schrodinger.application.mcpro.zmat module

Z-matrix classes and functions.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.mcpro.zmat.Zmat(title='', prot='', startCt=None, startReorderedCt=None, endCt=None, endReorderedCt=None, atom=[], rest=[], geo_var=[], filename='', tol={}, printZmatAtomLigStart=None, outfh=None)

class to store a single Zmat and related objects

adapt_dummy_types(ct, end)

set the proper atom type for an FEP dummy atom

add_lig_solvent_cap(curr_ct)

solvent cap will be added to the current ligand zmat at the center of atoms defined in the incoming ct.

add_prot_solvent_cap(capCt)

solvent cap will be added to the current zmat at the center of atoms defined in the incoming ct. Both zmat and incoming ct are expected to have the same frame of reference

conv_int(string)

Convert boss integers such as ‘0002’to ‘ 2’

create_zmat(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 For ligands use Wolfgang’s preparation method For proteins use pepz Options:

currentNumericType: value numeric types will begin with (if possible) flexSolute: “flex” for flexible solutes, “fixed” for rigid solutes

forceConsistentResnum(ct)

Return a ct where all atoms have the same residue number taken from the first atom. If the first atom doesn’t have a residue number the number 999 is used

getLargestNumericType()

Routine identifies the largest numeric atomtype (linking atom numbers to Coul/vdW parameters - can be taken from atom or QM blocks

get_residues(atomsList, ct)

Take a list of atoms and return the list of residues those atoms are part of

merge(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. These cts must be in the same reference frame. If addTerz is True than TERZ will be added between self and the merged molecule. If addTerz is False all of the possible 6 degrees of intramolecular freedom will be added to the zmatrix

modify_title(title)

myslice(string, start, end)

Create slices from string starting at postion start and ending at end. Really shouldn’t be needed but having weird problems with slices in this script

print_Zmat(swap, end_available, fileH, ligOnly=0)

print Zmat to a file, if ligOnly=1 ligand residue numbering will start at 1

read_zmat(filename, startCt=None, endCt=None, prot='', nocap=0, nonFepDummies=[])

read a boss/mcpro zmat nocap = 0 read all atoms including CAP

1 read all atoms except CAP

reduced_set(list, delim=' ')

Takes a list, orders it and returns a reduced representation string, ie. [ 1 2 3 4 5 ] would return 1-5

rigidify_geo_vars()

method to ensure no geometry variation is set as flexible in the MCPRO zmatrix

set_geometry_variations(end_ct, nonFepDummies)

Set geometry variations from differences in end_ct and zmat object

class schrodinger.application.mcpro.zmat.ZmatAddAng(a1=0, a2=0, a3=0)

Class to store additional angles

class schrodinger.application.mcpro.zmat.ZmatAddBnd(a1=0, a2=0)

Class to store additional bonds

class schrodinger.application.mcpro.zmat.ZmatAddDih(a1=0, a2=0, a3=0, a4=0, t1=0, t2=0)

Class to store additional dihedrals

class schrodinger.application.mcpro.zmat.ZmatAtom(nr=0, symbol='', iztype=0, iftype=0, iz1=0, iz2=0, iz3=0, zpar1=0.0, zpar2=0.0, zpar3=0.0, resname='', terz='', resnum=0, element=0, printZmatAtomLigStart=None)

class to store an atom of a zmat

printSwapZmatAtom(fileH)

print Zmat Atom

printZmatAtom(fileH, ligOnly=0)

print Zmat Atom

class schrodinger.application.mcpro.zmat.ZmatBondAtomtypes(a1=0, a2=0, r0=0.0, k0=0.0, r1=0.0, k1=0.0)

Class to store explicitly written stretch parameters

class schrodinger.application.mcpro.zmat.ZmatDomDef(d1a1=0, d1a2=0, d2a1=0, d2a2=0)

Class to store domain definitions

class schrodinger.application.mcpro.zmat.ZmatGeoVar(iz=0, type=0, var=0.0)

class to store geometry variations

class schrodinger.application.mcpro.zmat.ZmatHarCons(i1=0, i2=0, f1=0.0, f2=0.0, f3=0.0, f4=0.0)

Class to store harmonic constraints

class schrodinger.application.mcpro.zmat.ZmatNonBond(type=0, ele=0, symbol='', chg=0, eps=0, sig=0)

Class to store explicitly written non-bond parameters

class schrodinger.application.mcpro.zmat.ZmatVarDih(atom=0, type1=0, type2=0, vary=0)

Class to store variable dihedrals

class schrodinger.application.mcpro.zmat.proteinHandler(outfh=None)

Class provides methods to write the pepz input file

exportReceptor(outfile, pdb_version)

Export the receptor structure in *.pdb format

getCt()

Method to return the current protein ct

importReceptor(pdbOrder, infile='', inpProtCt='', changeCys=False)

Import the receptor assumed to be in pdb grouped order in *.pdb or *.mae format

reorderResidues()

Method to reorder protein residues sequentially Acts on the self.prot_ct object. If chain=0 the chains are removed. If chain != 0 chains are kept

write_ct_pdb_psp(ct, filename, pdb_version, mode='write', error_handler=None)

Write a CT to a PDB format file with MMPDB_PSP_MODE option active to ensure residue names in ct are output to PDB file

schrodinger.application.mcpro.zmat.removeOrientDummyAtoms(ct)

Method to identify and remove fep dummy atoms indicated by b_mcp_orient_dummy atom property added by mcpro_zmat