def minimize(selection='all', forcefield='MMFF94s', method='conjugate gradients', nsteps=500, conv=0.0001, cutoff=False, cut_vdw=6.0, cut_elec=8.0):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
mol.AddHydrogens()
ff = ob.OBForceField.FindForceField(forcefield) # GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if cutoff == True:
ff.EnableCutOff(True)
ff.SetVDWCutOff(cut_vdw)
ff.SetElectrostaticCutOff(cut_elec)
if method == 'conjugate gradients':
ff.ConjugateGradients(nsteps, conv)
else:
ff.SteepestDescent(nsteps, conv)
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
if name == 'all':
name = 'all_'
cmd.read_pdbstr(pdb_string, name)
print '#########################################'
print 'The Energy of %s is %8.2f %s ' % (name, nrg, ff.GetUnit())
print '#########################################'
def gpssPeptide(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get ligand surfaces
peptideInfo = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=peptideInfo"
)
# Get pocket atoms
for peptideSurface in peptideInfo:
peptideSurfaceFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/"
+ "gpssServerPymol.php?pdbId="
+ pdbCode
+ "&surfaceId="
+ peptideSurface
+ "&mode=peptideSurface"
)
peptideId = peptideSurface.split(".")
objectId = "Peptide-" + peptideId[1]
cmd.read_pdbstr(peptideSurfaceFile.read(), objectId)
cmd.do("hide everything," + objectId)
cmd.do("show surface," + objectId)
cmd.do("set transparency=0.2," + objectId)
cmd.do("zoom GPSS-" + pdbCode)
def pdbDisplay(self):
'''creates an actual pdb object of the protein or just the part near the
surface/group of interest'''
pdbText = "\n".join(self.pdbDatas[-1].rawData)
cmd.read_pdbstr(
pdbText, self.pdbNames[-1] + "." + str(self.drawCount) + ".pdb")
self.drawCount += 1
def gpssCastp(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get pocket count
castpInfo = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=castpInfo"
)
castpLength = int(castpInfo.readlines()[-1][13:16])
# Get pocket atoms
while castpLength > 0:
castpSurfaceFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/"
+ "gpssServerPymol.php?pdbId="
+ pdbCode
+ "&surfaceId="
+ str(castpLength)
+ "&mode=castpSurface"
)
objectId = "CASTp-" + str(castpLength)
cmd.read_pdbstr(castpSurfaceFile.read(), objectId)
cmd.do("hide everything," + objectId)
cmd.do("show surface," + objectId)
cmd.do("set transparency=0.2," + objectId)
castpLength -= 1
cmd.do("zoom GPSS-" + pdbCode)
def gpssLigand(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get ligand surfaces
ligandInfo = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=ligandInfo"
).read()
if ligandInfo:
ligandInfoArray = ligandInfo.split(":")
# Get pocket atoms
for ligandSurface in ligandInfoArray:
ligandSurfaceFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/"
+ "gpssServerPymol.php?pdbId="
+ pdbCode
+ "&surfaceId="
+ ligandSurface
+ "&mode=ligandSurface"
)
ligandId = ligandSurface.split(".")
objectId = "Ligand-" + ligandId[1] + "." + ligandId[2] + "." + ligandId[3]
cmd.read_pdbstr(ligandSurfaceFile.read(), objectId)
cmd.do("hide everything," + objectId)
cmd.do("show surface," + objectId)
cmd.do("show sticks," + objectId + " and resn " + ligandId[1])
cmd.do("zoom GPSS-" + pdbCode)
def gpssMetal(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get ligand surfaces
metalInfo = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=metalInfo"
).read()
if metalInfo:
metalInfoArray = metalInfo.split(":")
# Get pocket atoms
for metalSurface in metalInfoArray:
metalSurfaceFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/"
+ "gpssServerPymol.php?pdbId="
+ pdbCode
+ "&surfaceId="
+ metalSurface
+ "&mode=metalSurface"
)
metalId = metalSurface.split(".")
objectId = "Metal-" + metalId[1] + "." + metalId[2] + "." + metalId[3]
cmd.read_pdbstr(metalSurfaceFile.read(), objectId)
cmd.do("hide everything," + objectId)
cmd.do("show surface," + objectId)
cmd.do("show sphere," + objectId + " and resn " + metalId[1])
cmd.do("zoom GPSS-" + pdbCode)
def deepshifts_load(index,
objname=None,
host='localhost',
port=7000,
atom_props=None):
'''
deepshifts_load(index, objname=None, host='localhost', port=7000)
'''
# get data
req = requests.get('http://{}:{}/index/{}?fmt=proteindatabank'.format(
host, port, index))
data = req.json()
# load object
if objname is None:
objname = 'obj-' + str(index)
cmd.read_pdbstr(data['request'], objname)
cmd.set_title(objname, 1, data['energy'][0])
# load properties
if atom_props is None:
atom_props = ''
props = {p: data[p] for p in atom_props.split() if p in data}
for prop, values in props.iteritems():
#for n,value in enumerate(values):
# selection = 'id %d in %s'%(n, objname)
# cmd.set_atom_property(prop, value, selection)
cmd.iterate(objname,
'p["{}"]=l.pop(0)'.format(prop),
space={'l': values})
pprint.pprint(data)
def getSasa(sel="sele", normalized=0, probeSize=1.4):
name = "SASA %3.1f" % probeSize
if (normalized):
name = "normSASA %3.1f" % probeSize
cmd.read_pdbstr(
PythonMSL.getSasa(cmd.get_pdbstr(sel), normalized, probeSize), name)
def gpssMetal(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get ligand surfaces
metalInfo = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=metalInfo').read()
if metalInfo:
metalInfoArray = metalInfo.split(':')
# Get pocket atoms
for metalSurface in metalInfoArray:
metalSurfaceFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+ pdbCode +
'&surfaceId=' + metalSurface +
'&mode=metalSurface')
metalId = metalSurface.split('.')
objectId = 'Metal-' + metalId[1] + '.' + metalId[2] + '.' + metalId[3]
cmd.read_pdbstr(metalSurfaceFile.read(),objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show surface,' + objectId)
cmd.do('show sphere,' + objectId + ' and resn ' + metalId[1])
cmd.do('zoom GPSS-'+pdbCode)
def gpssLigand(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get ligand surfaces
ligandInfo = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=ligandInfo').read()
if ligandInfo:
ligandInfoArray = ligandInfo.split(':')
# Get pocket atoms
for ligandSurface in ligandInfoArray:
ligandSurfaceFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+ pdbCode +
'&surfaceId=' + ligandSurface +
'&mode=ligandSurface')
ligandId = ligandSurface.split('.')
