelClosedCallback(m, self.model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(m)
m.openState.active = False
z_near, z_far = clip_plane_positions()
self.set_depth(.5 * (z_near + z_far))
self.set_screen_position(self.screen_position)
self.orientation_cb()
return m
def toChimeraResId(resid):
"""Take a Modeller residue id and convert it to a chimera one"""
num, chain = resid.split(':')
insertCode = ''
while not str.isdigit(num[-1]):
insertCode = num[-1] + insertCode
num = num[:-1]
pos = int(num)
return chimera.MolResId(chain, pos, insert=insertCode)
def makedock(dirname, residueIds, outsideAtoms):
outfn = os.path.join(dirname, 'dock.ent')
out = open(outfn, 'w')
found_file = False
outsideResidueIds = set([id for id, name in outsideAtoms])
def isOutside(id, name):
if id not in outsideResidueIds:
return False
name = name.strip()
for oid, oname in outsideAtoms:
if id == oid and name == oname:
return True
return False
for fn in os.listdir(dirname):
if not fn.endswith('.pdb') or not pat.match(fn):
continue
found_file = True
number = int(fn[-12:-8])
print >> out, "REMARK Number:", number
conect = set()
f = open(os.path.join(dirname, fn), 'rU')
for line in f:
if line.startswith('CONECT'):
serial = int(line[6:11])
if serial in conect:
out.write(line)
continue
if not line.startswith('ATOM') \
and not line.startswith('HETATM'):
out.write(line)
continue
chain = line[21]
pos = int(line[22:26])
insertCode = line[26]
id = chimera.MolResId(chain, pos, insert=insertCode)
if id in residueIds or isOutside(id, line[12:16]):
serial = int(line[6:11])
conect.add(serial)
out.write(line)
f.close()
out.close()
if found_file:
return outfn
os.remove(outfn)
return None
def build_chimera_molecule(mmlib_structure):
from mmLib.Structure import fragment_id_split
import chimera
import numpy
from string import letters
modelMap = {} # mmLib structure to Chimera molecule
atoms = {} # mmLib atom to chimera atom mapping
residues = {} # fragment to chimera residue mapping
seq2frag = {} # entity-sequence to fragment mapping
sa2r = {} # sequence-asym_id to chimera residue mapping
e2c = {} # entity to chain mapping
# Make molecules
for mm in mmlib_structure.iter_models():
m = chimera.Molecule()
modelMap[mm] = m
seq2frag[m] = {}
sa2r[m] = {}
e2c[m] = {}
# Make atoms and residues as needed
name_to_element = element_table()
for mm in mmlib_structure.iter_models():
m = modelMap[mm]
for ma in mm.iter_all_atoms():
mf = ma.get_fragment()
try:
chain_id = ma.asym_id.strip()
except AttributeError:
chain_id = ma.chain_id.strip()
try:
r = residues[mf]
except KeyError:
seq, icode = fragment_id_split(mf.fragment_id)
if icode is None:
rid = chimera.MolResId(chain_id, seq)
else:
rid = chimera.MolResId(chain_id, seq, insert=icode)
r = m.newResidue(mf.res_name, rid)
residues[mf] = r
if not mf.is_standard_residue():
r.isHet = True
sf_key = (ma.label_entity_id, ma.label_seq_id)
d = seq2frag[m].setdefault(sf_key, {})
d[chain_id] = mf
sa2r[m][(ma.label_seq_id, ma.label_asym_id)] = r
s = e2c[m].setdefault(ma.label_entity_id, set([]))
s.add(chain_id)
if not ma.element:
ename = ma.name[0]
if len(ma.name) > 1 and ma.name[1] in letters:
ename += ma.name[1].lower()
