Topology

Topology

class sasmol.topology.Topology[source]

Bases: sasmol.charmm_topology.CharmmTopology

This class contains topology information used other modules.

add(dictionary, key, value, **kwargs)

This method is used by the self.read_topology method.

It will check whether the key is in the dictionary: if yes, append value to dictionary[key] if no, initialize dictionary[key] as [value]

Parameters

  • dictionary – dictionary : containing existing key, value pairs

  • key – dictionary key : key to query and perhaps intialize

  • value – dictionary value : value add

  • kwargs – optional future arguments

Return type

updated dictionary

Examples

>>> import sasmol.topology as topology
>>> d = {}
>>> d['ALA'] = 'RESI ALA'
>>> test = topology.CharmmTopology()
>>> test.add(d, 'GLU', 'GLU')
>>> d
{'GLU': ['GLU'], 'ALA': 'RESI ALA'}
>>> test.add(d, 'ASP', 'RESI ASP')
>>> d
{'ASP': ['RESI ASP'], 'GLU': ['GLU'], 'ALA': 'RESI ALA'}
charmm_names(**kwargs)
Parameters

kwargs – optional future arguments

Returns

dictionary : atom_name and list of atom names for hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorus, other

Return type

charmm_names

Examples

>>> import sasmol.properties as properties
>>> properties = properties.Atomic()
>>> properties.charmm_names()['sulfur']
['SG', 'SD', '1SG', '2SG']
check_charmm_atomic_order_reorganize(**kwargs)

re-organize the atomic list according to the charmm topology contract do nothing if the atomic order alreay match that in the charmm topology file meanwhile make sure there are no missing or extra atoms H-atoms are required Patch N-ter for the first residue and C-ter for the last residue in each segment

Parameters

kwargs – optional future arguments

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.check_charmm_atomic_order_reorganize()
Returns

list : with error code

Return type

error

Note

error code needs to be addressed and handled globally

compare_list_ignore_order(l1, l2, **kwargs)

Compare two lists while ignoring order

Parameters

  • l1 – list : list 1

  • l2 – list : list 2

  • kwargs – optional future arguments

Examples

>>> import sasmol.topology as topology
>>> test = topology.CharmmTopology()
>>> l1 = [1, 2, 4]
>>> l2 = [2, 1, 4]
>>> test.compare_list_ignore_order(l1, l2)
True
Return type

Boolean

create_fasta(**kwargs)[source]

Method to make a fasta file compatible lists of residue names

http://en.wikipedia.org/wiki/FASTA_format

Parameters

kwargs – optional future arguments

Returns

sets the fasta attribute in a system object

Return type

self._fasta

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule("hiv1_gag.pdb")
>>> molecule.create_fasta()
>>> print(molecule.fasta()[:5])
['G', 'A', 'R', 'A', 'S']

>>> molecule.create_fasta(fasta_format=True)
>>> print(molecule.fasta()[:5])
>
GAR
>>> molecule.create_fasta(fasta_format=True,width='60')
>>> print(molecule.fasta()[:-1])
>
GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQIL
GQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQAAAD
TGNNSQVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATP
QDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTS
TLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFY
KTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKAR
VIAEAMSQVTNSATIMMQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGH
QMKDCTERQAN

>>> molecule.create_fasta(fasta_format=True,width='60',name='aar')
>>> print(molecule.fasta()[:90])
>aar
GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQIL
GQLQPSLQTGSEELRSLYNTIAVL

Note

Other use types below

molecule.create_fasta(fasta_format=True,exclude_hetatm=True,by_chain=True) print(molecule.fasta())

print(‘>>> testing by_chain with HETATM (t.py): ‘)

molecule.create_fasta(fasta_format=True,by_chain=True) print(molecule.fasta())

print(‘>>> testing by_segname (t.py): ‘)

molecule.create_fasta(fasta_format=True,exclude_hetatm=True,by_segname=True) print(molecule.fasta())