objectId = 'Ligand-' + ligandId[1] + '.' + ligandId[2] + '.' + ligandId[3]
cmd.read_pdbstr(ligandSurfaceFile.read(),objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show surface,' + objectId)
cmd.do('show sticks,' + objectId + ' and resn ' + ligandId[1])
cmd.do('zoom GPSS-'+pdbCode)
def silent_load(filename, *tags, **kwds): # tags = empty loads all the strucutres. (kwds needed to eat a superflous _self parameter)
"""silent_load filename, [tags]
Load the given tags from the given Rosetta binary-format silent file into appropriately named structures in Pymol.
Tags can be zero or more comma separated tag. If no tags are given, load all availible tags.
Python-style regex expansion can be used to match multiple tags. Regexes must match the entire tag to be accepted.
"""
# Add start and end so we don't get partial matches.
# Strip out whitespace and quote marks (shouldn't occur in tags or regex, but might occur due to terminal quoting)
rextags = [ re.compile( "^" + t.strip().strip('"'+"'") + "$") for t in tags ]
with open(filename) as f:
while True:
line = f.readline()
if not line:
break # end of file
line = line.strip()
if not line:
continue
#In practice, ANNOTATED_SEQEUENCE always comes before coordiantes
if line.startswith("ANNOTATED_SEQUENCE:"):
tag = line.split()[-1]
if checktags(tag, rextags):
PDBLINES = load_struct(tag, line, f)
if PDBLINES:
if cmd is not None:
# Load the PDB into Pymol
print("-- Loading structure " + tag)
cmd.read_pdbstr( PDBLINES, tag )
else:
outfilename = tag+".pdb"
print("-- Saving file " + outfilename)
with open(outfilename,'w') as of:
of.write(PDBLINES)
pass
def minimize(selection='all',
forcefield='MMFF94s',
method='cg',
nsteps=2000,
conv=1E-6,
cutoff=False,
cut_vdw=6.0,
cut_elec=8.0):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
ff = ob.OBForceField.FindForceField(forcefield)
ff.Setup(mol)
if cutoff == True:
ff.EnableCutOff(True)
ff.SetVDWCutOff(cut_vdw)
ff.SetElectrostaticCutOff(cut_elec)
if method == 'cg':
ff.ConjugateGradients(nsteps, conv)
else:
ff.SteepestDescent(nsteps, conv)
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
if name == 'all':
name = 'all_'
cmd.read_pdbstr(pdb_string, name)
return nrg
def addH(self):
if reduceExe:
seles = self.h_sel.getvalue()
for sele in seles:
if sele != '':
pdbStr = cmd.get_pdbstr(sele)
args = '"' + reduceExe + '"' + ' -BUILD -DB ' + '"' + reduceDB + '" -'
print args + " "
p = subprocess.Popen(args,
shell=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
newpdb = p.communicate(pdbStr)[0]
mynewsel = sele + '_H'
if self.h_newSel.getvalue() != '':
mynewsel = self.h_newSel.getvalue()
if self.replVar.get() == 1:
mynewsel = sele
cmd.delete(sele)
cmd.read_pdbstr(newpdb, mynewsel)
else:
print "Could not determine selection"
else:
print reduceError
def jsoner(sel):
lens=[]
states=[]
q1=cmd.get_model(sel)
lens.append(len(q1.atom))
states.append(1)
proc = Popen("goreduce", shell=True, stdin=PIPE, stdout=PIPE)
options=json.dumps({"SelNames":[sel],"AtomsPerSel":lens,"StatesPerSel":states}) #, "IntOptions":[[5, 11]] })
proc.stdin.write(options+"\n")
for i in q1.atom:
atom,coords=gochem.Atom2gcRef(i)
proc.stdin.write(atom+"\n")
proc.stdin.write(coords+"\n")
proc.stdin.close()
# if proc.wait() != 1:
# print "There were some errors"
# for j in proc.stderr:
# print(json.loads(j))
# proc.stderr.close()
# for i in proc.stdout:
# print json.loads(i)
info = gochem.get_info(proc)
mod=gochem.get_model(proc,info,0)
cmd.load_model(mod,sel+"_Htmp",discrete=1,zoom=1)
modR=cmd.get_pdbstr(sel+"_Htmp")
cmd.read_pdbstr(modR,sel+"_H")
cmd.delete(sel+"_Htmp")
print "Jumalauta y wea"
def localSamplingBR(
system="all",
fragSel="sele and name CA",
bbqTable="/home/dwkulp/software/msl/tables/PiscesBBQTable.txt",
numResults=25):
cmd.read_pdbstr(
PythonMSL.localSamplingBR(cmd.get_pdbstr(system),
cmd.get_pdbstr(fragSel), numResults),
"fragmentsBR")
def create_model(self, name=None):
"""Creates PyMOL object connected with current structure (adds entry to Registry)"""
if name is None:
name = self.derived_from.name + "_" + \
self.__class__.__name__[
:4].lower() + str(Registry.get_next_number())
Registry.add(self, name, 0, structure_flag=True)
cmd.read_pdbstr(self.create_pdbstring(enumerate_atoms=True, transformed=True).read(), name, state=1) # pylint: disable=protected-access
cmd.set_title(name, 0, "PD")
def conf_search(selection="all", forcefield="MMFF94s", method="Weighted", nsteps=500, conformers=25, lowest_conf=5):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats("pdb", "pdb")
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
mol.AddHydrogens()
ff = ob.OBForceField.FindForceField(forcefield) ## GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if method == "Weighted":
ff.WeightedRotorSearch(conformers, nsteps)
elif method == "Random":
ff.RandomRotorSearch(conformers, nsteps)
else:
ff.SystematicRotorSearch(nsteps)
if name == "all":
name = "all_"
if method in ["Weighted", "Random"]:
ff.GetConformers(mol)
print "##############################################"
print " Conformer | Energy | RMSD"
nrg_unit = ff.GetUnit()
rmsd = 0
ff.GetCoordinates(mol)
nrg = ff.Energy()
conf_list = []
for i in range(conformers):
mol.SetConformer(i)
ff.Setup(mol)
