可用方法
1. 屏幕竖屏+常规截图
2. 借助csdn和浏览器插件
3. pycharm插件screenshot应用
方法1：系统-显示-更改方向
方法2：以下方代码为例
from rdkit import Chem
from rdkit.Chem import rdMolAlign
class PDBContainer:
"""Container for storage PDB information
Several operations with input structure as add/remove atoms, align against
reference structure and save to file using RDKit package.
Attributes:
atom_ids (dict): Relationship between PDB <residue name>/<atom name>
and atom ids of RDKit molecule representation
structure (rdkit.Chem.rdchem.Mol): RDKit container for structure
"""
def __init__(self, file, id_format):
"""Inititializing of container
Note: we disabled sanitizing step as well as removing of hydrogen atoms
to escape structural errors during reading PDB file. Also assumptions
about bonding of closely located also disabled.
Args:
file (str): File name of input structure
"""
self.id_format = id_format
self.atom_ids = {}
self.structure = Chem.rdmolfiles.MolFromPDBFile(file,
sanitize=False,
removeHs=False,
flavor=0,
proximityBonding=False)
self.update_atom_cache()
def update_atom_cache(self):
"""
Update state of atom_ids dictionary
"""
self.atom_ids = {}
for i, atom in enumerate(self.structure.GetAtoms()):
pdb_info = atom.GetPDBResidueInfo()
if pdb_info is not None:
atom_name = pdb_info.GetName().strip()
resi_name = pdb_info.GetResidueName().strip()
if self.id_format == 3:
resi_name = str(pdb_info.GetResidueNumber()) + " " + resi_name
resi_name = pdb_info.GetChainId().strip() + " " + resi_name
key = f"{resi_name} {atom_name}"
self.atom_ids[key] = i
def add_hetatm(self,
symbol,
coords=(0, 0, 0),
atom_name="D1",
res_name="LG1",
res_numb=1):
"""Add hetatm into structure
Args:
symbol (str): Any chemical element
coords (tuple, optional): 3D coordinate of added atom
atom_name (str, optional): PDB name of added atom
res_name (str, optional): PDB residue name of added atom
res_numb (int, optional): PDB residue number of added atom
Returns:
str: PDB <residue name>/<atom name> of added atom
"""
# prepare pdb information
pdb_info = Chem.AtomPDBResidueInfo()
pdb_info.SetName(atom_name)
pdb_info.SetResidueName(res_name)
pdb_info.SetResidueNumber(res_numb)
pdb_info.SetIsHeteroAtom(True)
# add pdb information into atom
atom = Chem.rdchem.Atom(symbol)
atom.SetMonomerInfo(pdb_info)
# add atom to structure
structure = Chem.rdchem.EditableMol(self.structure)
idx = structure.AddAtom(atom)
self.structure = structure.GetMol()
self.structure.GetConformer(0).SetAtomPosition(idx, coords)
a = self.structure.GetAtomWithIdx(idx)
pdb_info = a.GetPDBResidueInfo()
atom_name = pdb_info.GetName().strip()
resi_name = pdb_info.GetResidueName().strip()
if self.id_format == 3:
resi_name = str(pdb_info.GetResidueNumber()) + " " + resi_name
resi_name = pdb_info.GetChainId().strip() + " " + resi_name
key = f"{resi_name} {atom_name}"
self.update_atom_cache()
return key
def get_coordinates(self, atom_labels):
"""Return coordinates of given atoms
Args:
atom_labels (list): PDB labels of interested atoms
Returns:
list: coordinates of given atoms as nested list of X,Y,Z
coordinates
"""
x_coords, y_coords, z_coords = [], [], []
for label in atom_labels:
atom_id = self.atom_ids[label]
coord = self.structure.GetConformer(0).GetAtomPosition(atom_id)
x_coords.append(coord.x)
y_coords.append(coord.y)
z_coords.append(coord.z)
return x_coords, y_coords, z_coords
def align(self, reference, targ_atoms, ref_atoms, aln_iters):
"""Align structure against reference
Args:
reference (PDBContainer): Container of reference structure
targ_atoms (list): PDB atom labels of target using for alignment
ref_atoms (list): PDB atom labels of reference using for alignment
max_iters (int, optional): Max number of iterations for alignment
Returns:
float: RMSD between aligned targ_atoms and ref_atoms
"""
targ_dummy_atom_ids = []
targ_atom_ids = []
for i, atom in enumerate(targ_atoms):
if len(atom) > 1:
coords = self.get_coordinates(atom)
x_avg = sum(coords[0]) / len(coords[0])
