- MOFkit
- Linux
- GCC-5.4.0, need to support C ++ 11 and above
- Make
- compile all files -
makeormake all - compile specified function(
rm_mof_solvents/find_space_groups/in_cell/ICSD_classify/CSD_classify/format) -make func - delete executable -
make clean
- The program
Find Space Groupsis based on spglib. To use this function, you need to install and configure spglib.$ git clone https://github.com/atztogo/spglib.git $ module load gcc/5.4.0 (load gcc environment, this command only works if you use module tool in supercomputer/cluster) $ module load cmake/3.5.1 (load cmake environment) $ cd spglib $ mkdir _build $ cd _build $ cmake .. $ make $ make install
module load gcc/5.4.0
module load LAPACK/3.8.0-gcc-5.4.0
g++ ./src/icsd_classify_fp.cpp -o icsd_classify_fp -std=c++11 -L/WORK/app/LAPACK/3.8.0-gcc-5.4.0/lib64 -llapack -lblas -ltmglib
The program is a tool to remove solvents from MOF.
usage: ./bin/rm_mof_solvents --cif_in=string [options] ...
options:
-i, --cif_in input MOF cif file (string)
-o, --output_path output filepath (string [=])
-f, --force remove solvent molecules anyway
-?, --help print this message
$ ./bin/rm_mof_solvents -i ./examples/cod/ABAGAO.MOF_subset.cif -o ./examples/result
log
Parsing the cif file - ABAGAO.MOF_subset.cif
Getting some known resources...
Building base cell...
The number of bonded atom pairs is 80
Looking for solvent in ABAGAO.MOF_subset.cif
The calculated solvent molecule to be screened is [ H2O<known> ]
The MOF framework is [ C14CuH13N3O4 ]
Exporting result...
Export file ./example/result/ABAGAO_clean.cif successfully!
./examples/result/ABAGAO_clean.cif
#######################################################################
#
# Cambridge Crystallographic Data Centre
# CCDC
#
#######################################################################
#
# If this CIF has been generated from an entry in the Cambridge
# Structural Database, then it will include bibliographic, chemical,
# crystal, experimental, refinement or atomic coordinate data resulting
# from the CCDC's data processing and validation procedures.
#
#######################################################################
data_CSD_CIF_ABAGAO
_audit_creation_date 2016-11-22
_audit_creation_method CSD-ConQuest-V1
_database_code_CSD ABAGAO
_database_code_depnum_ccdc_archive 'CCDC 1498689'
_chemical_formula_sum 'C14 H15 Cu1 N3 O5'
_chemical_formula_moiety
;
(C14 H13 Cu1 N3 O4)n,H2 O1
;
_journal_coden_Cambridge 580
_journal_volume 119
_journal_year 2016
_journal_page_first 563
_journal_name_full 'Polyhedron '
loop_
_publ_author_name
"A.Timothy Royappa"
"A.D.Royappa"
"R.F.Moral"
"A.L.Rheingold"
"R.J.Papoular"
"D.M.Blum"
"T.Q.Duong"
"J.R.Stepherson"
"O.D.Vu"
"Banghao Chen"
"M.R.Suchomel"
"J.A.Golen"
"G.Andre"
"N.Kourkoumelis"
"A.D.Mercer"
"A.M.Pekarek"
"D.C.Kelly"
_chemical_name_systematic
;
catena-[(\m-ethanedioato)-(1-(pyridin-2-yl)-N-((pyridin-2-yl)methyl)methanamin
e)-copper(ii) monohydrate]
;
_chemical_name_common
;
catena-[(mu-oxalato)-(di-(2-picolyl)amine)-copper(ii) monohydrate]
;
_cell_volume 2959.318
_exptl_crystal_colour 'blue'
_exptl_crystal_density_diffrn 1.656
_exptl_crystal_description 'block'
_diffrn_ambient_temperature 100
#These two values have been output from a single CSD field.
