def __collectFrames( self, pdbs, castAll=0 ):
"""
Read coordinates from list of pdb files.
:param pdbs: list of file names
:type pdbs: [str]
:param castAll: analyze atom content of each frame for casting
(default: 0)
:type castAll: 0|1
:return: frames x (N x 3) Numpy array (of float)
:rtype: array
"""
frameList = []
i = 0
atomCast = None
if self.verbose: T.errWrite('reading %i pdbs...' % len(pdbs) )
refNames = self.ref.atomNames() ## cache for atom checking
for f in pdbs:
## Load
m = PDBModel(f)
## compare atom order & content of first frame to reference pdb
if castAll or i==0:
atomCast, castRef = m.compareAtoms( self.ref )
if castRef != list(range( len( self.ref ))):
## we can take away atoms from each frame but not from ref
raise TrajError("Reference PDB doesn't match %s."
%m.fileName)
if N0.all( atomCast == list(range( len( m ))) ):
atomCast = None ## no casting necessary
else:
if self.verbose: T.errWrite(' casting ')
## assert that frame fits reference
if atomCast:
m = m.take( atomCast )
## additional check on each 100st frame
if i%100 == 0 and m.atomNames() != refNames:
raise TrajError("%s doesn't match reference pdb."%m.fileName )
frameList.append( m.xyz )
i += 1
if i%10 == 0 and self.verbose:
T.errWrite('#')
if self.verbose: T.errWrite( 'done\n' )
## convert to 3-D Numpy Array
return N0.array(frameList).astype(N0.Float32)
class AmberParmBuilder:
"""
AmberParmBuilder
================
Create Amber topology and coordinate file from PDB.
- parmMirror():
...builds a fake parm that exactly mirrors a given PDB file.
This parm can be used for ptraj but not for simulations.
Currently, parmMirror only accepts amber-formatted PDBs as
input. It should be possible to create topologies that have
the same content and order of atoms as an xplor PDB but
some atoms will have different names.
- parmSolvated():
...builds a solvated system for PME simulations (incl. closing
of S-S bonds, capping of chain breaks). parmSolvated accepts
both xplor and amber-formatted PDBs as input.
Requires the amber programs C{tleap} and C{ambpdb}.
Requires leap template files in C{biskit/Biskit/data/amber/leap/}.
Note on forcefields:
The default forcefield used is specified in exe_tleap and currently
is ff10. This translates to loading amber11/dat/leap/cmd/leaprc.ff10
at the beginning of the leap run. As of 2011, ff10 is the recommended
default forcefield for proteins and nucleic acids.
Comment from Jason Swails on the Amber mailing list:
"
Try using ff99SB (which is the protein force field part of ff10, which is
the version I would actually suggest using). Despite its label, it is
actually a 2006 update of the ff99 force field which performs at least as
well (if not better) as ff03."
Unfortunately, ions are only "half" paramterized in ff10. Additional
parameters need to be loaded from a frmod file, typically
frcmod.ionsjc_tip3p. There are additional versions of this file optimized
for other water models than TIP3. frcmod.ionsjc_tip3p is set as the
default frmod file to include by parmSolvated and parmMirror. Please
include it if you provide your own list of frmod files.
.. note::
The design of AmberParmBuilder is less than elegant. It
would make more sense to split it into two classes that
are both derrived from Executor.
"""
## script to create a parm that exactly mirrors a given PDB
script_mirror_pdb = """
logFile %(f_out)s
source %(leaprc)s
%(fmod)s
%(fprep)s
p = loadPdb %(in_pdb)s
%(delete_atoms)s
saveAmberParm p %(out_parm)s %(out_crd)s
quit
"""
## tleap command to close a single S-S bond
ss_bond = "bond p.%i.SG p.%i.SG\n"
## leap script for solvated topology
F_leap_in = t.dataRoot() + '/amber/leap/solvate_box.leap'
## PDB with ACE capping residue
F_ace_cap = t.dataRoot() + '/amber/leap/ace_cap.pdb'
## PDB with NME capping residue
F_nme_cap = t.dataRoot() + '/amber/leap/nme_cap.pdb'
def __init__( self, model,
leap_template=F_leap_in,
leaprc=None,
leap_out=None, leap_in=None,
leap_pdb=None,
log=None,
debug=0,
verbose=0,
**kw ):
"""
:param model: model
:type model: PDBModel or str
:param leap_template: path to template file for leap input
:type leap_template: str
:param leaprc: forcefield parameter file or code (e.g. ff99)
:type leaprc: str
:param leap_out: target file for leap.log (default: discard)
:type leap_out: str
:param leap_in: target file for leap.in script (default: discard)
:type leap_in: str
:param kw: kw=value pairs for additional options in the leap_template
:type kw: key=value
"""
self.m = PDBModel( model )
self.leap_template = leap_template
self.leaprc = leaprc
self.leap_pdb = leap_pdb or tempfile.mktemp( '_leap_pdb' )
self.keep_leap_pdb = leap_pdb is not None
self.leap_in = leap_in
self.leap_out= leap_out
self.log = log or StdLog()
self.output = None # last output of leap
self.debug = debug
self.verbose = verbose
self.__dict__.update( kw )
def __runLeap( self, in_script, in_pdb, norun=0, **kw ):
"""
Create script file and run Leap.
