Package install :: Package MoSTBioDat :: Package DataBase :: Package ImportData :: Package Data2DB :: Module PDBFile
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Module PDBFile

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Classes [hide private]
  Residue
residue class INPUT: name - str, residue name num - int, residue number OUTPUT: class object
  Molecule
Molecule class INPUT: modelid - int, model id chainid - int, chain id molid - int, molecule id molname - str, molecule name molatnum - int, molecule atom number molinscode - str, molecule insertion code molfragnum - int, molecule fragment number molcoords - dict, molecule coordinates dictionary OUTPUT: class object
  Atom
atom class INPUT: name - str, atom name OUTPUT:
  createSDFile
create SDF file in specified directory INPUT: inboj - input ligand class object dirpath - str, directory path temporary - str, temporary directory path, default /tmp/Ligand sdf2pdb - boolean, convert sdf2pdb, default False aromaticflag - str, oe aromatic flag, default OEAroModelOpenEye addH - boolean, add hydrogen atoms, default False OUTPUT: file
  createPDBFile
create PDB file INPUT: macromolecule - input macromolecule dictionary dirpath - str, directory path pdbfile - str, output pdb file OUTPUT: file
Functions [hide private]
 
createPDBMol(ofs, mol)
create PDB file from molecule INPUT: ofs - output file stream mol - molecule object OUTPUT: file
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preprot(mol)
prepare molecule INPUT: mol - class object OUTPUT:
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iswater(formula)
check if is water molecule INPUT: formula - str, chemical formula OUTPUT: boolean
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checkres(r)
check residue INPUT: residue - residue class object INPUT: string
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printres(mol, cids, residues, restypes, natom, resnums)
print pdb file summary INPUT: mol - molecule object cids - chain id residues - residues object restypes - residue types natom - number of atom resnums - residue atom number OUTPUT: string
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defres(mol)
define residue INPUT: mol - molecule object OUTPUT: cids - chain id residues - residue object list restypes - residue types natom - number of atoms in residue resnums - residue names
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sortdictval(dictionary)
sort dictionary value INPUT: dictionary OUTPUT: sorted list of tuples
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parseres(mol, residue)
parse residue INPUT: mol - oe class object residue - residue class object repflag - boolean, report flag, default False
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PDBFile(pdbfilepath, repflag=1)
parse PDB file INPUT: pdbfilepath - str, file path repflag - boolean, residue flag, default True
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CanSmi(mol, iso, kek, verbose)
Create canonical smile (unique or absolute) INPUT: mol - molecule class object iso - boolean, create isomeric SMILE kek - boolean, Kekule aromatic form varbose - boolean, show warnings OUTPUT:
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