_refine_ls_R_factor_gt 0.0362
_refine_ls_wR_factor_gt 0.0362
_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_H-M 'P b c a'
_symmetry_Int_Tables_number 61
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
3 -x,1/2+y,1/2-z
4 1/2+x,1/2-y,-z
5 -x,-y,-z
6 -1/2+x,y,-1/2-z
7 x,-1/2-y,-1/2+z
8 -1/2-x,-1/2+y,z
_cell_length_a 18.5834(8)
_cell_length_b 8.3215(4)
_cell_length_c 19.1366(7)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 8
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
Cu 1.32
N 0.68
O 0.68
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Cu1 Cu 0.56165(2) 0.43062(4) 0.28700(2)
O1 O 0.64917(12) 0.5891(2) 0.34381(10)
O2 O 0.53447(12) 0.6511(2) 0.26192(10)
O3 O 0.65868(13) 0.8518(3) 0.36868(11)
O4 O 0.54528(12) 0.9114(2) 0.28233(11)
N1 N 0.50185(14) 0.4072(3) 0.37356(12)
N2 N 0.62594(15) 0.3848(3) 0.20563(12)
N3 N 0.60376(14) 0.2231(3) 0.32100(12)
H1 H 0.57550 0.13460 0.30130
C1 C 0.63138(17) 0.7346(4) 0.33832(15)
C2 C 0.59693(18) 0.2173(4) 0.39779(15)
H2 H 0.63600 0.27650 0.41940
H3 H 0.59900 0.10680 0.41390
C3 C 0.52577(18) 0.2912(4) 0.41742(15)
C4 C 0.67725(18) 0.2740(4) 0.21948(16)
C5 C 0.43969(19) 0.4820(4) 0.38716(16)
H4 H 0.42400 0.56200 0.35680
C6 C 0.56533(17) 0.7708(4) 0.29063(15)
C7 C 0.62106(19) 0.4481(4) 0.14073(16)
H5 H 0.58560 0.52410 0.13150
C8 C 0.39805(19) 0.4446(4) 0.44456(16)
H6 H 0.35500 0.49840 0.45300
C9 C 0.4219(2) 0.3252(4) 0.48922(17)
H7 H 0.39460 0.29690 0.52810
C10 C 0.67760(17) 0.2119(4) 0.29343(15)
H8 H 0.69380 0.10110 0.29430
H9 H 0.71010 0.27540 0.32190
C11 C 0.6675(2) 0.4028(4) 0.08760(17)
H10 H 0.66340 0.44730 0.04320
C12 C 0.4860(2) 0.2482(4) 0.47595(16)
H11 H 0.50260 0.16830 0.50590
C13 C 0.72500(19) 0.2248(4) 0.16824(18)
H12 H 0.76010 0.14840 0.17820
C14 C 0.7199(2) 0.2905(5) 0.10193(18)
H13 H 0.75190 0.25890 0.06710
Cu1B Cu 0.43835(2) 0.93062(4) 0.21300(2)
O4B O 0.45472(12) 0.4114(2) 0.21767(11)
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
Cu1 O1 2.359 1_555 1_555
O1 C1 1.259 1_555 1_555
O2 Cu1 1.963 1_555 1_555
O3 C1 1.243 1_555 1_555
O4 C6 1.238 1_555 1_555
N1 Cu1 2.004 1_555 1_555
N2 Cu1 1.999 1_555 1_555
N3 Cu1 2.004 1_555 1_555
H1 N3 0.980 1_555 1_555
C1 C6 1.559 1_555 1_555
C2 N3 1.476 1_555 1_555
H2 C2 0.970 1_555 1_555
H3 C2 0.971 1_555 1_555
C3 N1 1.354 1_555 1_555
C4 N2 1.353 1_555 1_555
C5 N1 1.338 1_555 1_555
H4 C5 0.930 1_555 1_555
C6 O2 1.274 1_555 1_555
C7 N2 1.352 1_555 1_555
H5 C7 0.930 1_555 1_555
C8 C5 1.379 1_555 1_555
H6 C8 0.931 1_555 1_555
C9 C8 1.383 1_555 1_555
H7 C9 0.931 1_555 1_555
C10 N3 1.473 1_555 1_555
H8 C10 0.970 1_555 1_555
H9 C10 0.970 1_555 1_555
C11 C7 1.386 1_555 1_555
H10 C11 0.930 1_555 1_555
C12 C3 1.389 1_555 1_555
H11 C12 0.930 1_555 1_555
C13 C4 1.384 1_555 1_555
H12 C13 0.931 1_555 1_555
C14 C11 1.377 1_555 1_555
H13 C14 0.931 1_555 1_555
Cu1B O4 2.395 1_555 1_555
O4B Cu1 2.395 1_555 1_555
C2 C3 1.506 1_555 1_555
C4 C10 1.507 1_555 1_555
C9 C12 1.376 1_555 1_555
C13 C14 1.385 1_555 1_555
#END
The program is used to obtain the space group information in the cif file.(base on spglib)
usage: ./bin/find_space_groups --input=string [options] ...
options:
-i, --input input cif file name (string)
-v, --version return the version of spglib
-w, --why this method is used to see roughly why spglib failed
-s, --spacegroup internatioanl space group short symbol and number are obtained as a string
-m, --symmetry symmetry operations are obtained as a dictionary
-r, --refine standardized crystal structure is obtained as a tuple of lattice (a 3x3 numpy array), atomic scaled positions (a numpy array of [number_of_atoms,3]), and atomic numbers (a 1D numpy array) that are symmetrized following space group type.