nrg = ff.Energy()
conf_list.append((nrg, i))
conf_list.sort()
lenght_conf_list = len(conf_list)
if lowest_conf > lenght_conf_list:
lowest_conf = lenght_conf_list
for i in range(lowest_conf):
nrg, orden = conf_list[i]
name_n = "%s%02d" % (name, i)
cmd.delete(name_n)
mol.SetConformer(orden)
pdb_string = obconversion.WriteString(mol)
cmd.read_pdbstr(pdb_string, name_n)
if i != 0:
rmsd = cmd.fit(name_n, "%s00" % name, quiet=1)
print "%15s | %10.2f%9s |%6.1f" % (name_n, nrg, nrg_unit, rmsd)
print "##############################################"
else:
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
cmd.read_pdbstr(pdb_string, name)
print "#########################################"
print "The Energy of %s is %8.2f %s " % (name, nrg, ff.GetUnit())
print "#########################################"
def conf_search(selection='all', forcefield='MMFF94s', method='Weighted', nsteps=500, conformers=25, lowest_conf=5):
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
mol.AddHydrogens()
ff = ob.OBForceField.FindForceField(forcefield) # GAFF, MMFF94s, MMFF94, UFF, Ghemical
ff.Setup(mol)
if method == 'Weighted':
ff.WeightedRotorSearch(conformers, nsteps)
elif method == 'Random':
ff.RandomRotorSearch(conformers, nsteps)
else:
ff.SystematicRotorSearch(nsteps)
if name == 'all':
name = 'all_'
if method in ['Weighted', 'Random']:
ff.GetConformers(mol)
print '##############################################'
print ' Conformer | Energy | RMSD'
nrg_unit = ff.GetUnit()
rmsd = 0
ff.GetCoordinates(mol)
nrg = ff.Energy()
conf_list = []
for i in range(conformers):
mol.SetConformer(i)
ff.Setup(mol)
nrg = ff.Energy()
conf_list.append((nrg, i))
conf_list.sort()
lenght_conf_list = len(conf_list)
if lowest_conf > lenght_conf_list:
lowest_conf = lenght_conf_list
for i in range(lowest_conf):
nrg, orden = conf_list[i]
name_n = '%s%02d' % (name, i)
cmd.delete(name_n)
mol.SetConformer(orden)
pdb_string = obconversion.WriteString(mol)
cmd.read_pdbstr(pdb_string, name_n)
if i != 0:
rmsd = cmd.fit(name_n, '%s00' % name, quiet=1)
print '%15s | %10.2f%9s |%6.1f' % (name_n, nrg, nrg_unit, rmsd)
print '##############################################'
else:
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
cmd.read_pdbstr(pdb_string, name)
print '#########################################'
print 'The Energy of %s is %8.2f %s ' % (name, nrg, ff.GetUnit())
print '#########################################'
def localSamplingCCD(
system="all",
fragSel="sele and name CA",
bbqTable="/export/home/brettth/projectsS/code/tree/mslib/trunk/tables/PiscesBBQTable.txt",
angle=10,
numResults=25):
cmd.read_pdbstr(
PythonMSL.localSamplingCCD(cmd.get_pdbstr(system),
cmd.get_pdbstr(fragSel), numResults, angle,
bbqTable), "fragmentsCCD")
def remote(self,pdbCode):
pdbCode = pdbCode.upper()
try:
pdbFile = urllib.urlopen('http://www.rcsb.org/pdb/cgi/export.cgi/' +
pdbCode + '.pdb.gz?format=PDB&pdbId=' +
pdbCode + '&compression=gz')
cmd.read_pdbstr(zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS), pdbCode)
except:
print("Unexpected error: "+sys.exc_info()[0])
tkinter.messagebox.showerror('Invalid Code',
'You entered an invalid pdb code:' + pdbCode)
def load_chimerax(filename):
"""
Load a UCSF ChimeraX file written by SwissDock
Parameters
----------
filename : str
chimerax file (XML file with URL of target and ligands cluster)
"""
# UCSF Chimera Web Data Format
# www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html
docked = get_docked()
print(f" PyViewDock: Loading \"{filename}\"")
# read ChimeraX file as XML
try:
chimerax_xml = ET.parse(filename).getroot()
target_url = chimerax_xml.find('web_files').find('file').get('loc')
commands = chimerax_xml.find('commands').find('py_cmd').text
cluster_url = re.findall('"(http[^"]+pdb)"', commands)[0]
target_filename = target_url.split('/')[-1]
cluster_filename = cluster_url.split('/')[-1]
if not all(
[target_url, cluster_url, target_filename, cluster_filename]):
raise ValueError
except FileNotFoundError:
print(" PyViewDock: Failed reading 'chimerax' file. File not found.")
except:
print(" PyViewDock: Failed reading 'chimerax' file. Invalid format.")
else:
# fetch files from server
try:
target_pdb = urlopen(target_url).read().decode('utf-8')
cluster_pdb = urlopen(cluster_url).readlines()
cluster_pdb = [i.decode('utf-8') for i in cluster_pdb]
cmd.read_pdbstr(target_pdb, 'target')
docked.load_dock4(cluster_pdb, 'cluster', 0)
except HTTPError:
print(
" PyViewDock: Failed reading 'chimerax' file. Bad server response. Too old?"
)
# find local files that match names in .chimerax directory
chimerax_directory = os.path.dirname(os.path.realpath(filename))
target_file = os.path.join(chimerax_directory, target_filename)
cluster_file = os.path.join(chimerax_directory, cluster_filename)
if os.path.isfile(target_file) and os.path.isfile(target_file):
print(
f" PyViewDock: Files found locally ({target_filename}, {cluster_filename}). Loading..."
)
importing.load(target_file)
load_dock4(cluster_file)
def minimize(selection='tmp',
forcefield='MMFF94',
method='steepest descent',
nsteps=2000,
conv=1E-6,
cutoff=False,
cut_vdw=6.0,
cut_elec=8.0,
rigid_geometry=True):
"""
Use openbabel to minimize the energy of a molecule.
