Add a from_csd function

[qzhu2017]

If the CSD python is available, we can import the structure from CSD

[qzhu2017]

import warnings
warnings.filterwarnings('ignore')

from pyxtal import pyxtal
c = pyxtal(molecular=True)

for csd in [#'ACSALA', 'TROXAN', 'TRIZIN', 'HXMTAM', 'PYRZIN', 
            #'PYRZOL', 'CYHEXO', 'CYTSIN', 'ADAMAN01', 'IMAZOL01', 
            #'URACIL', 'ACETAC', 'CYANAM01', 'FORMAM', 'SUCACB02',
            'ECARBM01', 'XAFQAZ', 'KONTIQ09', 'XATJOT', 'XAFQON']:
    c.from_CSD(csd)
    print(c)

------Crystal from CSD: ECARBM01------
Dimension: 3
Composition: [CCOC(N)=O]2
Group: P-1 (2)
triclinic lattice:   5.0510   7.0110   7.5430  78.6300  75.4200  76.6500
Wyckoff sites:
	H7C3N1O2     @ [ 0.0448  0.5792  0.2108]  WP [2i] Site [1] Euler [   0.0    0.0    0.0]

------Crystal from CSD: XAFQAZ------
Dimension: 3
Composition: [OC(=O)c1cc(cc(c1)N(=O)=O)N(=O)=O]4[Cc1ccc2N3CN(Cc2c1)c1ccc(C)cc1C3]4
Group: P21/c (14)
monoclinic lattice:  10.4240  27.5781   8.1258  90.0000 109.5640  90.0000
Wyckoff sites:
	H4C7N2O6     @ [ 0.8215  0.0296  0.3667]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]
	H18C17N2     @ [ 0.4518  0.1954  0.4124]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]

------Crystal from CSD: KONTIQ09------
Dimension: 3
Composition: [OC(=O)c1cc(O)c(O)c(O)c1]4[O]4
Group: P21/c (14)
monoclinic lattice:   9.7573   3.5579  21.5170  90.0000  91.3380  90.0000
Wyckoff sites:
	H6C7O5       @ [ 0.6927  0.9477  0.1405]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]
	H2O1         @ [ 0.8928  0.5034  0.9280]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]

------Crystal from CSD: XATJOT------
Dimension: 3
Composition: [[nH+]1cccc2cccnc12]4[OC(=O)C=CC(=O)[O-]]4
Group: Pca21 (29)
orthorhombic lattice:  23.5010   3.7141  12.6535  90.0000  90.0000  90.0000
Wyckoff sites:
	H7C8N2       @ [ 0.2272  0.3356  0.8232]  WP [4a] Site [1] Euler [   0.0    0.0    0.0]
	H3C4O4       @ [ 0.9672  0.0993  0.5601]  WP [4a] Site [1] Euler [   0.0    0.0    0.0]
[19:50:26] Warning: molecule is tagged as 3D, but all Z coords are zero
[19:50:26] Warning: molecule is tagged as 3D, but all Z coords are zero

------Crystal from CSD: XAFQON------
Dimension: 3
Composition: [[Cl-]]4[NC(=[NH2+])SC=CC(O)=O]4[O]4
Group: P21/c (14)
monoclinic lattice:   3.9906  21.2366  10.1014  90.0000  97.8331  90.0000
Wyckoff sites:
	Cl1          @ [ 0.0512  0.7257  0.2944]  WP [4e] Site [1]
	H7C4S1N2O2   @ [ 0.7169  0.9374  0.6596]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]
	H2O1         @ [ 0.9830  0.6826  0.5663]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]

[qzhu2017]

Todo:

• Enable function to extract unique CSD_code from a given family
• Enable the read of co-crystal d0ff9bb

[qzhu2017]

Some structures cannot match the original one after loading. Needs to check!!!

[qzhu2017]

Fully debugged at 15de1dc

To run more tests with different csd structures

[qzhu2017]

• if smiles returns duplicates, merge it to one.