-p, --primitive is found, lattice parameters (a 3x3 numpy array), scaled positions (a numpy array of [number_of_atoms,3]), and atomic numbers (a 1D numpy array) is returned.
-d, --dataset dataset,cell and symprec;angle_tolerance;hall_number;number;choice;transformation_matrix;origin shift;wyckoffs;site_symmetry_symbols;equivalent_atoms;mapping_to_primitive;rotations and translations;pointgroup;std_lattice;std_positions;std_types;std_rotation_matrix;std_mapping_to_primitive
-c, --symmfdset A set of crystallographic symmetry operations corresponding to hall_number is returned by a dictionary where rotation parts and translation parts are accessed by the keys rotations and translations, respectively.
-f, --spgfdset This function allows to directly access to the space-group-type database in spglib (spg_database.c). A dictionary is returned. To specify the space group type with a specific choice, hall_number is used.
-n, --niggli Niggli reduction is achieved using this method.
-l, --delaunay Delaunay reduction is achieved using this method.
-k, --irrkpoints Irreducible k-points are obtained from a sampling mesh of k-points
-?, --help print this message
$ ./bin/find_space_groups -i ./examples/cod/WAJZUE.cif -s
Parsing the cif file - WAJZUE.cif
Getting some known resources...
The space group is: Pbca 61
$ ./bin/find_space_groups -i ./examples/in-cell/ABETIN_clean.cif -s
Parsing the cif file - ABETIN_clean.cif
Getting some known resources...
The space group is: I4_1/acd 142
-
error while loading shared libraries: libsymspg.so.1: cannot open shared object file: No such file or directory because the program will default to
/lib64/libsymspg.sonot in/lib64/.Therefore, the following commands need to be added to allow the program to find the library in the directory of the instruction.export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./include/spglib/_buildspglib path please change according to the actual
This program will obtain its in-cell structure based on the space group information of the unit cell.
usage: ./bin/in_cell --input_path=string --output_path=string [options] ...
options:
-i, --input_path input MOF cif file (string)
-o, --output_path output file path (string)
-?, --help print this message
$ ./bin/in_cell -i ./examples/cod/WAJZUE.cif -o ./examples/result
log
Getting some known resources...
Parsing the cif file - WAJZUE.cif
Exporting in-cell result...
Export file ./examples/result/WAJZUE_in_cell.cif successfully!
./examples/result/WAJZUE_in_cell.cif
#######################################################################
#
# Cambridge Crystallographic Data Centre
# CCDC
#
#######################################################################
#
# If this CIF has been generated from an entry in the Cambridge
# Structural Database, then it will include bibliographic, chemical,
# crystal, experimental, refinement or atomic coordinate data resulting
# from the CCDC's data processing and validation procedures.
#
#######################################################################
data_WAJZUE
_symmetry_space_group_name_H-M "P 1"
_symmetry_int_tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
_cell_length_a 11.489(2)
_cell_length_b 22.733(5)
_cell_length_c 8.156(2)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 2130.18
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