"""
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
if rigid_geometry:
constraints = ob.OBFFConstraints()
for angle in ob.OBMolAngleIter(mol):
b, a, c = [mol.GetAtom(x + 1) for x in angle]
value = mol.GetAngle(a, b, c)
b, a, c = [x + 1 for x in angle]
constraints.AddAngleConstraint(a, b, c, value)
for i in ob.OBMolBondIter(mol):
a, b = (i.GetBeginAtomIdx(), i.GetEndAtomIdx())
value = i.GetLength()
constraints.AddDistanceConstraint(a, b, value)
ff = ob.OBForceField.FindForceField(forcefield)
ff.Setup(mol, constraints)
ff.SetConstraints(constraints)
else:
ff = ob.OBForceField.FindForceField(forcefield)
ff.Setup(mol)
if cutoff:
ff.EnableCutOff(True)
ff.SetVDWCutOff(cut_vdw)
ff.SetElectrostaticCutOff(cut_elec)
if method == 'conjugate gradients':
ff.ConjugateGradients(nsteps, conv)
else:
ff.SteepestDescent(nsteps, conv)
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
if name == 'all':
name = 'all_'
cmd.delete(selection)
cmd.read_pdbstr(pdb_string, selection)
return nrg
def wrapped_load_structure(self, code, *args, **kwargs):
"""Wrapped load_structure method: loads structures from databases or from local copy of PDB file.
Creates PyMOL objects and returns a list of PyDesc structures connected with those objects.
Arguments:
code -- str, pdb code; check PyDesc documentation for more information.
"""
list_of_structures = current_load_structure(self, code, *args, **kwargs)
for structure_index, structure_obj in enumerate(list_of_structures):
cmd.read_pdbstr(structure_obj.create_pdbstring(transformed=False).read(), structure_obj.name, state=structure_index + 1) # pylint: disable=protected-access
Registry.add(structure_obj, structure_obj.name, structure_index + 1, structure_flag=True)
cmd.set_title(structure_obj.name, structure_index + 1, "PD")
return list_of_structures
def localSamplingPDB(
system="all",
fragSel="sele and name CA",
fragDB="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/nr1000.fragdb",
numRes=-1,
rmsdTol=0.0,
bbqTable="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/PiscesBBQTable.txt",
numResults=25):
cmd.read_pdbstr(
PythonMSL.localSamplingPDB(cmd.get_pdbstr(system),
cmd.get_pdbstr(fragSel), fragDB, numRes,
rmsdTol, numResults, bbqTable),
"fragmentsPDB")
def LoadNew(model, name, template=None, PDBstr=False, state=0, discrete=0):
if PDBstr:
tmpname = name + "_tmp"
cmd.load_model(model, tmpname, discrete=discrete, zoom=1)
modR = cmd.get_pdbstr(tmpname)
cmd.read_pdbstr(modR, name)
cmd.delete(tmpname)
return
if template:
model.bond = template.bond
else:
add_bonds(model)
cmd.load_model(model, name, state=state, discrete=discrete)
def resiCBpick(seletedChain=False):
'''处理表位残基序列，获取其中的CB原子信息,该函数依赖 resiPick()'''
cblist = []
i = resipick(seletedChain)
cb = "cb_left"
test = "test"
cmd.read_pdbstr(i, test)
cmd.select(cb, "name cb " + " in " +
test)
cblist = cmd.get_pdbstr('cb')
return cblist
def _gpssLoadPdb(pdbCode,reinitialize):
pdbCode = pdbCode.lower()
GPSSpdbCode = 'GPSS_' + pdbCode
_gpssVersionCheck('0.3');
if cmd.get_names().count(GPSSpdbCode) < 1:
if reinitialize==1:
cmd.do('reinitialize')
pdbFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=pdbFile').read()
if pdbFile:
pdbFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=pdbFile')
cmd.read_pdbstr(pdbFile.read(),GPSSpdbCode)
# Make structure pretty
# David Borhani, 14-JAN-2009
# Changed to color by chain, show lines only, keep user's bg color.
#cmd.do('set bg_rgb=[1,1,1]')
#cmd.do('hide everything')
cmd.hide('everything', GPSSpdbCode)
#cmd.do('dss')
cmd.dss(GPSSpdbCode)
#util.cbc(selection='(GPSS-' + pdbCode + ')',first_color=7,quiet=1,legacy=1,_self=cmd)
#sel_string = '("' + GPSSpdbCode + '")'
#cmd.do('util.cbc(selection=' + sel_string + ',first_color=9,quiet=1,legacy=1)')
cmd.do('util.cbc(selection=("' + GPSSpdbCode + '"),first_color=9,quiet=1,legacy=1)')
#cmd.do('show lines, ' + GPSSpdbCode)
cmd.show('lines', GPSSpdbCode)
#cmd.do('show cartoon, ' + GPSSpdbCode)
#cmd.do('color gray')
return True
else:
tkMessageBox.showerror('GPSS ',
pdbCode + ' was not found on the GPSS server.')