:param in_script: content of ptraj script with place holders
:type in_script: str
:param in_pdb: PDB file to load into tleap
:type in_pdb: str
:param norun: 1 - only create leap scrip (default: 0)
:type norun: 1|0
:param kw: key=value pairs for filling place holders in script
:type kw: key=value
:raise AmberError: if missing option for leap input file or
if could not create leap input file
"""
x = AmberLeap( in_script,
in_pdb=in_pdb,
log=self.log, verbose=self.verbose, debug=self.debug,
catch_out=True,
f_in=self.leap_in,
f_out=self.leap_out,
**kw )
if norun:
x.generateInp()
else:
x.run()
self.output = x.output
## ## create leap script
## try:
## ## use own fields and given kw as parameters for leap script
## d = copy.copy( self.__dict__ )
## d.update( kw )
## in_script = in_script % d
## f = open( self.leap_in, 'w')
## f.write( in_script )
## f.close()
## if self.verbose:
## self.log.add('leap-script: ')
## self.log.add( in_script )
## except IOError:
## raise AmberError('Could not create leap input file')
## except:
## raise AmberError('missing option for leap input file\n'+\
## 'available: %s' % (str( d.keys() ) ))
## ## run tleap
## args = '-f %s' % self.leap_in
## if not norun:
## self.exe = Executor('tleap', args, log=self.log,verbose=1,
## catch_out=0)
## self.output, self.error, self.status = self.exe.run()
## if not os.path.exists( kw['out_parm'] ):
## raise AmberError, "tleap failed"
## ## clean up
## if not self.keep_leap_in and not self.debug:
## t.tryRemove( self.leap_in )
## if not self.keep_leap_out and not self.debug:
## t.tryRemove( self.leap_out)
def parm2pdb( self, f_parm, f_crd, f_out, aatm=0 ):
"""
Use ambpdb to build PDB from parm and crd.
:param f_parm: existing parm file
:type f_parm: str
:param f_crd: existing crd file
:type f_crd: str
:param f_out: target file name for PDB
:type f_out: str
:return: f_out, target file name for PDB
:rtype: str
:raise AmberError: if ambpdb fail
"""
## cmd = '%s -p %s -aatm < %s > %s' % \
args = '-p %s %s' % (f_parm, '-aatm'*aatm )
x = Executor('ambpdb', args, f_in=f_crd, f_out=f_out,
log=self.log, verbose=self.verbose, catch_err=1)
output,error,status = x.run()
if not os.path.exists( f_out ):
raise AmberError('ambpdb failed.')
return f_out
def __ssBonds( self, model, cutoff=4. ):
"""
Identify disulfide bonds.
:param model: model
:type model: PDBModel
:param cutoff: distance cutoff for S-S distance (default: 4.0)
:type cutoff: float
:return: list with numbers of residue pairs forming S-S
:rtype: [(int, int)]
"""
m = model.compress( model.mask( ['SG'] ) )
if len( m ) < 2:
return []
pw = MU.pairwiseDistances( m.xyz, m.xyz )
pw = N0.less( pw, cutoff )
r = []
for i in range( len( pw ) ):
for j in range( i+1, len(pw) ):
if pw[i,j]:
r += [ (m.atoms['residue_number'][i],
m.atoms['residue_number'][j]) ]
return r
def __cys2cyx( self, model, ss_residues ):
"""
Rename all S-S bonded CYS into CYX.
:param model: model
:type model: PDBModel
:param ss_residues: original residue numbers of S-S pairs
:type ss_residues: [(int, int)]
"""
ss = []
for a,b in ss_residues:
ss += [a,b]
for a in model:
if a['residue_number'] in ss:
a['residue_name'] = 'CYX'
def capACE( self, model, chain ):
"""
Cap N-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose)
return cleaner.capACE( model, chain, breaks=True )
def capNME( self, model, chain ):
"""
Cap C-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose )
return cleaner.capNME( model, chain, breaks=True)
def centerModel( self, model ):
"""
Geometric centar of model.
:param model: model
:type model: PDBMode
"""
center = N0.average( model.getXyz() )
model.setXyz( model.xyz - center )
def leapModel( self, hetatm=0, center=True ):
"""
Get a clean PDBModel for input into leap.
