mmLib.Library

Package mmLib :: Module Library

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Module mmLib.Library

Monomer and element library data classes. The Library classes are used for the identification and construction of biopolymers and ligands.

Classes
`ElementDesc`	Element description class returned by library_get_element_desc().
`MonomerDesc`	Monomer description class returned by library_get_monomer_desc().

Function Summary
	`library_construct_element_desc(symbol)` Constructs the ElementDesc object for the given element symbol.
	`library_construct_monomer_desc(res_name)` Constructs the MonomerDesc object for the given residue name.
	`library_get_element_desc(symbol)` Loads/caches/returns a instance of the ElementDesc class for the given element symbol.
	`library_get_monomer_desc(res_name)` Loads/caches/returns the monomer description objec MonomerDesc for the given monomer residue name.
	`library_guess_element_from_name(name0, res_name)` Try everything I can possibly think of to extract the element symbol from the atom name.
	`library_is_amino_acid(res_name)` Returns True if the res_name is a amino acid.
	`library_is_nucleic_acid(res_name)` Returns True if the res_name is a nucleic acid.
	`library_is_water(res_name)` Return True if the res_name is water.
	`test_module()`

Variable Summary
`dict`	`ALT_RES_NAME_DICT` = `{'C+': 'C', '+C': 'C', '+A': 'A', '+...`
`dict`	`AMINO_ACID13_DICT` = `{'A': 'ALA', 'C': 'CYS', 'E': 'GLU',...`
`dict`	`AMINO_ACID31_DICT` = `{'CYS': 'C', 'GLN': 'Q', 'ILE': 'I',...`
`list`	`AMINO_ACID3_LIST` = `['GLY', 'ALA', 'VAL', 'LEU', 'ILE', '...`
`dict`	`ELEMENT_CACHE` = `{}`
`mmCIFFile`	`ELEMENT_CIF_FILE` = `[[[{'van_der_walls_radius': '1.200000...`
`str`	`ELEMENT_DATA_PATH` = `'/home/jpaint/pymmlib/trunk/pymmlib/...`
`dict`	`ELEMENT_SYMBOL_DICT` = `{'BE': True, 'Yb': True, 'BA': Tru...`
`str`	`MMLIB_MONOMER_DATA_PATH` = `'/home/jpaint/pymmlib/trunk/py...`
`mmCIFFile`	`MMLIB_MONOMERS_CIF` = `[[[{'one_letter_code': 'G', 'chem_t...`
`dict`	`MONOMER_RES_NAME_CACHE` = `{}`
`list`	`NUCLEIC_ACID_LIST` = `['A', 'G', 'C', 'T', 'U']`
`dict`	`NUCLEIC_ACID_RES_NAME_DICT` = `{'C+': 'C', '+C': 'C', 'C':...`
`str`	`RCSB_MONOMER_DATA_FILE` = `'/home/jpaint/pymmlib/trunk/pym...`
`str`	`RCSB_MONOMER_DATA_PATH` = `'/home/jpaint/pymmlib/trunk/pym...`
`NoneType`	`RCSB_USE_ZIP` = None
`NoneType`	`RCSB_ZIP` = None

Function Details

library_construct_element_desc(symbol)

Constructs the ElementDesc object for the given element symbol.

library_construct_monomer_desc(res_name)

Constructs the MonomerDesc object for the given residue name.

library_get_element_desc(symbol)

Loads/caches/returns a instance of the ElementDesc class for the given element symbol. The source of the element data is the mmLib/Data/elements.cif file.

library_get_monomer_desc(res_name)

Loads/caches/returns the monomer description objec MonomerDesc for the given monomer residue name.

library_guess_element_from_name(name0, res_name)

Try everything I can possibly think of to extract the element symbol from the atom name. If availible, use the monmer dictionary to help narrow down the search.

library_is_amino_acid(res_name)

Returns True if the res_name is a amino acid.

library_is_nucleic_acid(res_name)

Returns True if the res_name is a nucleic acid.

library_is_water(res_name)

Return True if the res_name is water.

Variable Details

ALT_RES_NAME_DICT

Type:: dict
Value:: {'+A': 'A', '+C': 'C', '+G': 'G', '+T': 'T', '+U': 'U', 'A+': 'A', 'Ar': 'A', 'C+': 'C', ...