#cmd.do('zoom GPSS-'+pdbCode)
cmd.zoom(GPSSpdbCode, animate=0)
else:
return True
def resiCApick(seletedChain=False):
calist = []
i = resipick(seletedChain)
ca = "ca_left"
test = "test"
cmd.read_pdbstr(i, test)
cmd.select(ca, "name ca " + " in " + test)
calist = cmd.get_pdbstr('ca')
cmd.delete(test)
cmd.delete(ca)
return calist
def resiCApick(seletedChain=False):
'''处理表位残基序列，获取其中的CA原子信息,该函数依赖 resiPick()'''
calist = []
i = resipick(seletedChain)
ca = "ca_left"
test = "test"
cmd.read_pdbstr(i, test)
cmd.select(ca, "name ca " + " in " +
test)
calist = cmd.get_pdbstr('ca')
#resiPick的结果包含了全序列和残基序列，需要将位于后部的残基序列单独提取
return calist
def testSaveANISO(self):
cmd.read_pdbstr(v_pdbstr_anisou, 'm1')
v = cmd.get_pdbstr()
self.assertEqual(v, v_pdbstr_anisou, 'ANISOU records missing:\n' + v)
cmd.rotate('y', 30, object='m1')
cmd.translate([20, 0, 0], object='m1')
cmd.rotate('z', 20, object='m1')
v = cmd.get_pdbstr()
self.assertEqual(v, v_pdbstr_rotated, 'ANISOU not rotated in PDB string' + v)
v = cmd.get_model('m1').atom[0].u_aniso
self.assertArrayEqual(v, [0.183853, 0.378995, 0.309052, -0.103350, 0.125751, 0.050349],
1e-5, 'ANISOU not rotated in chempy model')
def gpssDna(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get sites
dna = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=dnaSurface').read()
if dna:
objectId = 'DNA-'+pdbCode;
cmd.read_pdbstr(dna,objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show surface,' + objectId)
cmd.do('set transparency=0.2,'+ objectId)
cmd.do('zoom GPSS-'+pdbCode)
def gpssDna(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get sites
dna = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=dnaSurface"
).read()
if dna:
objectId = "DNA-" + pdbCode
cmd.read_pdbstr(dna, objectId)
cmd.do("hide everything," + objectId)
cmd.do("show surface," + objectId)
cmd.do("set transparency=0.2," + objectId)
cmd.do("zoom GPSS-" + pdbCode)
def gpssSitesCsa(pdbCode, reinitialize):
if _gpssLoadPdb(pdbCode, reinitialize):
# Get sites
sites = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=sitesCsa"
).read()
if sites:
objectId = "SITES-CSA-" + pdbCode
cmd.read_pdbstr(sites, objectId)
cmd.do("hide everything," + objectId)
cmd.do("show spheres," + objectId)
cmd.do("color yellow," + objectId)
cmd.do("zoom GPSS-" + pdbCode)
def gpssSitesCsa(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get sites
sites = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=sitesCsa').read()
if sites:
objectId = 'SITES-CSA-'+pdbCode;
cmd.read_pdbstr(sites,objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show spheres,' + objectId)
cmd.do('color yellow,' + objectId)
cmd.do('zoom GPSS-'+pdbCode)
def minimize(selection='tmp', forcefield='MMFF94', method='steepest descent', nsteps= 2000, conv=1E-6, cutoff=False, cut_vdw=6.0, cut_elec=8.0, rigid_geometry=True):
"""
Write Me!
"""
pdb_string = cmd.get_pdbstr(selection)
name = cmd.get_legal_name(selection)
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('pdb', 'pdb')
mol = ob.OBMol()
obconversion.ReadString(mol, pdb_string)
if rigid_geometry:
constraints = ob.OBFFConstraints()
for angle in ob.OBMolAngleIter(mol):
b, a, c = [mol.GetAtom(x+1) for x in angle]
value = mol.GetAngle(a, b, c)
b, a, c = [x+1 for x in angle]
constraints.AddAngleConstraint(a, b, c, value)
for i in ob.OBMolBondIter(mol):
a, b = (i.GetBeginAtomIdx(), i.GetEndAtomIdx())
value = i.GetLength()
constraints.AddDistanceConstraint(a, b, value)
ff = ob.OBForceField.FindForceField(forcefield)
ff.Setup(mol, constraints)
ff.SetConstraints(constraints)
else:
ff = ob.OBForceField.FindForceField(forcefield)
ff.Setup(mol)
if cutoff:
ff.EnableCutOff(True)
ff.SetVDWCutOff(cut_vdw)
ff.SetElectrostaticCutOff(cut_elec)
if method == 'conjugate gradients':
ff.ConjugateGradients(nsteps, conv)
else:
ff.SteepestDescent(nsteps, conv)
ff.GetCoordinates(mol)
nrg = ff.Energy()
pdb_string = obconversion.WriteString(mol)
cmd.delete(name)
if name == 'all':
name = 'all_'
cmd.delete(selection)
cmd.read_pdbstr(pdb_string, selection)
return nrg
def test(self):
cmd.read_pdbstr(v_pdbstr_anisou, 'm1')
with testing.mktemp('.mae') as maefilename:
cmd.save(maefilename, 'm1')
cmd.delete('*')
cmd.load(maefilename, 'm1')
self.assertEqual(cmd.get_pdbstr('m1'), v_pdbstr_anisou)
cmd.read_pdbstr(v_pdbstr_rotated, 'm2')
cmd.align('m1', 'm2')
with testing.mktemp('.mae') as maefilename:
cmd.save(maefilename, 'm1')
cmd.delete('*')
cmd.load(maefilename, 'm1')
# Attention: Not sure if rotation is numerically stable across
# platforms. Fuzzy comparison might be needed.
self.assertEqual(cmd.get_pdbstr('m1'), v_pdbstr_rotated)
def gpssPeptide(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get ligand surfaces
peptideInfo = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=peptideInfo')
# Get pocket atoms
for peptideSurface in peptideInfo:
peptideSurfaceFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+ pdbCode +
'&surfaceId=' + peptideSurface +
'&mode=peptideSurface')
peptideId = peptideSurface.split('.')
objectId = 'Peptide-' + peptideId[1]
cmd.read_pdbstr(peptideSurfaceFile.read(),objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show surface,' + objectId)
cmd.do('set transparency=0.2,'+ objectId)
cmd.do('zoom GPSS-'+pdbCode)
def gzload(id):
# if filename doesn't exist, try it as a PDBID
if not os.path.exists(id):
filename = pdbutils.pdbfilename(id)
label = id
else:
filename = id
label = os.path.basename(filename)
# Abort if file doesn't exist
if not filename or not os.path.exists(filename):
print "Error: id=%(id)s Can not find %(filename)s" % vars()
return
# read the data
fh = gzip.open(filename)
data = fh.read()
fh.close()
# load it into pymol
cmd.read_pdbstr(data,label)
def reduce_object(obj, flip=1):
"""Add hydrogens to a copy of a loaded PyMOL object with Reduce.
TODO: more doc here
"""
# Run reduce with specified flips
pdbstr = cmd.get_pdbstr(obj)
reduced_pdbstr = generate_reduce_output(pdbstr, flip_type=flip)
# Fail gracefully if no output is generated.
if not reduced_pdbstr:
msg = "Failed to generate Reduce output for {}.".format(obj)
logger.error(msg)
return
withflips = " with flips" if flip else ""
logger.info("Generated Reduce output{} for '{}'.".format(withflips, obj))
# Process the output string for flips
flips_list = process_reduce_output(reduced_pdbstr)
logger.info("Processed Reduce output to extract list of flips.")