:param hetatm: keep HETATM records (default: 0)
:type hetatm: 1|0
:return: model
:rtype: PDBMod
"""
m = self.m.clone()
m.xplor2amber()
cleaner = PDBCleaner( m, log=self.log, verbose=self.verbose )
m = cleaner.process( keep_hetatoms=hetatm, amber=1 )
m.renumberResidues( addChainId=1 )
if center:
self.centerModel( m )
return m
def __fLines( self, template, values ):
if not type( values ) is list:
values = [ values ]
return ''.join( [ template % v for v in values ] )
def parmSolvated( self, f_out, f_out_crd=None, f_out_pdb=None,
hetatm=0, norun=0,
cap=0, capN=[], capC=[],
fmod=['frcmod.ionsjc_tip3p'], fprep=[],
box=10.0, center=True, **kw ):
"""
:param f_out: target file for parm (topology)
:type f_out: str
:param f_out_crd: target file for crd (coordinates)
(default:|f_out_base|.crd)
:type f_out_crd: str
:param f_out_pdb: target file for pdb (default:|f_out_base|.pdb)
:type f_out_pdb: str
:param hetatm: keep hetero atoms (default: 0)
:type hetatm: 1|0
:param cap: put ACE and NME capping residue on chain breaks
(default: 0)
:type cap: 1|0
:param capN: indices of chains that should get ACE cap (default: [])
:type capN: [int]
:param capC: indices of chains that should get NME cap (default: [])
:type capC: [int]
:param box: minimal distance of solute from box edge (default: 10.0)
:type box: float
:param center: re-center coordinates (default: True)
:type center: bool
:param fmod: list of files with amber parameter modifications
to be loaded into leap with loadAmberParams
(default:['frcmod.ionsjc_tip3p'] ... mod file needed for
default Amber ff10 ions -- topology saving will fail if this
one is missing)
:type fmod: [str]
:param fprep: list of files with amber residue definitions
(to be loaded into leap with loadAmberPrep) (default: [])
:type fprep: [str]
:param kw: additional key=value pairs for leap input template
:type kw: key=value
:raise IOError:
"""
f_out = t.absfile( f_out )
f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
f_out_pdb = t.absfile( f_out_pdb ) or t.stripSuffix( f_out ) +\
'_leap.pdb'
## removed: (bugfix 3434136)
#fmod = [ t.absfile( f ) for f in t.toList( fmod ) ]
#fprep = [ t.absfile( f ) for f in t.toList( fprep ) ]
try:
if self.verbose: self.log.add( '\nCleaning PDB file for Amber:' )
m = self.leapModel( hetatm=hetatm, center=center )
if cap:
end_broken = m.atom2chainIndices( m.chainBreaks() )
capC = MU.union( capC, end_broken )
capN = MU.union( capN, N0.array( end_broken ) + 1 )
for i in capN:
if self.verbose:
self.log.add( 'Adding ACE cap to chain %i' % i )
m = self.capACE( m, i )
for i in capC:
if self.verbose:
self.log.add( 'Adding NME cap to chain %i' % i )
m = self.capNME( m, i )
m.renumberResidues( addChainId=1 ) ## again, to accomodate capping
template = open( self.leap_template ).read()
leap_mod = self.__fLines( 'm = loadAmberParams %s\n', fmod )
leap_prep= self.__fLines( 'loadAmberPrep %s\n', fprep )
ss = self.__ssBonds( m, cutoff=4. )
self.__cys2cyx( m, ss )
leap_ss = self.__fLines( self.ss_bond, ss )
if self.verbose:
self.log.add('Found %i disulfide bonds: %s' % (len(ss),str(ss)))
if self.verbose:
self.log.add( 'writing cleaned PDB to %s' % self.leap_pdb )
m.writePdb( self.leap_pdb, ter=3 )
self.__runLeap( template, in_pdb=self.leap_pdb,
out_parm=f_out, out_crd=f_out_crd,
ss_bonds=leap_ss, fmod=leap_mod,
fprep=leap_prep, norun=norun,
box=box, **kw )
if not norun:
parm_pdb = self.parm2pdb( f_out, f_out_crd, f_out_pdb )
if not self.keep_leap_pdb and not self.debug:
t.tryRemove( self.leap_pdb )
except IOError as why:
raise IOError(why)
def __deleteAtoms( self, m, i_atoms ):
"""
Delet atoms
:param m: model
:type m: PDBMode
:param i_atoms: atom index
:type i_atoms: [int]
:return: leap statements for deleting given atoms
:rtype: [str]
"""
cmd = 'remove p.%(res)i p.%(res)i.%(atom)i'
rM = m.resMap()
rI = m.resIndex()
s = []
for i in i_atoms:
res = m.atoms['residue_number'][i]
## substract atom index of first atom in of this residue
atm = i - rI[ rM[ i ] ] + 1
s += [ cmd % {'res':res, 'atom':atm} ]
return '\n'.join( s )
def __inverseIndices( self, model, i_atoms ):
"""
:param model: model
:type model: PDBMode
:param i_atoms: atom index
:type i_atoms: [int]
:return: remaining atom indices of m that are NOT in i_atoms
:rtype: [int]
"""
mask = N0.zeros( len( model ),N0.Int )
N0.put( mask, i_atoms, 1 )
return N0.nonzero( N0.logical_not( mask ) )
def parmMirror( self, f_out, f_out_crd=None, fmod=['frcmod.ionsjc_tip3p'],
fprep=[], **kw ):
"""
Create a parm7 file whose atom content (and order) exactly mirrors
the given PDBModel. This requires two leap runs. First we get a
temporary topology, then we identify all atoms added by leap and
build a final topology where these atoms are deleted.
