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src/c/o/cogent-1.5.3/cogent/format/pdb.py   cogent(Download)
from itertools import chain
 
from cogent.struct.selection import einput
from cogent.data.protein_properties import AA_NAMES
from cogent.parse.pdb import dict2pdb, dict2ter
def PDBWriter(f, entities, header_=None, trailer_=None):
        structure = einput(entities, level='A', name='atoms')
        # hierarchy: args, dicts
        try:
            header = (header_ or entities.raw_header or entities.header)
    q_mode = (q_mode or 'number')   # Q
 
    entities = einput(entities, level)
 
    for entity in entities:
        q_data = eval(q_mode)(entity.xtra.get(q_key), b_val) # occupancy
        b_data = eval(b_mode)(entity.xtra.get(b_key), q_val) # b-factor
 
        if level != 'A':
            atoms = einput(entity, 'A')

src/p/y/pycogent-HEAD/cogent/format/pdb.py   pycogent(Download)
from itertools import chain
 
from cogent.struct.selection import einput
from cogent.data.protein_properties import AA_NAMES
from cogent.parse.pdb import dict2pdb, dict2ter
def PDBWriter(f, entities, header_=None, trailer_=None):
        structure = einput(entities, level='A', name='atoms')
        # hierarchy: args, dicts
        try:
            header = (header_ or entities.raw_header or entities.header)
    q_mode = (q_mode or 'number')   # Q
 
    entities = einput(entities, level)
 
    for entity in entities:
        q_data = eval(q_mode)(entity.xtra.get(q_key), b_val) # occupancy
        b_data = eval(b_mode)(entity.xtra.get(b_key), q_val) # b-factor
 
        if level != 'A':
            atoms = einput(entity, 'A')

src/c/o/cogent-1.5.3/cogent/format/xyzrn.py   cogent(Download)
 
from itertools import chain
from cogent.struct.selection import einput
from cogent.data.protein_properties import AREAIMOL_VDW_RADII
from cogent.data.ligand_properties import LIGAND_AREAIMOL_VDW_RADII
def XYZRNWriter(f, entities, radius_type=None, header=None, trailer=None):
    """Function which writes XYZRN files from ``Entity`` instances."""
    radius_type = (radius_type or 'AREAIMOL_VDW_RADII')
 
    structure = einput(entities, level='A', name='structure')

src/p/y/pycogent-HEAD/cogent/format/xyzrn.py   pycogent(Download)
 
from itertools import chain
from cogent.struct.selection import einput
from cogent.data.protein_properties import AREAIMOL_VDW_RADII
from cogent.data.ligand_properties import LIGAND_AREAIMOL_VDW_RADII
def XYZRNWriter(f, entities, radius_type=None, header=None, trailer=None):
    """Function which writes XYZRN files from ``Entity`` instances."""
    radius_type = (radius_type or 'AREAIMOL_VDW_RADII')
 
    structure = einput(entities, level='A', name='structure')

src/c/o/cogent-1.5.3/cogent/struct/asa.py   cogent(Download)
from cogent.app.stride import Stride
from cogent.parse.stride import stride_parser
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import sphere_points, coords_to_symmetry, \
    # First we mask all water residues and chains with all residues masked 
    # (water chains).
    lattice_residues = einput(entities, 'R')
    lattice_residues.maskChildren('H_HOH', 'eq', 'name')
    lattice_chains = einput(entities, 'C')
        # the following makes sure that masking changes by the above
        # tests are reverted.
        lattice_structures = einput(entities, 'S')
        lattice_structures.setUnmasked(force=True)
        raise ValueError('No unmasked atoms to build lattice.')
    # these are all atoms we can work with
    lattice_atoms = einput(entities, 'A')

