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| __init__(self,
title='',
prot='',
startCt=None,
startReorderedCt=None,
endCt=None,
endReorderedCt=None,
atom=[],
rest=[],
geo_var=[],
filename='',
tol={},
printZmatAtomLigStart=None,
outfh=None) |
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__copy__(self)
Method to copy a Zmat object |
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| modify_title(self,
title) |
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create_zmat(self,
startCt=None,
endCt=None,
prot='',
title='',
protFile='',
consFile='',
consSpec=0,
debug=0,
jobname='',
inpProtCt=None,
resStart=4.0,
consStart=8.0,
currentNumericType=800,
flexSolute='flex',
oplsvers=2005,
bndTol='',
angTol='',
torTol='',
initDum=1,
pdb_version=3.0)
Create an MCPRO zmatrix from input cts for protein or ligand systems... |
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reduced_set(self,
list,
delim=' ')
Takes a list, orders it and returns a reduced representation string,
ie. |
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forceConsistentResnum(self,
ct)
Return a ct where all atoms have the same residue number taken from
the first atom. |
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get_residues(self,
atomsList,
ct)
Take a list of atoms and return the list of residues those atoms are
part of |
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getLargestNumericType(self)
Routine identifies the largest numeric atomtype (linking atom numbers
to Coul/vdW parameters - can be taken from atom or QM blocks |
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rigidify_geo_vars(self)
method to ensure no geometry variation is set as flexible in the
MCPRO zmatrix |
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read_zmat(self,
filename,
startCt=None,
endCt=None,
prot='',
nocap=0,
nonFepDummies=[])
read a boss/mcpro zmat ... |
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add_lig_solvent_cap(self,
curr_ct)
solvent cap will be added to the current ligand zmat at the center of
atoms defined in the incoming ct. |
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add_prot_solvent_cap(self,
capCt)
solvent cap will be added to the current zmat at the center of atoms
defined in the incoming ct. |
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merge(self,
ligZmat,
addTerz,
resname="LIG")
lig_zmat will be merged at the end of the self zmat Note that
lig_zmat is expected to be a ligand with startReorderedCt defined and
self is expected to be a protein wtih protReorderedCt defined. |
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myslice(self,
string,
start,
end)
Create slices from string starting at postion start and ending at
end. |
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conv_int(self,
string)
Convert boss integers such as '0002'to ' 2' |
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print_Zmat(self,
swap,
end_available,
fileH,
ligOnly=0)
print Zmat to a file, if ligOnly=1 ligand residue numbering will
start at 1 |
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adapt_dummy_types(self,
ct,
end)
set the proper atom type for an FEP dummy atom |
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set_geometry_variations(self,
end_ct,
nonFepDummies)
Set geometry variations from differences in end_ct and zmat object |
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