This parm is hence NOT suited for simulations but can be used to parse
e.g. a trajectory or PDB into ptraj.
:param f_out: target parm file
:type f_out: str
:param f_out_crd: target crd file (default: f_out but ending .crd)
:type f_out_crd: str
:param fmod : list of amber Mod files (loaded with loadAmberParams)
:type fmod : [str]
:param fmod : list of amber Prep files (loaded with loadAmberPrep)
:type fmod : [str]
"""
f_out = t.absfile( f_out )
f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
## if there are hydrogens, recast them to standard amber names
aatm = 'HA' in self.m.atomNames() ## 'HB2' in self.m.atomNames()
## First leap round ##
m_ref = self.m.clone()
m_ref.xplor2amber( aatm=aatm, parm10=True )
tmp_in = tempfile.mktemp( 'leap_in0.pdb' )
m_ref.writePdb( tmp_in, ter=3 )
tmp_parm = tempfile.mktemp( '_parm0' )
tmp_crd = tempfile.mktemp( '_crd0' )
leap_mod = self.__fLines( 'm = loadAmberParams %s\n', fmod )
leap_prep= self.__fLines( 'loadAmberPrep %s\n', fprep )
self.__runLeap( self.script_mirror_pdb,
leaprc=self.leaprc, fmod=leap_mod, fprep=leap_prep,
in_pdb=tmp_in, out_parm=tmp_parm, out_crd=tmp_crd,
delete_atoms='' )
tmp_pdb = self.parm2pdb( tmp_parm, tmp_crd,
tempfile.mktemp( 'leap_out.pdb' ), aatm=aatm )
if not self.debug:
t.tryRemove( tmp_parm )
t.tryRemove( tmp_crd )
t.tryRemove( tmp_in )
## load model with missing atoms added by leap
m_leap = PDBModel( tmp_pdb )
## compare atom content
iLeap, iRef = m_leap.compareAtoms( m_ref )
## check that ref model doesn't need any change
if iRef != list(range( len( m_ref ))):
uLeap, uRef = m_leap.unequalAtoms( m_ref, iLeap, iRef )
atms = m_ref.reportAtoms( uRef, n=6 )
raise AmberError("Cannot create exact mirror of %s.\n" % tmp_in +\
"Leap has renamed/deleted original atoms in %s:\n"% tmp_pdb+\
atms)
## indices of atoms that were added by leap
delStr = self.__deleteAtoms( m_leap,
self.__inverseIndices( m_leap, iLeap ) )
## Second leap round ##
self.__runLeap( self.script_mirror_pdb, leaprc=self.leaprc,
in_pdb=tmp_pdb, fmod=leap_mod, fprep=leap_prep,
out_parm=f_out, out_crd=f_out_crd,
delete_atoms=delStr )
if not self.debug:
t.tryRemove( tmp_pdb )
class Test(BT.BiskitTest):
"""Test class """
def prepare(self):
from biskit import LogFile
import tempfile
def test_PDBCleaner(self):
"""PDBCleaner general test"""
## Loading PDB...
self.c = PDBCleaner(t.testRoot() + '/rec/1A2P_rec_original.pdb',
log=self.log,
verbose=self.local)
self.m = self.c.process()
self.assertAlmostEqual(self.m.mass(), 34029.0115499993, 7)
def test_DNACleaning(self):
"""PDBCleaner DNA test"""
## Loading PDB...
self.c = PDBCleaner(t.testRoot() + 'amber/entropy/0_com.pdb',
log=self.log,
verbose=self.local)
self.dna = self.c.process(amber=True)
self.assertAlmostEqual(self.dna.mass(), 26953.26, 1)
def test_Capping(self):
"""PDBCleaner.capTerminals test"""
