Package schrodinger :: Package protein :: Module _reliability :: Class ModelCheck

[frames] | no frames]

Class ModelCheck

Instance Methods

[hide private]

__init__(self, ct, do_calc=True, save_ct=True, settings={})
Create a ModelCheck instance.

_getTitle(self)
Get protein title

_process_ligand_inputs(self, ligand_setting)
This function parses the ligand inputs, which could be in several formats.

_get_binding_site(self, ligand_list, site_asl=None)

calc(self)

is_donor(self, ct, iatom)

is_acceptor(self, ct, iatom)

hbond_da_type(self, ct, iatom)

within_three_bonds(self, ct, iatom, target_atom)

filter_data_by_chain(self, chain)
get the violations only related to the specified chain name

get_site_info(self, site_asl)

add_set(self, calc_set)

reset(self)

check_packing(self)

check_hb(self)

hb_buried_donor(self, ct)

hb_buried_acceptor(self, ct)

hb_check_buried(self, ct, unbonded_list, calc_set)

hb_unsatis_water(self, ct)

isolated_waters(self)

missing_loop(self)

missing_loop_chainbreak(self)

check_xray(self)

analyze_pr_set(self, data_set)
analyze one set of results from ProteinReport @type data_set: ProteinReport.data_set @param data_set: one of ProteinReport data set

analyzeStericClashes(self, data_set)
Analyze the steric clash results

schrodinger.structure._StructureAtom

_getSecondAtom(self, descriptor, residue_dict)
Get the second atom described in the specified descriptor

in_site(self, descriptor)

set_bubble_look(self)

read_data_from_CT(self)
read the data from CT into memory.

save_data_to_CT(self)
Save all data to CT properties

get_results(self)
returns results

get_quick_results(self)
Abbreviented output that can be used to quickly validate if the protein is suitable for FEP calculations

add_notes(self)
add notes about each calc_set

text_report(self, out_text_file='')
write out the details of each calc_set

bubble_plot(self, show)
draw a bubble plot

Class Variables

[hide private]

RES_RE = '([\\w_ ]): # chain name\n ...

DESCRIPTOR_RE = re.compile(r'(?x)([\w_ ]):\s*\w*\s*(-?\d*)([A-...

Method Details

[hide private]

init(self, ct, do_calc=True, save_ct=True, settings=`{}`)
(Constructor)

Create a ModelCheck instance. Which runs Protein Report and some other calculations and then summarize the metrics.

_process_ligand_inputs(self, ligand_setting)


This function parses the ligand inputs, which could be in several
formats.
a) within the same CT as the protein, more than one ligands can be
   defined.  Example:  A:128
b) ligands may automatically detected if 'ligand_setting == 'auto'
   automatically

analyze_pr_set(self, data_set)


analyze one set of results from ProteinReport
@type data_set: ProteinReport.data_set
@param data_set: one of ProteinReport data set

bad_points: violations within the binding site
count: raw count of bad points
bubble_scale: normalized scale, usually from 'count'
              0-1: acceptable; >1: bad; -1: no data

analyzeStericClashes(self, data_set)

Analyze the steric clash results

Parameters:

data_set (schrodinger.protein.analysis.report. steric_clash_data_set) - The data set to analyze

_getSecondAtom(self, descriptor, residue_dict)

Get the second atom described in the specified descriptor

Parameters:

descriptor (str) - String describing two clashing residues, formatted similar to "A:GLU 1: N - A:GLN 55: N *"
residue_dict (dict) - A dictionary used as an optimization to speed up the search. Key: (chain, resnum, inscode) Value: _Residue object

Returns: schrodinger.structure._StructureAtom

The second atom described in descriptor

read_data_from_CT(self)

read the data from CT into memory. return False for error

Class Variable Details

[hide private]

RES_RE

Value:

'''([\\w_ ]):           # chain name
                 \\s*\\w*\\s*           # residue name
                 (-?\\d*)([A-Za-z]?): # residue number and insertion c
ode
                 \\s*(\\w*)\\s*         # atom name
                 '''

DESCRIPTOR_RE

Value:

re.compile(r'(?x)([\w_ ]):\s*\w*\s*(-?\d*)([A-Za-z]?):\s*(\w*)\s*\s*-\
s*([\w_ ]):\s*\w*\s*(-?\d*)([A-Za-z]?):\s*(\w*)\s*\s*\*\s*')

Class ModelCheck

__init__(self, ct, do_calc=True, save_ct=True, settings={}) (Constructor)

_process_ligand_inputs(self, ligand_setting)

analyze_pr_set(self, data_set)

analyzeStericClashes(self, data_set)

_getSecondAtom(self, descriptor, residue_dict)

read_data_from_CT(self)

RES_RE

DESCRIPTOR_RE

init(self, ct, do_calc=True, save_ct=True, settings=`{}`)
(Constructor)