AMINO_ACID13_DICT

Type:: dict
Value:: {'A': 'ALA', 'C': 'CYS', 'D': 'ASP', 'E': 'GLU', 'F': 'PHE', 'G': 'GLY', 'H': 'HIS', 'I': 'ILE', ...

AMINO_ACID31_DICT

Type:: dict
Value:: {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLN': 'Q', 'GLU': 'E', 'GLY': 'G', ...

AMINO_ACID3_LIST

Type:: list
Value:: ['GLY', 'ALA', 'VAL', 'LEU', 'ILE', 'PRO', 'PHE', 'TYR', 'TRP']

ELEMENT_CACHE

Type:: dict
Value:: {}

ELEMENT_CIF_FILE

Type:: mmCIFFile
Value:: [[[{'van_der_walls_radius': '1.200000', 'name': 'Hydrogen', 'symbol': \ 'H', 'covalent_radius': '0.320', 'number': '1', 'color_rgb': '#FFFFFF'\ , 'atomic_weight': '1.007940'}], [{'b4': '57.799698', 'c': '0.003038',\ 'a3': '0.140191', 'a1': '0.493002', 'charge': '0', 'a2': '0.322912', \ 'a4': '0.040810', 'b2': '26.125700', 'b3': '3.142360', 'wavelength': '\ CuKa', 'b1': '10.510900'}, {'b4': '3.567090', 'c': '0.002389', 'a3': '\ 0.415815', 'a1': '0.897661', 'charge': '-1', 'a2': '0.565616', 'a4': '\ 0.116973', 'b2': '15.187000', 'b3': '186.575989', 'wavelength': 'CuKa'\ ...

ELEMENT_DATA_PATH

Type:: str
Value:: '/home/jpaint/pymmlib/trunk/pymmlib/mmLib/Data/elements.cif'

ELEMENT_SYMBOL_DICT

Type:: dict
Value:: {'BA': True, 'BE': True, 'BI': True, 'CS': True, 'DY': True, 'Ru': True, 'Yb': True, 'gd': True, ...

MMLIB_MONOMER_DATA_PATH

Type:: str
Value:: '/home/jpaint/pymmlib/trunk/pymmlib/mmLib/Data/monomers.cif'

MMLIB_MONOMERS_CIF

Type:: mmCIFFile
Value:: [[[{'one_letter_code': 'G', 'chem_type': 'aliphatic', 'id': 'GLY'}]], \ [[{'one_letter_code': 'A', 'chem_type': 'aliphatic', 'id': 'ALA'}]], [\ [{'one_letter_code': 'V', 'chem_type': 'aliphatic', 'id': 'VAL'}], [{'\ atom4': 'CG1', 'atom3': 'CB', 'name': 'chi1', 'atom2': 'CA', 'atom1': \ 'N'}]], [[{'one_letter_code': 'L', 'chem_type': 'aliphatic', 'id': 'LE\ U'}], [{'atom4': 'CG', 'atom3': 'CB', 'name': 'chi1', 'atom2': 'CA', '\ atom1': 'N'}, {'atom4': 'CD1', 'atom3': 'CG', 'name': 'chi2', 'atom2':\ 'CB', 'atom1': 'CA'}]], [[{'one_letter_code': 'I', 'chem_type': 'alip\ ...

MONOMER_RES_NAME_CACHE

Type:: dict
Value:: {}

NUCLEIC_ACID_LIST

Type:: list
Value:: ['A', 'G', 'C', 'T', 'U']

NUCLEIC_ACID_RES_NAME_DICT

Type:: dict
Value:: {'+A': 'A', '+C': 'C', '+G': 'G', '+T': 'T', '+U': 'U', 'A': 'A', 'A+': 'A', 'Ar': 'A', ...

RCSB_MONOMER_DATA_FILE

Type:: str
Value:: '/home/jpaint/pymmlib/trunk/pymmlib/mmLib/Data/Monomers.zip'

RCSB_MONOMER_DATA_PATH

Type:: str
Value:: '/home/jpaint/pymmlib/trunk/pymmlib/mmLib/Data/Monomers'

RCSB_USE_ZIP

Type:: NoneType
Value:: None

RCSB_ZIP

Type:: NoneType
Value:: None

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