## Loading PDB...
self.model = PDBModel(t.testRoot() + '/rec/1A2P_rec_original.pdb')
self.c = PDBCleaner(self.model, log=self.log, verbose=self.local)
self.m2 = self.c.capTerminals(breaks=True)
self.assertTrue(self.m2.atomNames() == self.model.atomNames())
self.m3 = self.model.clone()
self.m3.removeRes([10, 11, 12, 13, 14, 15])
self.m4 = self.m3.clone()
self.c = PDBCleaner(self.m3, log=self.log, verbose=self.local)
self.m3 = self.c.capTerminals(breaks=True, capC=[0], capN=[0, 1])
self.assertEqual(
self.m3.takeChains([0]).sequence()[:18], 'XVINTFDGVADXXKLPDN')
if self.local:
self.log.add('\nTesting automatic chain capping...\n')
self.c = PDBCleaner(self.m4, log=self.log, verbose=self.local)
self.m4 = self.c.capTerminals(auto=True)
self.assertEqual(
self.m4.takeChains([0]).sequence()[:18], 'XVINTFDGVADXXKLPDN')
def test_capping_internal(self):
self.m3 = PDBModel(t.testRoot('pdbclean/foldx_citche.pdb'))
self.m3 = self.m3.takeChains([1]) # pick second chain; has chain break
self.c3 = PDBCleaner(self.m3, verbose=self.local, log=self.log)
m = self.c3.capACE(self.m3, 1, checkgap=False)
self.assertEqual(
m.lenChains(breaks=True) - 1, self.m3.lenChains(breaks=True))
class Test(BT.BiskitTest):
"""Test class """
def prepare(self):
from biskit import LogFile
import tempfile
def test_PDBCleaner( self ):
"""PDBCleaner general test"""
## Loading PDB...
self.c = PDBCleaner( t.testRoot() + '/rec/1A2P_rec_original.pdb',
log=self.log,
verbose=self.local)
self.m = self.c.process()
self.assertAlmostEqual( self.m.mass(), 34029.0115499993, 7 )
def test_DNACleaning( self ):
"""PDBCleaner DNA test"""
## Loading PDB...
self.c = PDBCleaner( t.testRoot() + 'amber/entropy/0_com.pdb',
log=self.log, verbose=self.local )
self.dna = self.c.process(amber=True)
self.assertAlmostEqual( self.dna.mass(), 26953.26, 1 )
def test_Capping( self ):
"""PDBCleaner.capTerminals test"""
## Loading PDB...
self.model = PDBModel(t.testRoot() + '/rec/1A2P_rec_original.pdb')
self.c = PDBCleaner( self.model, log=self.log, verbose=self.local )
self.m2 = self.c.capTerminals( breaks=True )
self.assertTrue( self.m2.atomNames() == self.model.atomNames() )
self.m3 = self.model.clone()
self.m3.removeRes( [10,11,12,13,14,15] )
self.m4 = self.m3.clone()
self.c = PDBCleaner( self.m3, log=self.log, verbose=self.local )
self.m3 = self.c.capTerminals( breaks=True, capC=[0], capN=[0,1])
self.assertEqual( self.m3.takeChains([0]).sequence()[:18],
'XVINTFDGVADXXKLPDN' )
if self.local:
self.log.add( '\nTesting automatic chain capping...\n' )
self.c = PDBCleaner( self.m4, log=self.log, verbose=self.local )
self.m4 = self.c.capTerminals( auto=True )
self.assertEqual( self.m4.takeChains([0]).sequence()[:18],
'XVINTFDGVADXXKLPDN' )
def test_capping_internal(self):
self.m3 = PDBModel(t.testRoot('pdbclean/foldx_citche.pdb'))
self.m3 = self.m3.takeChains([1]) # pick second chain; has chain break
self.c3 = PDBCleaner(self.m3, verbose=self.local, log=self.log)
m = self.c3.capACE(self.m3, 1, checkgap=False)
self.assertEqual(m.lenChains(breaks=True) -1,
self.m3.lenChains(breaks=True))
class AmberParmBuilder:
"""
AmberParmBuilder
================
Create Amber topology and coordinate file from PDB.
- parmMirror():
...builds a fake parm that exactly mirrors a given PDB file.
This parm can be used for ptraj but not for simulations.
Currently, parmMirror only accepts amber-formatted PDBs as
input. It should be possible to create topologies that have
the same content and order of atoms as an xplor PDB but
some atoms will have different names.
- parmSolvated():
...builds a solvated system for PME simulations (incl. closing
of S-S bonds, capping of chain breaks). parmSolvated accepts
both xplor and amber-formatted PDBs as input.
Requires the amber programs C{tleap} and C{ambpdb}.
Requires leap template files in C{biskit/Biskit/data/amber/leap/}.
Note on forcefields:
The default forcefield used is specified in exe_tleap and currently
is ff10. This translates to loading amber11/dat/leap/cmd/leaprc.ff10
at the beginning of the leap run. As of 2011, ff10 is the recommended
default forcefield for proteins and nucleic acids.
Comment from Jason Swails on the Amber mailing list:
"
Try using ff99SB (which is the protein force field part of ff10, which is
the version I would actually suggest using). Despite its label, it is
actually a 2006 update of the ff99 force field which performs at least as
well (if not better) as ff03."
Unfortunately, ions are only "half" paramterized in ff10. Additional
parameters need to be loaded from a frmod file, typically
frcmod.ionsjc_tip3p. There are additional versions of this file optimized
for other water models than TIP3. frcmod.ionsjc_tip3p is set as the
default frmod file to include by parmSolvated and parmMirror. Please
include it if you provide your own list of frmod files.