elif len(ma.element) > 1:
ename = ma.element[0].upper() + ma.element[1:].lower()
else:
ename = ma.element
try:
element = name_to_element[ename]
except KeyError:
# Don't know what it is, guess carbon
element = name_to_element['C']
a = m.newAtom(ma.name.replace('*', "'"), element)
a.altLoc = ma.alt_loc
c = chimera.Coord()
c.x, c.y, c.z = ma.position
a.setCoord(c) # a.coord = c does not work
a.bfactor = ma.temp_factor
a.occupancy = ma.occupancy
if ma.U is not None:
a.anisoU = numpy.array(ma.U, 'f')
atoms[ma] = a
r.addAtom(a)
# Make bonds
numBonds = 0
for mm in mmlib_structure.iter_models():
m = modelMap[mm]
for ma in mm.iter_all_atoms():
for mb in ma.iter_bonds():
a1 = atoms[mb.get_atom1()]
a2 = atoms[mb.get_atom2()]
try:
m.newBond(a1, a2)
except TypeError:
pass
else:
numBonds += 1
# Make inter-residue bonds
from chimera.resCode import res3to1
from chimera import Sequence
residueAfter = {}
try:
table = mmlib_structure.cifdb["entity_poly_seq"]
except KeyError:
pass
else:
for m in modelMap.itervalues():
seqMap = {}
prevEntity = None
prevDict = None
for row in table.iter_rows():
thisEntity = row["entity_id"]
try:
chains = e2c[m][thisEntity]
except KeyError:
pass
else:
monomer = res3to1(row["mon_id"])
for chainId in chains:
try:
seq = seqMap[chainId]
except KeyError:
if chainId == " ":
name = Sequence.PRINCIPAL
else:
name = Sequence.CHAIN_FMT % chainId
seq = Sequence.Sequence(name)
seqMap[chainId] = seq
seq.append(monomer)
num = row["num"]
try:
thisDict = seq2frag[m][(thisEntity, num)]
except KeyError:
# leave the prev variables so we will connect
# residues in the same chain.
continue
if prevDict is not None and prevEntity == thisEntity:
for chain_id, prevR in prevDict.iteritems():
try:
thisR = thisDict[chain_id]
except KeyError:
continue
isAA = thisR.is_amino_acid()
isNA = thisR.is_nucleic_acid()
wasAA = prevR.is_amino_acid()
wasNA = prevR.is_nucleic_acid()
if isAA and wasAA:
numBonds += connectResidues(
prevR, ["C"], thisR, ["N"], atoms,
residueAfter)
if isNA and wasNA:
numBonds += connectResidues(
prevR, ["O3'", "O3*"], thisR, ["P"], atoms,
residueAfter)
prevDict = thisDict
prevEntity = thisEntity
m.cifPolySeq = seqMap
# If no bonds were made, make them
if numBonds == 0:
import chimera
for m in modelMap.itervalues():
chimera.connectMolecule(m)
# Assign secondary structure (helix and turn)
try:
table = mmlib_structure.cifdb["struct_conf"]
except KeyError:
pass
else:
for m in modelMap.itervalues():
for row in table.iter_rows():
typeId = row["conf_type_id"]
if typeId.startswith("HELX"):
ssType = "isHelix"
elif typeId.startswith("TURN"):
ssType = "isTurn"
else:
continue
bAsymId = row["beg_label_asym_id"]
bSeqId = row["beg_label_seq_id"]
eAsymId = row["end_label_asym_id"]
eSeqId = row["end_label_seq_id"]
try:
bRes = sa2r[m][(bSeqId, bAsymId)]
except KeyError:
print "No residue match asym_id=%s seq_id=%s" % (bAsymId,
bSeqId)
continue
try:
eRes = sa2r[m][(eSeqId, eAsymId)]
except KeyError:
print "No residue match asym_id=%s seq_id=%s" % (eAsymId,
eSeqId)
continue
# Make sure we have a clear list of residues
# from beginning to end
r = bRes
while r is not eRes and r is not None:
r = residueAfter.get(r, None)
if r is None:
print "Non-consecutive residues (%s.%s) -> (%s.%s)" % (
bSeqId, bAsymId, eSeqId, eAsymId)
continue
r = bRes
while r is not eRes:
setattr(r, ssType, True)
r = residueAfter[r]
setattr(eRes, ssType, True)
# Assign secondary structure (sheet)
try:
table = mmlib_structure.cifdb["struct_sheet_range"]
except KeyError:
pass
else:
for m in modelMap.itervalues():
for row in table.iter_rows():
bAsymId = row["beg_label_asym_id"]
bSeqId = row["beg_label_seq_id"]
eAsymId = row["end_label_asym_id"]
eSeqId = row["end_label_seq_id"]
try:
bRes = sa2r[m][(bSeqId, bAsymId)]
except KeyError:
print "No residue match asym_id=%s seq_id=%s" % (bAsymId,
bSeqId)
continue
try:
eRes = sa2r[m][(eSeqId, eAsymId)]
except KeyError:
print "No residue match asym_id=%s seq_id=%s" % (eAsymId,
eSeqId)
continue
# Make sure we have a clear list of residues
# from beginning to end
r = bRes
while r is not eRes and r is not None:
r = residueAfter.get(r, None)
if r is None:
print "Non-consecutive residues (%s.%s) -> (%s.%s)" % (
bSeqId, bAsymId, eSeqId, eAsymId)
continue
r = bRes
while r is not eRes:
r.isSheet = True
r = residueAfter[r]
eRes.isSheet = True
# Add any modres information to resCode dictionaries
try:
table = mmlib_structure.cifdb["struct_conn"]
except KeyError:
pass
else:
from chimera import resCode
dicts = (resCode.regex3to1, resCode.nucleic3to1, resCode.protein3to1,
resCode.standard3to1)
for row in table.iter_rows():
if row["conn_type_id"] != "modres":
continue
try:
name = row["ptnr1_auth_comp_id"]
except KeyError:
name = row["ptnr1_label_comp_id"]
stdName = row["pdbx_ptnr1_standard_comp_id"]
for d in dicts:
if stdName in d:
d[name] = d[stdName]
return modelMap.values()
def ReadMol ( fpath, log=False ) :
from random import random
cif, loops = ReadCif ( fpath, log )
# descriptions by chain id:
descrByEntityId = GetEntityDescr ( cif, loops )
try :
atoms = loops['_atom_site']['data']
print " - %d atom records" % len(atoms)
except :
print " - no atoms in cif?"
return None
labels = loops['_atom_site']['labels']
if 0 :
print "Labels:"
for l in labels :
print " : ", l
import time
start = time.time()
rmap = {}
nmol = chimera.Molecule()
from os import path
#nmol.name = path.splitext ( path.split (fpath)[1] )[0]
nmol.name = path.split (fpath) [1]
nmol.openedAs = [ fpath, [] ]
nmol.cif = cif
nmol.cifLoops = loops
nmol.chainColors = {}
nmol.chainDescr = {}
numQ = 0
first = True
for at in atoms :
mp = at['asMap']
if log and first :
#for label, val in mp.iteritems () :
for li, label in enumerate ( labels ) :
print " %d : %s : %s" % (li+1, label, mp[label])
first = False
atType = mp['type_symbol']
atName = mp['label_atom_id']
rtype = mp['label_comp_id']
chainId = mp['label_asym_id']
chainEId = mp['label_entity_id']
px = mp['Cartn_x']
py = mp['Cartn_y']
pz = mp['Cartn_z']
occ = mp['occupancy']
bfactor = mp['B_iso_or_equiv']
altLoc = mp['label_alt_id']
if altLoc == "." : altLoc = ''
if chainEId in descrByEntityId :
nmol.chainDescr [chainId] = descrByEntityId [chainEId]
resId = ResId ( mp )
if resId == None :
continue
ris = "%s%d" % (chainId, resId)
res = None
if not ris in rmap :
res = nmol.newResidue ( rtype, chimera.MolResId(chainId, resId) )