# Store flips list and raw reduced_pdbstr in MPObject
o = get_or_create_object(obj)
o.flips = flips_list
o.reduce_output = reduced_pdbstr
# Store current group_auto_mode setting
gam = cmd.get('group_auto_mode')
cmd.set('group_auto_mode', 2)
# Load the output PDB into a copy of the original and disable the original.
name = o.pdb['reduce']
cmd.create(name, obj) # duplicate original to preserve representation
cmd.read_pdbstr(reduced_pdbstr, name, state=1)
cmd.disable(obj)
# Restore original group_auto_mode
cmd.set('group_auto_mode', gam)
def test(self, matrix_mode):
cmd.viewport(100, 100)
cmd.set('matrix_mode', matrix_mode)
cmd.set('ambient', 1.0)
cmd.read_pdbstr(v_pdbstr_anisou, 'm1', zoom=0)
cmd.read_pdbstr(v_pdbstr_rotated, 'm2', zoom=0)
self._rep()
cmd.set_view(views[0])
ref = self.get_imagearray()
self.assertImageHasColor('yellow')
cmd.align('m1', 'm2')
cmd.set_view(views[1])
self.assertImageEqual(ref,
count=100,
delta=1,
msg='ANISOU not aligned on display')
pdbstr = cmd.get_pdbstr('m1')
cmd.delete('*')
cmd.read_pdbstr(pdbstr, 'm1', zoom=0)
self._rep()
self.assertImageEqual(ref, count=100, msg='ANISOU not aligned in PDB')
def reduce_object(obj, flip=1):
"""Add hydrogens to a copy of a loaded PyMOL object with Reduce.
TODO: more doc here
"""
# Run reduce with specified flips
pdbstr = cmd.get_pdbstr(obj)
reduced_pdbstr = generate_reduce_output(pdbstr, flip_type=flip)
# Fail gracefully if no output is generated.
if not reduced_pdbstr:
msg = "Failed to generate Reduce output for {}.".format(obj)
logger.error(msg)
return
withflips = " with flips" if flip else ""
logger.info("Generated Reduce output{} for '{}'.".format(withflips, obj))
# Process the output string for flips
flips_list = process_reduce_output(reduced_pdbstr)
logger.info("Processed Reduce output to extract list of flips.")
# Store flips list and raw reduced_pdbstr in MPObject
o = get_or_create_object(obj)
o.flips = flips_list
o.reduce_output = reduced_pdbstr
# Store current group_auto_mode setting
gam = cmd.get('group_auto_mode')
cmd.set('group_auto_mode', 2)
# Load the output PDB into a copy of the original and disable the original.
name = o.pdb['reduce']
cmd.create(name, obj) # duplicate original to preserve representation
cmd.read_pdbstr(reduced_pdbstr, name, state=1)
cmd.disable(obj)
# Restore original group_auto_mode
cmd.set('group_auto_mode', gam)
def _gpssLoadPdb(pdbCode, reinitialize):
pdbCode = pdbCode.lower()
_gpssVersionCheck("0.3")
if cmd.get_names().count("GPSS-" + pdbCode) < 1:
if reinitialize == 1:
cmd.do("reinitialize")
pdbFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=pdbFile"
).read()
if pdbFile:
pdbFile = urllib2.urlopen(
"http://gpss.mcsg.anl.gov/webservices/" + "gpssServerPymol.php?pdbId=" + pdbCode + "&mode=pdbFile"
)
cmd.read_pdbstr(pdbFile.read(), "GPSS-" + pdbCode)
# Make structure pretty
cmd.do("set bg_rgb=[1,1,1]")
cmd.do("hide everything")
cmd.do("dss")
cmd.do("show cartoon, GPSS-" + pdbCode)
cmd.do("color gray")
return True
else:
tkMessageBox.showerror(
"GPSS ", pdbCode + " was not found on the GPSS server."
)
cmd.do("zoom GPSS-" + pdbCode)
else:
return True
def _gpssLoadPdb(pdbCode,reinitialize):
pdbCode = pdbCode.lower()
_gpssVersionCheck('0.1');
if cmd.get_names().count('GPSS-'+pdbCode) < 1:
if reinitialize==1:
cmd.do('reinitialize')
pdbFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=pdbFile').read()
if pdbFile:
pdbFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=pdbFile')
cmd.read_pdbstr(pdbFile.read(),'GPSS-'+pdbCode)
# Make structure pretty
cmd.do('set bg_rgb=[1,1,1]')
cmd.do('hide everything')
cmd.do('dss')
cmd.do('show cartoon, GPSS-' + pdbCode)
cmd.do('color gray')
return True
else:
tkMessageBox.showerror('GPSS ',
pdbCode + ' was not found on the GPSS server.')