.. note::
The design of AmberParmBuilder is less than elegant. It
would make more sense to split it into two classes that
are both derrived from Executor.
"""
## script to create a parm that exactly mirrors a given PDB
script_mirror_pdb = """
logFile %(f_out)s
source %(leaprc)s
%(fmod)s
%(fprep)s
p = loadPdb %(in_pdb)s
%(delete_atoms)s
saveAmberParm p %(out_parm)s %(out_crd)s
quit
"""
## tleap command to close a single S-S bond
ss_bond = "bond p.%i.SG p.%i.SG\n"
## leap script for solvated topology
F_leap_in = t.dataRoot() + '/amber/leap/solvate_box.leap'
## PDB with ACE capping residue
F_ace_cap = t.dataRoot() + '/amber/leap/ace_cap.pdb'
## PDB with NME capping residue
F_nme_cap = t.dataRoot() + '/amber/leap/nme_cap.pdb'
def __init__( self, model,
leap_template=F_leap_in,
leaprc=None,
leap_out=None, leap_in=None,
leap_pdb=None,
log=None,
debug=0,
verbose=0,
**kw ):
"""
:param model: model
:type model: PDBModel or str
:param leap_template: path to template file for leap input
:type leap_template: str
:param leaprc: forcefield parameter file or code (e.g. ff99)
:type leaprc: str
:param leap_out: target file for leap.log (default: discard)
:type leap_out: str
:param leap_in: target file for leap.in script (default: discard)
:type leap_in: str
:param kw: kw=value pairs for additional options in the leap_template
:type kw: key=value
"""
self.m = PDBModel( model )
self.leap_template = leap_template
self.leaprc = leaprc
self.leap_pdb = leap_pdb or tempfile.mktemp( '_leap_pdb' )
self.keep_leap_pdb = leap_pdb is not None
self.leap_in = leap_in
self.leap_out= leap_out
self.log = log or StdLog()
self.output = None # last output of leap
self.debug = debug
self.verbose = verbose
self.__dict__.update( kw )
def __runLeap( self, in_script, in_pdb, norun=0, **kw ):
"""
Create script file and run Leap.
:param in_script: content of ptraj script with place holders
:type in_script: str
:param in_pdb: PDB file to load into tleap
:type in_pdb: str
:param norun: 1 - only create leap scrip (default: 0)
:type norun: 1|0
:param kw: key=value pairs for filling place holders in script
:type kw: key=value
:raise AmberError: if missing option for leap input file or
if could not create leap input file
"""
x = AmberLeap( in_script,
in_pdb=in_pdb,
log=self.log, verbose=self.verbose, debug=self.debug,
catch_out=True,
f_in=self.leap_in,
f_out=self.leap_out,
**kw )
if norun:
x.generateInp()
else:
x.run()
self.output = x.output
## ## create leap script
## try:
## ## use own fields and given kw as parameters for leap script
## d = copy.copy( self.__dict__ )
## d.update( kw )
## in_script = in_script % d
## f = open( self.leap_in, 'w')
## f.write( in_script )
## f.close()
## if self.verbose:
## self.log.add('leap-script: ')
## self.log.add( in_script )
## except IOError:
## raise AmberError('Could not create leap input file')
## except:
## raise AmberError('missing option for leap input file\n'+\
## 'available: %s' % (str( d.keys() ) ))
## ## run tleap
## args = '-f %s' % self.leap_in
## if not norun:
## self.exe = Executor('tleap', args, log=self.log,verbose=1,
## catch_out=0)
## self.output, self.error, self.status = self.exe.run()
## if not os.path.exists( kw['out_parm'] ):
## raise AmberError, "tleap failed"
## ## clean up
## if not self.keep_leap_in and not self.debug:
## t.tryRemove( self.leap_in )
## if not self.keep_leap_out and not self.debug:
## t.tryRemove( self.leap_out)
def parm2pdb( self, f_parm, f_crd, f_out, aatm=0 ):
"""
Use ambpdb to build PDB from parm and crd.
:param f_parm: existing parm file
:type f_parm: str
:param f_crd: existing crd file
:type f_crd: str
:param f_out: target file name for PDB
:type f_out: str
:return: f_out, target file name for PDB
:rtype: str
:raise AmberError: if ambpdb fail
"""
## cmd = '%s -p %s -aatm < %s > %s' % \
args = '-p %s %s' % (f_parm, '-aatm'*aatm )
x = Executor('ambpdb', args, f_in=f_crd, f_out=f_out,
log=self.log, verbose=self.verbose, catch_err=1)
output,error,status = x.run()
if not os.path.exists( f_out ):
raise AmberError('ambpdb failed.')
return f_out
def __ssBonds( self, model, cutoff=4. ):
"""
Identify disulfide bonds.