rmap[ris] = res
else :
res = rmap[ris]
clr = None
if not chainId in nmol.chainColors :
clr = chimera.MaterialColor ( random(), random(), random(), 1.0 )
nmol.chainColors[chainId] = clr
if 0 and log :
print " - chain %s" % chainId
else :
clr = nmol.chainColors [chainId]
nat = nmol.newAtom ( atName, chimera.Element(atType) )
drawRib = rtype in protein3to1 or rtype in nucleic3to1
#aMap[at] = nat
res.addAtom( nat )
nat.setCoord ( chimera.Point( float(px), float(py), float(pz) ) )
nat.altLoc = altLoc
nat.occupancy = float(occ)
nat.bfactor = float(bfactor)
if 'Q-score' in mp :
try :
Q = float ( mp['Q-score'] )
nat.Q = Q
numQ += 1
except :
#print " - q score is", mp['Q-score']
pass
end = time.time()
print " - created %d atoms, %.1fs, %d q-scores" % ( len(nmol.atoms), end-start, numQ )
return nmol
def LoadMolCh_ ( fpath, log=False, task=None ) :
mol = ReadMol ( fpath, log=False )
from chimera.resCode import nucleic3to1
from chimera.resCode import protein3to1, protein1to3
protein3to1['HSD'] = protein3to1['HIS']
protein3to1['HSE'] = protein3to1['HIS']
nucleic1to3 = { 'T':'THY', 'C':'CYT', 'G':'GUA', 'A':'ADE', 'U':'URA'}
nucleic3to1['GDP'] = nucleic3to1['GUA']
crmap = {}
rmolmap = {}
print " - adding bonds"
import time
start = time.time()
for r in mol.residues :
if not r.id.chainId in crmap :
crmap[r.id.chainId] = { r.id.position : r }
else :
crmap[r.id.chainId][r.id.position] = r
chains = mol.chainColors.keys()
print "%d residues - %d chains" % ( len(mol.residues), len(chains) )
from os.path import splitext
chMols = {}
for ch in chains :
start = time.time()
chMol = chimera.Molecule()
chMol.name = splitext ( mol.name )[0] + "_" + ch
rmap0 = crmap[ch]
chMols[ch] = chMol
print " - %s - %d residues" % (ch, len(rmap0)),
rmap = {}
for ri, res in rmap0.iteritems() :
nr = chMol.newResidue ( res.type, chimera.MolResId(ch, res.id.position) )
rmap[nr.id.position] = nr
for at in res.atoms :
nat = chMol.newAtom ( at.name, at.element )
nr.addAtom ( nat )
nat.setCoord ( at.coord() )
print ", %d atoms" % len(chMol.atoms),
for ri, r in rmap.iteritems() :
#if ri % 100 == 0 :
# print "%d/%d" % ( ri, len(mol.residues) )
# if task :
# task.updateStatus( "%d/%d" % ( ri, len(mol.residues) ) )
rmol = None
rtype = r.type.upper()
if rtype.lower() in rmolmap :
rmol = rmolmap[ rtype.lower() ]
else :
rmol = GetResMol ( rtype.lower() )
if rmol != None :
rmolmap[rtype.lower()] = rmol
if rmol != None :
for b in rmol.bonds :
a1n, a2n = b.atoms[0].name, b.atoms[1].name
if a1n in r.atomsMap and a2n in r.atomsMap :
for a1 in r.atomsMap[a1n] :
for a2 in r.atomsMap[a2n] :
#print "%s - %s" % ( At(a1), At(a2) )
nb = chMol.newBond ( a1, a2 )
pass
else :
print " - rmol %s not found" % rtype
if 1 :
if r.type.upper() in protein3to1 :
if r.id.position-1 in rmap :
pres = rmap[r.id.position-1]
if pres.type.upper() in protein3to1 :
#GetSS ( pres, r )
if "C" in pres.atomsMap and "N" in r.atomsMap :
for a1 in pres.atomsMap["C"] :
for a2 in r.atomsMap["N"] :
#print a1.name, pres.id.position, a2.name, r.id.position
nb = chMol.newBond ( a1, a2 )
pass
if r.type.upper() in nucleic1to3 or r.type.upper() in nucleic3to1 :
if r.id.position-1 in rmap :
pres = rmap[r.id.position-1]
