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src/c/o/cogent-1.5.3/cogent/core/entity.py   cogent(Download)
from cogent.core.annotation import SimpleVariable
from numpy import (sqrt, arctan2, power, array, mean, sum)
from cogent.data.protein_properties import AA_NAMES, AA_ATOM_BACKBONE_ORDER, \
                                   AA_ATOM_REMOTE_ORDER, AREAIMOL_VDW_RADII, \
                                   DEFAULT_AREAIMOL_VDW_RADIUS, AA_NAMES_3to1
    def residue(res_id1, res_id2):
        r1, r2 = 1, 1
        if res_id1 in AA_NAMES: r1 = 2
        if res_id1 in HOH_NAMES: r1 = 0
        if res_id2 in AA_NAMES: r2 = 2
    def getSeq(self, moltype ='PROTEIN'):
        """Returns a Sequence object from the ordered residues.
        The "seq_type" determines allowed residue names."""
        if moltype == 'PROTEIN':
            valid_names = AA_NAMES

src/p/y/pycogent-HEAD/cogent/core/entity.py   pycogent(Download)
from cogent.core.annotation import SimpleVariable
from numpy import (sqrt, arctan2, power, array, mean, sum)
from cogent.data.protein_properties import AA_NAMES, AA_ATOM_BACKBONE_ORDER, \
                                   AA_ATOM_REMOTE_ORDER, AREAIMOL_VDW_RADII, \
                                   DEFAULT_AREAIMOL_VDW_RADIUS, AA_NAMES_3to1
    def residue(res_id1, res_id2):
        r1, r2 = 1, 1
        if res_id1 in AA_NAMES: r1 = 2
        if res_id1 in HOH_NAMES: r1 = 0
        if res_id2 in AA_NAMES: r2 = 2
    def getSeq(self, moltype ='PROTEIN'):
        """Returns a Sequence object from the ordered residues.
        The "seq_type" determines allowed residue names."""
        if moltype == 'PROTEIN':
            valid_names = AA_NAMES

src/c/o/cogent-1.5.3/cogent/format/pdb.py   cogent(Download)
 
from cogent.struct.selection import einput
from cogent.data.protein_properties import AA_NAMES
from cogent.parse.pdb import dict2pdb, dict2ter
 
    for atom in atoms.sortedvalues():
        fields = atom.getDict()
        if (old_fields['chain_id'] != fields['chain_id']) and old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
                coords.append(dict2ter(old_fields))
        if (old_fields['model'] != fields['model']) and old_fields['model'] != '': # model can be 0 :)
                if old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
        coords.append(dict2pdb(fields))
        old_fields = fields
    if fields['res_name'] in AA_NAMES:
        coords.append(dict2ter(fields))
    coords.append('ENDMDL\n')

src/p/y/pycogent-HEAD/cogent/format/pdb.py   pycogent(Download)
 
from cogent.struct.selection import einput
from cogent.data.protein_properties import AA_NAMES
from cogent.parse.pdb import dict2pdb, dict2ter
 
    for atom in atoms.sortedvalues():
        fields = atom.getDict()
        if (old_fields['chain_id'] != fields['chain_id']) and old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
                coords.append(dict2ter(old_fields))
        if (old_fields['model'] != fields['model']) and old_fields['model'] != '': # model can be 0 :)
                if old_fields['chain_id'] and old_fields['res_name'] in AA_NAMES:
        coords.append(dict2pdb(fields))
        old_fields = fields
    if fields['res_name'] in AA_NAMES:
        coords.append(dict2ter(fields))
    coords.append('ENDMDL\n')

src/c/o/cogent-1.5.3/cogent/parse/pdb.py   cogent(Download)
from numpy import array, linalg
 
from cogent.data.protein_properties import AA_NAMES
from cogent.core.entity import StructureBuilder, ConstructionWarning, ConstructionError
 

src/p/y/pycogent-HEAD/cogent/parse/pdb.py   pycogent(Download)
from numpy import array, linalg
 
from cogent.data.protein_properties import AA_NAMES
from cogent.core.entity import StructureBuilder, ConstructionWarning, ConstructionError