:param model: model
:type model: PDBModel
:param cutoff: distance cutoff for S-S distance (default: 4.0)
:type cutoff: float
:return: list with numbers of residue pairs forming S-S
:rtype: [(int, int)]
"""
m = model.compress( model.mask( ['SG'] ) )
if len( m ) < 2:
return []
pw = MU.pairwiseDistances( m.xyz, m.xyz )
pw = N0.less( pw, cutoff )
r = []
for i in range( len( pw ) ):
for j in range( i+1, len(pw) ):
if pw[i,j]:
r += [ (m.atoms['residue_number'][i],
m.atoms['residue_number'][j]) ]
return r
def __cys2cyx( self, model, ss_residues ):
"""
Rename all S-S bonded CYS into CYX.
:param model: model
:type model: PDBModel
:param ss_residues: original residue numbers of S-S pairs
:type ss_residues: [(int, int)]
"""
ss = []
for a,b in ss_residues:
ss += [a,b]
for a in model:
if a['residue_number'] in ss:
a['residue_name'] = 'CYX'
def capACE( self, model, chain ):
"""
Cap N-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose)
return cleaner.capACE( model, chain, breaks=True )
def capNME( self, model, chain ):
"""
Cap C-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose )
return cleaner.capNME( model, chain, breaks=True)
def centerModel( self, model ):
"""
Geometric centar of model.
:param model: model
:type model: PDBMode
"""
center = N0.average( model.getXyz() )
model.setXyz( model.xyz - center )
def leapModel( self, hetatm=0, center=True ):
"""
Get a clean PDBModel for input into leap.
:param hetatm: keep HETATM records (default: 0)
:type hetatm: 1|0
:return: model
:rtype: PDBMod
"""
m = self.m.clone()
m.xplor2amber()
cleaner = PDBCleaner( m, log=self.log, verbose=self.verbose )
m = cleaner.process( keep_hetatoms=hetatm, amber=1 )
m.renumberResidues( addChainId=1 )
if center:
self.centerModel( m )
return m
def __fLines( self, template, values ):
if not type( values ) is list:
values = [ values ]
return ''.join( [ template % v for v in values ] )
def parmSolvated( self, f_out, f_out_crd=None, f_out_pdb=None,
hetatm=0, norun=0,
cap=0, capN=[], capC=[],
fmod=['frcmod.ionsjc_tip3p'], fprep=[],
box=10.0, center=True, **kw ):
"""
:param f_out: target file for parm (topology)
:type f_out: str
:param f_out_crd: target file for crd (coordinates)
(default:|f_out_base|.crd)
:type f_out_crd: str
:param f_out_pdb: target file for pdb (default:|f_out_base|.pdb)
:type f_out_pdb: str
:param hetatm: keep hetero atoms (default: 0)
:type hetatm: 1|0
:param cap: put ACE and NME capping residue on chain breaks
(default: 0)
:type cap: 1|0
:param capN: indices of chains that should get ACE cap (default: [])
:type capN: [int]
:param capC: indices of chains that should get NME cap (default: [])
:type capC: [int]
:param box: minimal distance of solute from box edge (default: 10.0)
:type box: float
:param center: re-center coordinates (default: True)
:type center: bool
:param fmod: list of files with amber parameter modifications
to be loaded into leap with loadAmberParams
(default:['frcmod.ionsjc_tip3p'] ... mod file needed for
default Amber ff10 ions -- topology saving will fail if this
one is missing)
:type fmod: [str]
:param fprep: list of files with amber residue definitions
(to be loaded into leap with loadAmberPrep) (default: [])
:type fprep: [str]
:param kw: additional key=value pairs for leap input template
:type kw: key=value
:raise IOError:
"""
f_out = t.absfile( f_out )
f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
f_out_pdb = t.absfile( f_out_pdb ) or t.stripSuffix( f_out ) +\
'_leap.pdb'
## removed: (bugfix 3434136)
#fmod = [ t.absfile( f ) for f in t.toList( fmod ) ]
#fprep = [ t.absfile( f ) for f in t.toList( fprep ) ]
try:
if self.verbose: self.log.add( '\nCleaning PDB file for Amber:' )
m = self.leapModel( hetatm=hetatm, center=center )
if cap:
end_broken = m.atom2chainIndices( m.chainBreaks() )
capC = MU.union( capC, end_broken )
capN = MU.union( capN, N0.array( end_broken ) + 1 )
for i in capN:
if self.verbose:
self.log.add( 'Adding ACE cap to chain %i' % i )
m = self.capACE( m, i )
for i in capC:
if self.verbose:
self.log.add( 'Adding NME cap to chain %i' % i )
m = self.capNME( m, i )
m.renumberResidues( addChainId=1 ) ## again, to accomodate capping