Note that this creates a simple string that is associated with the molecule (self) and it will return without assigning a string if a non-standard three letter code is supplied.

make_backbone_pdb_from_fasta(filename, moltype, **kwargs)[source]

Method to write a PDB file of one atom per residue based on input FASTA sequence

http://en.wikipedia.org/wiki/FASTA_format

Parameters

  • string (moltype) –

  • string – -> ‘protein’ ; fasta sequence of a protein -> ‘nucleic’ ; fasta sequence of a nucleic acid

  • kwargs – optional future arguments

Returns

sets the fasta attribute in a system object

Return type

self._fasta

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule("hiv1_gag.pdb")
>>> molecule.create_fasta()
>>> molecule.fasta()[:5]
['G', 'A', 'R', 'A', 'S']

>>> molecule.make_backbone_pdb_from_fasta('sequence.pdb', 'protein')

Note

Only protein and nucleic acid one-letter codes are supported Protein PDB files are written with one “CA” atom per residue Nucleic acid PDF files are written with on “O5’” atom per residue

Protein PDB residue names are written as standard residue names; terminal patch names such as GLYP and PROP belong in topology/psfgen contexts.

All coordinate values are set to 0.000

make_constraint_pdb(filename, basis_type, **kwargs)[source]

Method to rename attribute fields and assign values of 1.00 for the given basis type.

“beta” is the default attribute field to reassign

Default usage sets all attribute fields to zero prior to re-assigning basis type atoms to 1.00

Parameters

  • string (filename) –

  • types (basis) –

    ‘heavy : all atoms except hydrogen

    ’protein’ : all atoms in moltype protein

    ’nucleic’ : all atoms in moltype nucleic

    ’backbone’

    -> proteins: N, CA, C, O

    ’solute’ : all protein and nucleic

kwargs

optional arguments

field=’beta’ : write 1.00 to beta field

field=’occupancy’ : write 1.00 to occupancy field

reset=Trueset all values to 0.00 before setting

individual vaules to 1.00

reset=False: only change desired values to 1.00

ignoring all other values

Returns

updated system object writes pdb to disk

Return type

None

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.make_constraint_pdb('constrainted_backbone_hiv1_gag.pdb', 'backbone')

>>> molecule.make_constraint_pdb('constrainted_backbone_occupancy_hiv1_gag.pdb', 'backbone', field='occupancy')

constrtain all heavy atoms

>>> molecule.make_constraint_pdb('constrainted_heavy_hiv1_gag.pdb', 'heavy')

constrain all protein atoms

>>> molecule.make_constraint_pdb('constrainted_protein_hiv1_gag.pdb', 'protein')

constrain all non-solvent atoms

>>> molecule.make_constraint_pdb('constrainted_solute_hiv1_gag.pdb', 'solute')

Note

Only moltype protein and nucleic are supported.

Output PDB file will contain coordinates from frame 0

patch_charmm_residue_atoms(residue, patch, **kwargs)

Applies ‘patch’ to ‘residue’ based on the charmm topology definition to add / remove atoms as needed. Only ATOM and DELE records are accommodated

Parameters

  • residue – string : residue name

  • patch – string : patch name

  • kwargs – optional future arguments

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.check_charmm_atomic_order_reorganize()
>>> molecule.patch_charmm_residue_atoms('GLY','GLYP')
Return type

updated dictionary entry for residue in question

Note

Error list is defined and used, but not returned. Needs to be handled globally.

read_charmm_topology(topology_file_path='', topology_file_name='top_all27_prot_na.inp', **kwargs)

Read and parse the charmm topology file A comprehensive dictionary (topology_info) will be built to store all the topology information The strategy for parsing topology file is to split words in each line

Parameters

  • topology_file_path – string : default = ‘’

  • topology_file_name – string : default = ‘top_all27_prot_na.inp’