if pres.type.upper() in nucleic1to3 or pres.type.upper() in nucleic3to1 :
if "O3'" in pres.atomsMap and "P" in r.atomsMap :
for a1 in pres.atomsMap["O3'"] :
for a2 in r.atomsMap["P"] :
#print a1.name, pres.id.position, a2.name, r.id.position
nb = chMol.newBond ( a1, a2 )
pass
print ( ", %d bonds, %.1fs" % (len(chMol.bonds), time.time()-start) )
#start = time.time()
#chimera.openModels.add ( [chMol] )
#print " - added mol %ss, %.1fs" % (chMol.name, time.time()-start)
start = time.time()
for r in chMol.residues :
rt = r.type.upper()
if rt in protein3to1 or rt in nucleic3to1 or rt in nucleic1to3 :
r.ribbonDisplay = True
r.ribbonDrawMode = 2
r.ribbonColor = mol.chainColors[r.id.chainId]
for at in r.atoms :
at.display = False
at.drawMode = at.EndCap
if at.element.name.upper() in atomColors :
at.color = atomColors[at.element.name.upper()]
else :
at.color = mol.chainColors[r.id.chainId]
else :
for at in r.atoms :
at.display = True
at.drawMode = at.EndCap
if at.element.name.upper() in atomColors :
at.color = atomColors[at.element.name.upper()]
else :
at.color = mol.chainColors[r.id.chainId]
for b in mol.bonds :
b.drawMode = b.Stick
b.display = b.Smart
#print " - changed mol disp %s - %.1fs" % (chMol.name, time.time()-start)
return mol
def molecule_from_atoms(m, atoms):
import chimera
cm = chimera.Molecule()
cm.color = m.color
cm.display = m.display
for attr in ('name', 'openedAs'):
if hasattr(m, attr):
setattr(cm, attr, getattr(m, attr))
if hasattr(m, 'pdbHeaders'):
cm.setAllPDBHeaders(m.pdbHeaders)
rmap = {}
rlist = atom_residues(atoms)
rlist.sort(lambda r1, r2: cmp(r1.id.position, r2.id.position))
for r in rlist:
crid = chimera.MolResId(r.id.chainId, r.id.position)
cr = cm.newResidue(r.type, crid)
cr.isHet = r.isHet
cr.isHelix = r.isHelix
cr.isSheet = r.isSheet
cr.isTurn = r.isTurn
cr.ribbonColor = r.ribbonColor
cr.ribbonStyle = r.ribbonStyle
cr.ribbonDrawMode = r.ribbonDrawMode
cr.ribbonDisplay = r.ribbonDisplay
rmap[r] = cr
amap = {}
for a in atoms:
ca = cm.newAtom(a.name, a.element)
ca.setCoord(a.coord())
ca.altLoc = a.altLoc
ca.color = a.color
ca.drawMode = a.drawMode
ca.display = a.display
if hasattr(a, 'bfactor'):
ca.bfactor = a.bfactor
amap[a] = ca
cr = rmap[a.residue]
cr.addAtom(ca)
for b in atom_bonds(atoms):
a1, a2 = b.atoms
cb = cm.newBond(amap[a1], amap[a2])
cb.color = b.color
cb.drawMode = b.drawMode
cb.display = b.display
for am in m.associatedModels():
if not isinstance(am, chimera.PseudoBondGroup):
continue
if not am.category.startswith("coordination complexes"):
continue
for pb in am.pseudoBonds:
a1, a2 = pb.atoms
if a1 not in amap or a2 not in amap:
continue
cm.newBond(amap[a1], amap[a2])
return cm
def placePeptide(sequence,
phiPsis,
model="scratch",
position=None,
rotlib=None,
chainID='A'):
"""place a peptide sequence
'sequence' contains the (upper case) sequence
'phiPsis' is a list of phi/psi tuples, one per residue
'model' can either be a chimera.Molecule instance or a string.
If the latter, then a new model is created with the string as
its .name attribute.
'position' can either be a chimera.Point or None. If None, then
the fragment is positioned at the center of the view.
