Python from_pdb示例

示例#1

文件： test_forcefield.py 项目： sjbertolani/molecular-design-toolkit

def mol_from_pdb():
    mol = mdt.from_pdb('3aid')
    return mdt.Molecule(mol.chains['A'].residues['ARQ401'])

示例#2

文件： test_io.py 项目： xianqiangsun/molecular-design-toolkit

def test_from_pdb_mmcif_format():
    mol = mdt.from_pdb('3aid', usecif=True)
    assert mol.metadata.pdbid == '3aid'
    assert mol.metadata.sourceformat == 'mmcif'
    assert mol.metadata.sourceurl.split('.')[-1] == 'cif'
    assert mol.num_atoms == 1912

示例#3

文件： test_io.py 项目： xianqiangsun/molecular-design-toolkit

def test_mmcif_fallback_if_no_pdb_file():
    mol = mdt.from_pdb('4V5X')
    assert mol.metadata.pdbid.lower() == '4v5x'
    assert mol.metadata.sourceformat == 'mmcif'
    assert mol.metadata.sourceurl.split('.')[-1] == 'cif'

示例#4

文件： generate_residue_templates.py 项目： drancom/molecular-design-toolkit

#!/usr/bin/env python
""" A short script that assembles reasonable template geometries for standard amino acids
and DNA bases
"""
import moldesign as mdt
import json

protein = mdt.from_pdb('4F0A')
dna = mdt.build_bdna('ACTGAA')

residues = {}

for chain in protein.chains.values() + dna.chains.values():
    for residue in chain:
        if residue.type not in ('dna', 'protein'): continue
        if residue.type == 'dna' and (residue.is_5prime_end or residue.is_3prime_end):
            continue
        if residue.type == 'protein' and (residue.is_c_terminal or residue.is_n_terminal):
            continue

        residues[residue.resname] = mdt.clean_pdb(mdt.Molecule(residue))

residue_pdb = {k: m.write(format='pdb') for k,m in residues.iteritems()}

with open('residue_templates.json', 'w') as outfile:
    json.dump(residue_pdb, outfile)

示例#5

文件： test_io.py 项目： xianqiangsun/molecular-design-toolkit

def test_from_pdb_pdb_format():
    mol = mdt.from_pdb('3aid')
    assert mol.metadata.pdbid == '3aid'
    assert mol.metadata.sourceformat == 'pdb'
    assert mol.num_atoms == 1912

示例#6

def pdb3aid():
    mol = mdt.from_pdb('3AID')
    return mol

示例#7

#!/usr/bin/env python
""" A short script that assembles reasonable template geometries for standard amino acids
and DNA bases
"""
import moldesign as mdt
import json

protein = mdt.from_pdb('4F0A')
dna = mdt.build_bdna('ACTGAA')

residues = {}

for chain in list(protein.chains.values()) + list(dna.chains.values()):
    for residue in chain:
        if residue.type not in ('dna', 'protein'): continue
        if residue.type == 'dna' and (residue.is_5prime_end or residue.is_3prime_end):
            continue
        if residue.type == 'protein' and (residue.is_c_terminal or residue.is_n_terminal):
            continue

        residues[residue.resname] = mdt.clean_pdb(mdt.Molecule(residue))

residue_pdb = {k: m.write(format='pdb') for k,m in residues.items()}

with open('residue_templates.json', 'w') as outfile:
    json.dump(residue_pdb, outfile)

示例#8

文件： object_fixtures.py 项目： drancom/molecular-design-toolkit

def pdb3aid():
    mol = mdt.from_pdb('3AID')
    return mol

示例#9

文件： test_mm.py 项目： drancom/molecular-design-toolkit

def protein_default_amber_forcefield():
    mol = mdt.from_pdb('1YU8')
    newmol = mdt.assign_forcefield(mol)
    newmol.set_energy_model(mdt.models.ForceField)
    return newmol

示例#10

def from_pdb(pdbcode):
    import moldesign as mdt
    mol = mdt.from_pdb(pdbcode)
    mol.write('out.pkl')

示例#11

文件： test_io.py 项目： Autodesk/molecular-design-toolkit

def test_mmcif_fallback_if_no_pdb_file():
    mol = mdt.from_pdb('4V5X')
    assert mol.metadata.pdbid.lower() == '4v5x'
    assert mol.metadata.sourceformat == 'mmcif'
    assert mol.metadata.sourceurl.split('.')[-1] == 'cif'

示例#12

文件： test_io.py 项目： Autodesk/molecular-design-toolkit

def test_from_pdb_mmcif_format():
    mol = mdt.from_pdb('3aid', usecif=True)
    assert mol.metadata.pdbid == '3aid'
    assert mol.metadata.sourceformat == 'mmcif'
    assert mol.metadata.sourceurl.split('.')[-1] == 'cif'
    assert mol.num_atoms == 1912

示例#13

文件： test_io.py 项目： Autodesk/molecular-design-toolkit

def test_from_pdb_pdb_format():
    mol = mdt.from_pdb('3aid')
    assert mol.metadata.pdbid == '3aid'
    assert mol.metadata.sourceformat == 'pdb'
    assert mol.num_atoms == 1912

示例#14

文件： test_data_structures.py 项目： shiva16/molecular-design-toolkit

def pdb3aid():
    #FPATH = '../notebooks/data/3AID.pdb'
    #assert os.path.exists(FPATH)
    mol = mdt.from_pdb('3AID')
    return mol