template = open( self.leap_template ).read()
leap_mod = self.__fLines( 'm = loadAmberParams %s\n', fmod )
leap_prep= self.__fLines( 'loadAmberPrep %s\n', fprep )
ss = self.__ssBonds( m, cutoff=4. )
self.__cys2cyx( m, ss )
leap_ss = self.__fLines( self.ss_bond, ss )
if self.verbose:
self.log.add('Found %i disulfide bonds: %s' % (len(ss),str(ss)))
if self.verbose:
self.log.add( 'writing cleaned PDB to %s' % self.leap_pdb )
m.writePdb( self.leap_pdb, ter=3 )
self.__runLeap( template, in_pdb=self.leap_pdb,
out_parm=f_out, out_crd=f_out_crd,
ss_bonds=leap_ss, fmod=leap_mod,
fprep=leap_prep, norun=norun,
box=box, **kw )
if not norun:
parm_pdb = self.parm2pdb( f_out, f_out_crd, f_out_pdb )
if not self.keep_leap_pdb and not self.debug:
t.tryRemove( self.leap_pdb )
except IOError as why:
raise IOError(why)
def __deleteAtoms( self, m, i_atoms ):
"""
Delet atoms
:param m: model
:type m: PDBMode
:param i_atoms: atom index
:type i_atoms: [int]
:return: leap statements for deleting given atoms
:rtype: [str]
"""
cmd = 'remove p.%(res)i p.%(res)i.%(atom)i'
rM = m.resMap()
rI = m.resIndex()
s = []
for i in i_atoms:
res = m.atoms['residue_number'][i]
## substract atom index of first atom in of this residue
atm = i - rI[ rM[ i ] ] + 1
s += [ cmd % {'res':res, 'atom':atm} ]
return '\n'.join( s )
def __inverseIndices( self, model, i_atoms ):
"""
:param model: model
:type model: PDBMode
:param i_atoms: atom index
:type i_atoms: [int]
:return: remaining atom indices of m that are NOT in i_atoms
:rtype: [int]
"""
mask = N0.zeros( len( model ),N0.Int )
N0.put( mask, i_atoms, 1 )
return N0.nonzero( N0.logical_not( mask ) )
def parmMirror( self, f_out, f_out_crd=None, fmod=['frcmod.ionsjc_tip3p'],
fprep=[], **kw ):
"""
Create a parm7 file whose atom content (and order) exactly mirrors
the given PDBModel. This requires two leap runs. First we get a
temporary topology, then we identify all atoms added by leap and
build a final topology where these atoms are deleted.
This parm is hence NOT suited for simulations but can be used to parse
e.g. a trajectory or PDB into ptraj.
:param f_out: target parm file
:type f_out: str
:param f_out_crd: target crd file (default: f_out but ending .crd)
:type f_out_crd: str
:param fmod : list of amber Mod files (loaded with loadAmberParams)
:type fmod : [str]
:param fmod : list of amber Prep files (loaded with loadAmberPrep)
:type fmod : [str]
"""
f_out = t.absfile( f_out )
f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
## if there are hydrogens, recast them to standard amber names
aatm = 'HA' in self.m.atomNames() ## 'HB2' in self.m.atomNames()
## First leap round ##
m_ref = self.m.clone()
m_ref.xplor2amber( aatm=aatm, parm10=True )
tmp_in = tempfile.mktemp( 'leap_in0.pdb' )
m_ref.writePdb( tmp_in, ter=3 )
tmp_parm = tempfile.mktemp( '_parm0' )
tmp_crd = tempfile.mktemp( '_crd0' )
leap_mod = self.__fLines( 'm = loadAmberParams %s\n', fmod )
leap_prep= self.__fLines( 'loadAmberPrep %s\n', fprep )
self.__runLeap( self.script_mirror_pdb,
leaprc=self.leaprc, fmod=leap_mod, fprep=leap_prep,
in_pdb=tmp_in, out_parm=tmp_parm, out_crd=tmp_crd,
delete_atoms='' )
tmp_pdb = self.parm2pdb( tmp_parm, tmp_crd,
tempfile.mktemp( 'leap_out.pdb' ), aatm=aatm )
if not self.debug:
t.tryRemove( tmp_parm )
t.tryRemove( tmp_crd )
t.tryRemove( tmp_in )
## load model with missing atoms added by leap
m_leap = PDBModel( tmp_pdb )
## compare atom content
iLeap, iRef = m_leap.compareAtoms( m_ref )
## check that ref model doesn't need any change
if iRef != list(range( len( m_ref ))):
uLeap, uRef = m_leap.unequalAtoms( m_ref, iLeap, iRef )
atms = m_ref.reportAtoms( uRef, n=6 )
raise AmberError("Cannot create exact mirror of %s.\n" % tmp_in +\
"Leap has renamed/deleted original atoms in %s:\n"% tmp_pdb+\
atms)
## indices of atoms that were added by leap
delStr = self.__deleteAtoms( m_leap,
self.__inverseIndices( m_leap, iLeap ) )
## Second leap round ##
self.__runLeap( self.script_mirror_pdb, leaprc=self.leaprc,
in_pdb=tmp_pdb, fmod=leap_mod, fprep=leap_prep,
out_parm=f_out, out_crd=f_out_crd,
delete_atoms=delStr )
if not self.debug:
t.tryRemove( tmp_pdb )