"""
if not sequence:
raise ValueError("No sequence supplied")
sequence = sequence.upper()
if not sequence.isupper():
raise ValueError("Sequence contains non-alphabetic characters")
from chimera.resCode import protein1to3
for c in sequence:
if c not in protein1to3:
raise ValueError("Unrecognized protein 1-letter code:" " %s" % c)
if len(sequence) != len(phiPsis):
raise ValueError("Number of phi/psis not equal to" " sequence length")
if isinstance(model, basestring):
model = _newModel(model)
needFocus = False
if position is None:
if len(chimera.openModels.list()) == 1:
needFocus = True
xf = model.openState.xform
position = xf.inverse().apply(Point(*chimera.viewer.camera.center))
prev = [None] * 3
pos = 1
from Midas.addAA import DIST_N_C, DIST_CA_N, DIST_C_CA, DIST_C_O
from chimera.molEdit import findPt, addAtom, addDihedralAtom
serialNumber = None
residues = []
for c, phiPsi in zip(sequence, phiPsis):
phi, psi = phiPsi
while model.findResidue(chimera.MolResId(chainID, pos)):
pos += 1
r = model.newResidue(protein1to3[c], chainID, pos, ' ')
residues.append(r)
for backbone, dist, angle, dihed in (('N', DIST_N_C, 116.6, psi),
('CA', DIST_CA_N, 121.9, 180.0),
('C', DIST_C_CA, 110.1, phi)):
if prev[0] == None:
pt = Point(0.0, 0.0, 0.0)
elif prev[1] == None:
pt = Point(dist, 0.0, 0.0)
elif prev[2] == None:
pt = findPt(prev[0].coord(), prev[1].coord(),
Point(0.0, 1.0, 0.0), dist, angle, 0.0)
else:
pt = findPt(prev[0].coord(), prev[1].coord(), prev[2].coord(),
dist, angle, dihed)
a = addAtom(backbone,
Element(backbone[0]),
r,
pt,
serialNumber=serialNumber,
bondedTo=prev[0])
serialNumber = a.serialNumber + 1
prev = [a] + prev[:2]
o = addDihedralAtom("O",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
120.4,
180.0 + psi,
bonded=True)
# C terminus O/OXT at different angle than mainchain O
model.deleteAtom(o)
addDihedralAtom("O",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
117.0,
180.0 + psi,
bonded=True)
addDihedralAtom("OXT",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
117.0,
psi,
bonded=True)
from Rotamers import useBestRotamers
# have to process one by one, otherwise side-chain clashes will occur
kw = {}
if rotlib:
kw['lib'] = rotlib
for r in residues:
useBestRotamers("same", [r], criteria="cp", log=False, **kw)
# find peptide center
coords = []
for r in residues:
coords.extend([a.coord() for a in r.atoms])
center = Point(coords)
correction = position - center
for r in residues:
for a in r.atoms:
a.setCoord(a.coord() + correction)
from Midas import ksdssp
ksdssp([model])
if needFocus:
chimera.runCommand("focus")
return residues
def addAA(residue_type, residue_seq, last_res, conformation=None):
"""add an amino acid to a model.
"""
phi, psi = getPhiPsiVals(conformation)
if not isLastRes(last_res):
raise AddAAError, "Can only add to last residue."
last_bbone_ats = {}
## find 'C' atom of last residue
last_C = getBboneAtom(last_res, 'C')
if not last_C:
raise AddAAError, "Couldn't find 'C' backbone atom of last residue"
else:
last_bbone_ats['C'] = last_C
## find 'CA' atom of last residue
last_CA = getBboneAtom(last_res, 'CA')
if not last_CA:
raise AddAAError, "Couldn't find 'CA' backbone atom of last residue"
else:
last_atom_drawMode = last_CA.drawMode
last_bond_drawMode = last_CA.bondsMap[last_C].drawMode
last_bbone_ats['CA'] = last_CA
## find 'N' atom of last residue
last_N = getBboneAtom(last_res, 'N')
if not last_N:
raise AddAAError, "Couldn't find 'N' backbone atom of last residue"
else:
last_bbone_ats['N'] = last_N
## find 'O' atom of last residue
last_O = getBboneAtom(last_res, 'O')
if not last_O:
raise AddAAError, "Couldn't find 'O' backbone atom of last residue"
else:
last_bbone_ats['O'] = last_O
## make a new residue
insert_char = residue_seq[-1]
if insert_char.isalpha():
## insertion specified
residue_seq = residue_seq[:-1]
else:
insert_char = ' '
if residue_seq.isdigit():
residue_seq = int(residue_seq)
else:
raise AddAAError, "Residue sequence argument can contain at most one insertion character"
mol = last_res.molecule
mrid = chimera.MolResId(last_res.id.chainId,
residue_seq,
insert=insert_char)
if mol.findResidue(mrid):
raise AddAAError, "Can't add amino acid, model already contains residue with sequence '%s'." % \
residue_seq
new_res = mol.newResidue(residue_type, mrid, neighbor=last_res, after=True)
if conformation == 'alpha':
new_res.isHelix = True
elif conformation in ('abeta', 'pbeta'):
new_res.isSheet = True
bFac = getBFactor(mol)
## now delete any terminal atoms from the last residue, if there is one
## there.
try:
pruneLastResidue(last_res)
except AddAAError, what:
cleanUp(mol, new_res, [])
raise AddAAError, what