cmd.do('zoom GPSS-'+pdbCode)
else:
return True
def gpssCastp(pdbCode,reinitialize):
if _gpssLoadPdb(pdbCode,reinitialize):
# Get pocket count
castpInfo = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&mode=castpInfo')
castpLength = int(castpInfo.readlines()[-1][13:16])
# Get pocket atoms
while castpLength > 0:
castpSurfaceFile = urllib2.urlopen('http://gpss.mcsg.anl.gov/webservices/'+
'gpssServerPymol.php?pdbId='+
pdbCode + '&surfaceId='+str(castpLength)+
'&mode=castpSurface')
objectId = 'CASTp-'+str(castpLength)
cmd.read_pdbstr(castpSurfaceFile.read(),objectId)
cmd.do('hide everything,' + objectId)
cmd.do('show surface,' + objectId)
cmd.do('set transparency=0.2,'+ objectId)
castpLength-=1
cmd.do('zoom GPSS-'+pdbCode)
def displayPdb(self, tstD, tstName, group=False, pointGroupCacheTemp=None):
'''creates an actual pdb object of the protein or just the part near the
surface/group of interest'''
if not group: # just display the whole thing
pdbText = "\n".join(tstD.dict['PDB_RECORD'])
cmd.read_pdbstr(pdbText, tstName + "." + str(self.drawCount) + ".pdb")
else:
pointNearbyAtomList = tstD.dict['POINT_NEARBY_ATOM']
import sets
atomSet = sets.Set() # old since pymol is based on 2.3 forever
for pointNearbyAtom in pointNearbyAtomList:
try:
point = pointNearbyAtom[0]
groups = pointGroupCacheTemp[point]
if group in groups:
atomSet.update(pointNearbyAtom[1:])
except TypeError:
pass # means a point had no nearby atoms, which can happen given dist
#print point, groups, atomSet
pdbStr = ""
for atomLine in atomSet:
pdbStr += tstD.dict['PDB_RECORD'][int(atomLine)-1] + "\n"
cmd.read_pdbstr(
pdbStr, tstName + "." + str(self.drawCount) + ".pdb." + str(group))
def rpcLoadPDB(data, objName, colorScheme='', replace=1):
""" loads a molecule from a pdb string
Arguments:
data: the mol block
objName: name of the object to create
colorScheme: (OPTIONAL) name of the color scheme to use
for the molecule (should be either 'std' or one of the
color schemes defined in pymol.utils)
replace: (OPTIONAL) if an object with the same name already
exists, delete it before adding this one
"""
from pymol import util
if replace:
cmd.delete(objName)
res = cmd.read_pdbstr(data, objName)
colorObj(objName, colorScheme)
if res is not None:
return res
else:
return ''
def rpcLoadPDB(data, objName, colorScheme='', replace=1):
""" loads a molecule from a pdb string
Arguments:
data: the mol block
objName: name of the object to create
colorScheme: (OPTIONAL) name of the color scheme to use
for the molecule (should be either 'std' or one of the
color schemes defined in pymol.utils)
replace: (OPTIONAL) if an object with the same name already
exists, delete it before adding this one
"""
from pymol import util
if replace:
cmd.delete(objName)
res = cmd.read_pdbstr(data, objName)
colorObj(objName, colorScheme)
if res is not None:
return res
else:
return ''
def test(self, matrix_mode):
cmd.viewport(100,100)
cmd.set('matrix_mode', matrix_mode)
cmd.set('ambient', 1.0)
cmd.read_pdbstr(v_pdbstr_anisou, 'm1', zoom=0)
cmd.read_pdbstr(v_pdbstr_rotated, 'm2', zoom=0)
self._rep()
cmd.set_view(views[0])
ref = self.get_imagearray()
self.assertImageHasColor('yellow')
cmd.align('m1', 'm2')
cmd.set_view(views[1])
self.assertImageEqual(ref, count=100, delta=1, msg='ANISOU not aligned on display')
pdbstr = cmd.get_pdbstr('m1')
cmd.delete('*')
cmd.read_pdbstr(pdbstr, 'm1', zoom=0)
self._rep()
self.assertImageEqual(ref, count=100, msg='ANISOU not aligned in PDB')
def load_dock4(self, cluster, object, mode):
"""
Load a SwissDock's cluster of ligands from string list in PDB >Dock4 format
Parameters
----------
cluster : list of str
list of string lines from cluster of structures in PDB format
object : str
name to be include the new object
mode : {0, 1, 2}
0 - all molecules to same object
1 - only first molecule of each cluster to object (ClusterRank==0)
2 - all molecules to multiple objects according to clusters
"""
cluster = [line.strip() for line in cluster if line.strip()]
self.__init__()
# read all structures remarks/coordinates
i = 0
pdb = []
remark_re = re.compile(r'(?i)^REMARK\b\s+(\w+)\s*:\s*(-?\d+\.?\d*)')
while i < len(cluster):
pdb_keyword = cluster[i].split()[0].upper()
# process docking information in REMARKs
if pdb_keyword == 'REMARK':
remarks = dict()
# loop over REMARKs until no compliant found
while remark_re.match(cluster[i]):
match = remark_re.match(cluster[i])
key = str(match.group(1))
value = float(match.group(2)) if key not in (
'Cluster', 'ClusterRank') else int(match.group(2))
remarks[key] = value
i += 1
# take whole molecule PDB coordinate lines
elif pdb_keyword in ('ATOM', 'HETATM'):
i_0 = i
while cluster[i].split()[0].upper() in ('ATOM', 'HETATM'):
i += 1
pdb_molecule = "\n".join(cluster[i_0:i]) + '\nENDMDL\n'
# append to main attribute at the end of molecule
pdb.append(pdb_molecule)
self.entries.append({
'remarks': remarks,
'internal': deepcopy(self.internal_empty)
})
else:
i += 1
# equalize remarks for all entries
for n, i in enumerate(self.entries):
for j in self.remarks:
i['remarks'].setdefault(j, None)
# set internals
i['internal']['object'] = object
i['internal']['state'] = n + 1
# check if defined Cluster and ClusterRank
if mode in (
'1', '2'
) and not 'Cluster' in self.remarks or not 'ClusterRank' in self.remarks:
print(
" PyViewDock: Failed splitting while loading. Missing 'Cluster' or 'ClusterRank'."
)
return
# load only first of every cluster (ClusterRank == 0)
if mode == '1':
entries_tmp, pdb_tmp = [], []
n_state = 0
for e, p in zip(self.entries, pdb):
if e['remarks']['ClusterRank'] == 0:
pdb_tmp.append(p)
entries_tmp.append(e)
n_state += 1
entries_tmp[-1]['internal']['state'] = n_state
self.entries, pdb = deepcopy(entries_tmp), deepcopy(pdb_tmp)
cmd.read_pdbstr("".join(pdb), object)
# load all in different objects by Cluster
elif mode == '2':
pdb_tmp = dict()
for e, p in zip(self.entries, pdb):
object_new = object + '-' + str(e['remarks']['Cluster'])
pdb_tmp.setdefault(object_new, []).append(p)
e['internal']['object'] = object_new
e['internal']['state'] = len(pdb_tmp[object_new]) + 1
for object_new, p in pdb_tmp.items():
cmd.read_pdbstr("".join(p), object_new)
# load all in one object
else:
cmd.read_pdbstr("".join(pdb), object)
def load_gro(filename, object='', state=-1, quiet=1, zoom=-1):
'''
DESCRIPTION
Load a gro file (molecular structure in Gromos87 format).
http://manual.gromacs.org/online/gro.html
This command can handle larger ID and resi values than PDB files and thus
is better (but slower) than converting a gro file to PDB format using
editconf.