y_avg = sum(coords[1]) / len(coords[1])
z_avg = sum(coords[2]) / len(coords[2])
label = self.add_hetatm("H",
coords=(x_avg, y_avg, z_avg),
atom_name=f"D{i}",
res_name="LG1",
res_numb=1)
atom_id = self.atom_ids[label]
targ_dummy_atom_ids.append(label)
else:
atom_id = self.atom_ids[atom[0]]
targ_atom_ids.append(atom_id)
ref_dummy_atom_ids = []
ref_atom_ids = []
for i, atom in enumerate(ref_atoms):
if len(atom) > 1:
coords = reference.get_coordinates(atom)
x_avg = sum(coords[0]) / len(coords[0])
y_avg = sum(coords[1]) / len(coords[1])
z_avg = sum(coords[2]) / len(coords[2])
label = reference.add_hetatm("H",
coords=(x_avg, y_avg, z_avg),
atom_name=f"D{i}",
res_name="LG1",
res_numb=1)
atom_id = reference.atom_ids[label]
ref_dummy_atom_ids.append(label)
else:
atom_id = reference.atom_ids[atom[0]]
ref_atom_ids.append(atom_id)
atom_map = list(zip(targ_atom_ids, ref_atom_ids))
rmsd = Chem.rdMolAlign.AlignMol(self.structure,
reference.structure,
atomMap=atom_map,
maxIters=aln_iters)
self.delete_atoms(targ_dummy_atom_ids)
reference.delete_atoms(ref_dummy_atom_ids)
return rmsd
def delete_atoms(self, atoms):
"""Delete set of atoms
Args:
atoms (list): PDB labels of deleting atoms
"""
structure = Chem.rdchem.EditableMol(self.structure)
ids = set([self.atom_ids[a] for a in atoms if a in self.atom_ids])
for idx in sorted(ids, reverse=True):
structure.RemoveAtom(idx)
for a in atoms:
if a in self.atom_ids:
del self.atom_ids[a]
self.structure = structure.GetMol()
self.update_atom_cache()
def merge(self, compound):
"""Copy atoms and bonds of some structure to self
Args:
compound (PDBContainer): Structure that will be pasted into given
structure
"""
structure = Chem.rdchem.EditableMol(self.structure)
atoms_ids = {}
coords = {}
for i, a in enumerate(compound.structure.GetAtoms()):
idx = structure.AddAtom(a)
atoms_ids[i] = idx
coords[idx] = compound.structure.GetConformer(0).GetAtomPosition(i)
# Because the output is PDB without any CONNECT lines
# we can skip adding of bonds
# for bond in compound.structure.GetBonds():
# bgn = atoms_ids[bond.GetBeginAtomIdx()]
# end = atoms_ids[bond.GetEndAtomIdx()]
# structure.AddBond(bgn, end, bond.GetBondType())
self.structure = structure.GetMol()
for idx, coord in coords.items():
self.structure.GetConformer(0).SetAtomPosition(idx, coord)
self.update_atom_cache()
def save(self, file):
"""Summary
Args:
file (TYPE): Description
"""
Chem.rdmolfiles.MolToPDBFile(self.structure, file, flavor=2)
def delete_hetHs(self):
"""Remove HETATM hydrogens from the structure
"""
hetHs = []
for i, a in enumerate(self.structure.GetAtoms()):
pdb_info = a.GetPDBResidueInfo()
is_hetero = pdb_info.GetIsHeteroAtom()
atom_name = pdb_info.GetName().strip()
resi_name = pdb_info.GetResidueName().strip()
if is_hetero and a.GetSymbol() == "H":
key = resi_name + " " + atom_name
hetHs.append(key)
self.delete_atoms(hetHs)
self.update_atom_cache()
def rename(self, old_resn, new_resn, new_chain=None, new_resi=None, het=False):
"""Replace residue name and number as well as chain label
Args:
old_resn (str): Old residue name
new_resn (str): New residue name
new_chain (str, optional): New chain name
new_resi (str, optional): New residue number
"""
for i, a in enumerate(self.structure.GetAtoms()):
pdb_info = a.GetPDBResidueInfo()
if het:
pdb_info.SetIsHeteroAtom(True)
resi_name = pdb_info.GetResidueName().strip()
if self.id_format == 3:
resi_name = str(pdb_info.GetResidueNumber()) + " " + resi_name
resi_name = pdb_info.GetChainId().strip() + " " + resi_name
if resi_name == old_resn:
pdb_info.SetResidueName(new_resn)
if new_chain:
pdb_info.SetChainId(new_chain)
if new_resi:
pdb_info.SetResidueNumber(new_resi)
self.update_atom_cache()
使用getfire插件截取整个页面，后对代码部分进行截取（csdn网页页尾有发文选项不能清除，详情见下，故选取部分页面截图此处不适用）
方法3：pycharm工具使用 code screenshots，点击安装，后对插件进行设置，尤其记得把scale调小为1，才能避免截图生成速度过慢，占用内存过大。padding那个选项笔者没有太过研究，如果友友们对此有更好的设置或更好的方法欢迎互相交流~~
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