def outputMolecule(singleMol, dataDir):
molecule = Molecule([], [])
for site in singleMol:
molecule.append(str(site.specie), site.coords)
xyzObj = XYZ(molecule)
os.chdir(dataDir)
os.system('mkdir singleMolecule')
xyzObj.write_file(dataDir + '/singleMolecule/singleMol.xyz')
def outputMolecule(singleMol, dataDir):
molecule = Molecule([], [])
singlemolpath = os.path.join(dataDir, 'singlemolecule')
for siteIndex in singleMol.keys():
molecule.append(str(singleMol[siteIndex].specie), singleMol[siteIndex].coords)
xyzObj = XYZ(molecule)
if "singleMol.xyz" in os.listdir(singlemolpath):
decision = None
print('You have one \'singleMol.xyz\' file inside the single molecule path.')
print('This previous file will be overwritten.')
while decision != 'Y' and decision != 'N':
decision = input('Do you want to proceed? Y for yes, N for no.')
if decision == 'Y':
xyzObj.write_file(os.path.join(singlemolpath, 'singleMol.xyz'))
print('The single molecule structure is saved under:', os.path.join(dataDir, 'singlemolecule.singleMol.xyz'))
elif decision == 'N':
print('The previous file is not changed. ')
sys.exit()
else:
print('Not eligible response!!!\n')
else:
xyzObj.write_file(os.path.join(singlemolpath, 'singleMol.xyz'))
print('The single molecule structure is saved under:', os.path.join(dataDir, 'singlemolecule/singleMol.xyz'))
def test_expand_structure(self):
molecule = ColorVonoroi.expand_structure(self.struc)
xyz = XYZ(molecule)
xyz.write_file(
"/Users/yao/Google Drive/mmtools/data/expaned_structure.xyz")
mol = Molecule(["C", "H", "H", "H", "H"], coords)
print("mol:", mol)
print("\n")
print("mol[0]:", mol[0])
print("mol[1]:", mol[1])
print("\n")
#断连index为0和1两个原子之间的化学键，有上面的输出可以看到这两个位c和H,但是很奇怪为何会出现如下的结果？可能与空间结构有关系？
for frag in mol.break_bond(0, 1):
print("frag:", frag)
print("\n")
print("neighbors of mol[0]:", mol.get_neighbors(mol[0], 3))
#得到分子中的共价键
print("covalent_bonds of:", mol.get_covalent_bonds())
print("\n")
#Creates a Structure from a Molecule by putting the Molecule in
#the center of a orthorhombic box. Useful for creating Structure
#for calculating molecules using periodic codes.
#通过把分子放在正交晶（orthorhombic）的盒子box里，从分子Molecule生存结构Structure。
#创建结构Structure，用于通过周期代码计算分子。
structure = mol.get_boxed_structure(10, 10, 10)
print("structure:", structure)
#xyz format是用来表示分子几何结构的文件，需要定分子中原子的坐标。
from pymatgen.io.xyz import XYZ
xyz = XYZ(mol)
xyz.write_file("methane.xyz")