src/p/y/pycogent-HEAD/cogent/struct/asa.py   pycogent(Download)
from cogent.app.stride import Stride
from cogent.parse.stride import stride_parser
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import sphere_points, coords_to_symmetry, \
    # First we mask all water residues and chains with all residues masked 
    # (water chains).
    lattice_residues = einput(entities, 'R')
    lattice_residues.maskChildren('H_HOH', 'eq', 'name')
    lattice_chains = einput(entities, 'C')
        # the following makes sure that masking changes by the above
        # tests are reverted.
        lattice_structures = einput(entities, 'S')
        lattice_structures.setUnmasked(force=True)
        raise ValueError('No unmasked atoms to build lattice.')
    # these are all atoms we can work with
    lattice_atoms = einput(entities, 'A')

src/c/o/cogent-1.5.3/cogent/struct/manipulation.py   cogent(Download)
from cogent.core.entity import HIERARCHY, copy, StructureHolder, ModelHolder
from cogent.maths.geometry import coords_to_symmetry, coords_to_crystal
from cogent.struct.selection import einput
 
 
    conflicts = []
    changes = []
    residues = einput(entities, 'R')
    id_r = [[None, None, None]]
    for r in residues.sortedvalues():  # sort by id, ic, name
    mxs = sh['uc_mxs']
    # get initial coordinates
    atoms = einput(model, 'A')
    coords = array(atoms.getData('coords'))
    # expand the coordinates to symmetry
        # copy model
        new_model = copy(model) # with additional models which
        new_atoms = einput(new_model, 'A')
        # patch with coordinates
        new_coords = all_coords[i]
    omx = sh['uc_omx']
    # get initial coorinates
    atoms = einput(structure, 'A')
    coords = array([atoms.getData('coords')]) # fake 3D
    # expand the coordinates to crystal

src/p/y/pycogent-HEAD/cogent/struct/manipulation.py   pycogent(Download)
from cogent.core.entity import HIERARCHY, copy, StructureHolder, ModelHolder
from cogent.maths.geometry import coords_to_symmetry, coords_to_crystal
from cogent.struct.selection import einput
 
 
    conflicts = []
    changes = []
    residues = einput(entities, 'R')
    id_r = [[None, None, None]]
    for r in residues.sortedvalues():  # sort by id, ic, name
    mxs = sh['uc_mxs']
    # get initial coordinates
    atoms = einput(model, 'A')
    coords = array(atoms.getData('coords'))
    # expand the coordinates to symmetry
        # copy model
        new_model = copy(model) # with additional models which
        new_atoms = einput(new_model, 'A')
        # patch with coordinates
        new_coords = all_coords[i]
    omx = sh['uc_omx']
    # get initial coorinates
    atoms = einput(structure, 'A')
    coords = array([atoms.getData('coords')]) # fake 3D
    # expand the coordinates to crystal

src/c/o/cogent-1.5.3/cogent/struct/contact.py   cogent(Download)
"""Classes and functions for computing and manipulating accessible 
surface areas (ASA)."""
 
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
    # if not specified otherwise the lattice is the first model
    lattice = model or structure[(0,)]
    lents = einput(lattice, level)
    lents_ids = lents.getData('getFull_id', forgiving=False, method=True)
    lcoords = array(lents.getData('coords', forgiving=False))
    qents = einput(query, level)
    """
    xtra_key = xtra_key or 'CONTACTS'
    structures = einput(query, 'S')
    if len(structures.values()) > 1:
        raise ValueError('Entities from multiple structures are not supported.')

src/p/y/pycogent-HEAD/cogent/struct/contact.py   pycogent(Download)
"""Classes and functions for computing and manipulating accessible 
surface areas (ASA)."""
 
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
    # if not specified otherwise the lattice is the first model
    lattice = model or structure[(0,)]
    lents = einput(lattice, level)
    lents_ids = lents.getData('getFull_id', forgiving=False, method=True)
    lcoords = array(lents.getData('coords', forgiving=False))
    qents = einput(query, level)
    """
    xtra_key = xtra_key or 'CONTACTS'
    structures = einput(query, 'S')
    if len(structures.values()) > 1:
        raise ValueError('Entities from multiple structures are not supported.')

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