Based on a script from Tsjerk Wassenaar, posted on pymol-users mailing list.
http://www.mail-archive.com/[email protected]/msg09394.html
'''
from . import pymol_version
if pymol_version >= 1.74:
print(
' Notice: native gro file support available in PyMOL since 1.7.4')
if object == '':
object = os.path.basename(filename).rsplit('.', 1)[0]
_pdbAtomLine = 'ATOM %5i %-3s %3s%2s%4i %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s '
_pdbBoxLine = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1'
def pdbAtom(line):
''' Parses a gro atom line and returns a pdb ATOM line '''
resi = int(line[:5])
resn = line[5:10].strip()
name = line[10:15].strip()
ID = int(line[15:20])
x, y, z = 10 * float(line[20:28]), 10 * float(line[28:36]), 10 * float(
line[36:44])
segi = '%02d%02d' % (ID / 100000, resi / 10000)
ID, resi = ID % 100000, resi % 10000
return _pdbAtomLine % (ID, name[:3], resn[:3], 'A', resi, x, y, z, 1,
0, segi, name[0])
def pdbBox(line):
''' Parses a gro box line and returns a pdb CRYST1 line '''
from math import degrees
from chempy.cpv import length, get_angle
v = [10 * float(i)
for i in line.split()] + 6 * [0] # Padding for rectangular boxes
v1, v2, v3 = (v[0], v[3], v[4]), (v[5], v[1], v[6]), (v[7], v[8], v[2])
a = length(v1)
b = length(v2)
c = length(v3)
alpha = degrees(get_angle(v2, v3))
beta = degrees(get_angle(v1, v3))
gamma = degrees(get_angle(v1, v2))
return _pdbBoxLine % (a, b, c, alpha, beta, gamma)
pdb = ['']
stream = open(filename)
for model in range(1, 9999):
title = stream.readline()
natoms = stream.readline().strip()
if natoms == '':
break
natoms = int(natoms)
pdb.append('MODEL %8d' % model)
for i in range(natoms):
pdb.append(pdbAtom(stream.readline()))
pdb.append('ENDMDL')
boxline = stream.readline()
if model == 1:
pdb[0] = pdbBox(boxline)
stream.close()
pdb.extend(['END', ''])
cmd.read_pdbstr('\n'.join(pdb),
object,
int(state),
quiet=int(quiet),
zoom=int(zoom))
cmd.alter(
object,
'(ID,resi,segi) = (ID+100000*int(segi[:2]),resv+10000*int(segi[2:]),"")'
)
try:
# Importing the PyMOL module will create the window.
import pymol #@UnresolvedImport
from pymol import cmd #@UnresolvedImport
except:
print "Failed to import pymol; python will stack dump next:"
# Tell PyMOL we don't want any GUI features.
__main__.pymol_argv = [ 'pymol', '-Gi' ]
# Call the function below before using any PyMOL modules.
pymol.finish_launching()
cmd.stereo('walleye')
cmd.set('stereo_shift', 0.23)
cmd.set('stereo_angle', 1.0)
cmd.spectrum()
try:
pdbCode = '1brv'
pdbFile = urllib2.urlopen('file:///Users/jd/workspace35/cing/data/Tests/pdb/'+
pdbCode + '/pdb' +
pdbCode + '.ent')
cmd.read_pdbstr(pdbFile.read(), pdbCode)
except:
print "Unexpected error:", sys.exc_info()[0]
time.sleep(5)
#cmd.quit()
def load_pose_into_object(pose_name):
'''Load the pose into the object.'''
pdb_os = rosetta.std.ostringstream()
poses[pose_name].dump_pdb(pdb_os)
cmd.read_pdbstr(pdb_os.str(), pose_name)
cmd.color('green', '{0} and (n. c*)'.format(pose_name))
COLOR, 0.2, 1.0, 0.2,
SPHERE, 1.0+math.cos(a/10.0), 1.0+math.sin(a/20.0), 1.0+math.cos(a/10.0), 0.2+math.cos(a/5.0)/10.0,
COLOR, 1.0, 0.2, 0.2,
SPHERE, 2.0-math.cos(a/10.0), 1.0+math.sin(0.5+a/10.0), 1.0+math.cos(a/10.0), 0.2+math.cos(a/5.0)/10.0,
]
obj = axes + balls
cmd.load_cgo(obj,'cgo01',c)
c = c + 1
# counter label
pdb_list = [
"HETATM%5d C UNK 1 %8.3f%8.3f%8.3f 1.00 10.00\n"%(c,2.0,0,2.0),
]
cmd.read_pdbstr(string.join(pdb_list,''),'lab1',c,discrete=1)
cmd.label("(lab1 and id %d)"%c,"'frame %d %6.3f'"%(c,math.sin(a/10.0)))
cmd.hide("nonbonded","lab1")
# axes labels
pdb_list = [
"HETATM 1 X UNK 1 %8.3f%8.3f%8.3f 1.00 10.00\n"%(3.2,0,0),
"HETATM 2 Y UNK 2 %8.3f%8.3f%8.3f 1.00 10.00\n"%(0,3.2,0),
"HETATM 3 Z UNK 3 %8.3f%8.3f%8.3f 1.00 10.00\n"%(0,0,3.2),]
cmd.read_pdbstr(string.join(pdb_list,''),'lab2')
cmd.hide('(lab2)')
cmd.label('lab2','name')
def __init__(self=None):
cmd.extend('webload', webload)
def webload(pdbid):
import sys, os
import StringIO
import gzip
import urllib
label = pdbid
url = _PDB_URL % vars()
try:
datafh = StringIO.StringIO(urllib.urlopen(url).read())
data = gzip.GzipFile(fileobj=datafh).read()
except Exception, e:
print "Error: pdbid=%(pdbid)s" % vars(), e
return
if not data:
print "Invalid PDB id %(pdbid)s" % vars()
return
# load it into pymol
cmd.read_pdbstr(data, label)
if __name__ == 'pymol':
__init__()
def push2pymol(self, name, state=1):
cmd.read_pdbstr(self.pdbstr(), name, state)
def quench(sel="sele", rounds=10):
cmd.read_pdbstr(PythonMSL.quickQuench(cmd.get_pdbstr(sel), rounds),
"quench")
def testReadPdbstr(self):
cmd.read_pdbstr(pdbstr, 'm1')
self.assertEqual(7, cmd.count_atoms())
cmd.read_pdbstr(pdbstr, 'm1')
self.assertEqual(2, cmd.count_states())