  • kwargs – optional future arguments

Examples

>>> import pprint
>>> import sasmol.topology as topology
>>> test = topology.CharmmTopology()
>>> test.read_charmm_topology()
>>> pprint.pprint(test.topology_info['NTER'],width=100)
{'ATOM': [['N', 'NH3', '-0.30'],
    ['HT1', 'HC', '0.33'],
    ['HT2', 'HC', '0.33'],
    ['HT3', 'HC', '0.33'],
    ['CA', 'CT1', '0.21'],
    ['HA', 'HB', '0.10']],
'BOND': [['HT1', 'N'], ['HT2', 'N'], ['HT3', 'N']],
'DELE': [['ATOM', 'HN']],
'DONO': ['HT1', 'N', 'HT2', 'N', 'HT3', 'N'],
'IC': [['HT1', 'N', 'CA', 'C', '0.0000', '0.0000', '180.0000', '0.0000', '0.0000'],
        ['HT2', 'CA', '*N', 'HT1', '0.0000', '0.0000', '120.0000', '0.0000', '0.0000'],
        ['HT3', 'CA', '*N', 'HT2', '0.0000', '0.0000', '120.0000', '0.0000', '0.0000']],
'TOTAL_CHARGE': '1.00'}
Returns

list : with error code

Return type

error

Note

error code needs to be addressed and handled globally

renumber(**kwargs)[source]

Method to renumber index and resid fields

Parameters

kwargs – index : resid :

Returns

updated system object

index resid

Return type

None

Examples

>>> import sasmol.system as system
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> molecule.index()[0]
1
>>> molecule.resid()[0]
1

default renumber() with no arguments renumbers both index and resid starting at 1

>>> molecule.renumber()
>>> molecule.index()[0]
1
>>> molecule.resid()[0]
1

passing a kwarg with a value will renumber appropriate attribute with value passed

>>> molecule.renumber(index=3)
>>> molecule.index()[0]
3
>>> molecule.resid()[0]
1

>>> molecule.renumber(resid=8)
>>> molecule.index()[0]
3
>>> molecule.resid()[0]
8

>>> molecule.renumber(index=223, resid=18)
>>> molecule.index()[0]
223
>>> molecule.resid()[0]
18
setup_charmm_residue_atoms(**kwargs)

Build the atom list of all the residues in the charmm topology file

Parameters

kwargs – optional future arguments

Examples

>>> import sasmol.topology as topology
>>> test = topology.CharmmTopology()
>>> test.read_charmm_topology()
>>> test.setup_charmm_residue_atoms()
Returns

self.charmm_residue_atoms

Return type

new dictionary entry for residue in question

setup_cys_patch_atoms_simple(**kwargs)

A way to set up cys patch atoms simply remove HG1 atom from the atom list

Parameters

kwargs – optional future arguments

Examples

>>> import sasmol.topology as topology
>>> import pprint
>>> test = topology.CharmmTopology()
>>> test.read_charmm_topology()
>>> pprint.pprint(self.topology_info['CYS']['ATOM'])
[['N', 'NH1', '-0.47'],
['HN', 'H', '0.31'],
['CA', 'CT1', '0.07'],
['HA', 'HB', '0.09'],
['CB', 'CT2', '-0.11'],
['HB1', 'HA', '0.09'],
['HB2', 'HA', '0.09'],
['SG', 'S', '-0.23'],
['HG1', 'HS', '0.16'],
['C', 'C', '0.51'],
['O', 'O', '-0.51']]
>>> pprint.pprint(test.setup_cys_patch_atoms_simple(), width=80)
[['N', 'NH1', '-0.47'],
['HN', 'H', '0.31'],
['CA', 'CT1', '0.07'],
['HA', 'HB', '0.09'],
['CB', 'CT2', '-0.11'],
['HB1', 'HA', '0.09'],
['HB2', 'HA', '0.09'],
['SG', 'S', '-0.23'],
['C', 'C', '0.51'],
['O', 'O', '-0.51']]
Return type

updated dictionary entry for residue in question