Br1 Br 0.06709 0.19491 0.88381 1.000
Br2 Br 0.06709 0.30509 0.38381 1.000
Br3 Br 0.43291 0.69491 0.88381 1.000
Br4 Br 0.43291 0.80509 0.38381 1.000
Br5 Br 0.56709 0.19491 0.61619 1.000
Br6 Br 0.56709 0.30509 0.11619 1.000
Br7 Br 0.93291 0.69491 0.61619 1.000
Br8 Br 0.93291 0.80509 0.11619 1.000
C1 C 0.0042 0.63258 0.4821 1.000
C2 C 0.0042 0.86742 0.9821 1.000
C3 C 0.0513 0.6596 0.3253 1.000
C4 C 0.0513 0.8404 0.8253 1.000
C5 C 0.0535 0.5712 0.7403 1.000
C6 C 0.0535 0.9288 0.2403 1.000
C7 C 0.059 0.6075 0.9012 1.000
C8 C 0.059 0.8925 0.4012 1.000
C9 C 0.0987 0.59869 0.578 1.000
C10 C 0.0987 0.90131 0.078 1.000
C11 C 0.1417 0.52908 0.8228 1.000
C12 C 0.1417 0.97092 0.3228 1.000
C13 C 0.1596 0.6968 0.3524 1.000
C14 C 0.1596 0.8032 0.8524 1.000
C15 C 0.1607 0.5697 0.964 1.000
C16 C 0.1607 0.9303 0.464 1.000
C17 C 0.2083 0.63515 0.5989 1.000
C18 C 0.2083 0.86485 0.0989 1.000
C19 C 0.2467 0.161 0.4388 1.000
C20 C 0.2467 0.339 0.9388 1.000
C21 C 0.2533 0.661 0.4388 1.000
C22 C 0.2533 0.839 0.9388 1.000
C23 C 0.2917 0.13515 0.5989 1.000
C24 C 0.2917 0.36485 0.0989 1.000
C25 C 0.3393 0.0697 0.964 1.000
C26 C 0.3393 0.4303 0.464 1.000
C27 C 0.3404 0.1968 0.3524 1.000
C28 C 0.3404 0.3032 0.8524 1.000
C29 C 0.3583 0.02908 0.8228 1.000
C30 C 0.3583 0.47092 0.3228 1.000
C31 C 0.4013 0.09869 0.578 1.000
C32 C 0.4013 0.40131 0.078 1.000
C33 C 0.441 0.1075 0.9012 1.000
C34 C 0.441 0.3925 0.4012 1.000
C35 C 0.4465 0.0712 0.7403 1.000
C36 C 0.4465 0.4288 0.2403 1.000
C37 C 0.4487 0.1596 0.3253 1.000
C38 C 0.4487 0.3404 0.8253 1.000
C39 C 0.4958 0.13258 0.4821 1.000
C40 C 0.4958 0.36742 0.9821 1.000
C41 C 0.5042 0.63258 0.0179 1.000
C42 C 0.5042 0.86742 0.5179 1.000
C43 C 0.5513 0.6596 0.1747 1.000
C44 C 0.5513 0.8404 0.6747 1.000
C45 C 0.5535 0.5712 0.7597 1.000
C46 C 0.5535 0.9288 0.2597 1.000
C47 C 0.559 0.6075 0.5988 1.000
C48 C 0.559 0.8925 0.0988 1.000
C49 C 0.5987 0.59869 0.922 1.000
C50 C 0.5987 0.90131 0.422 1.000
C51 C 0.6417 0.52908 0.6772 1.000
C52 C 0.6417 0.97092 0.1772 1.000
C53 C 0.6596 0.6968 0.1476 1.000
C54 C 0.6596 0.8032 0.6476 1.000
C55 C 0.6607 0.5697 0.536 1.000
C56 C 0.6607 0.9303 0.036 1.000
C57 C 0.7083 0.63515 0.9011 1.000
C58 C 0.7083 0.86485 0.4011 1.000
C59 C 0.7467 0.161 0.0612 1.000
C60 C 0.7467 0.339 0.5612 1.000
C61 C 0.7533 0.661 0.0612 1.000
C62 C 0.7533 0.839 0.5612 1.000
C63 C 0.7917 0.13515 0.9011 1.000
C64 C 0.7917 0.36485 0.4011 1.000
C65 C 0.8393 0.0697 0.536 1.000
C66 C 0.8393 0.4303 0.036 1.000
C67 C 0.8404 0.1968 0.1476 1.000
C68 C 0.8404 0.3032 0.6476 1.000
C69 C 0.8583 0.02908 0.6772 1.000
C70 C 0.8583 0.47092 0.1772 1.000
C71 C 0.9013 0.09869 0.922 1.000
C72 C 0.9013 0.40131 0.422 1.000
C73 C 0.941 0.1075 0.5988 1.000
C74 C 0.941 0.3925 0.0988 1.000
C75 C 0.9465 0.0712 0.7597 1.000
C76 C 0.9465 0.4288 0.2597 1.000
C77 C 0.9487 0.1596 0.1747 1.000
C78 C 0.9487 0.3404 0.6747 1.000
C79 C 0.9958 0.13258 0.0179 1.000
C80 C 0.9958 0.36742 0.5179 1.000
H1 H 0.0086 0.1839 0.2238 1.000
H2 H 0.0086 0.3161 0.7238 1.000
H3 H 0.0107 0.1042 0.5324 1.000
H4 H 0.0107 0.3958 0.0324 1.000
H5 H 0.0524 0.0116 0.8466 1.000
H6 H 0.0524 0.4884 0.3466 1.000
H7 H 0.0571 0.1046 0.048 1.000
H8 H 0.0571 0.3954 0.548 1.000
H9 H 0.0696 0.6283 0.2485 1.000
H10 H 0.0696 0.8717 0.7485 1.000
H11 H 0.0796 0.6484 0.884 1.000
H12 H 0.0796 0.8516 0.384 1.000
H13 H 0.14 0.7309 0.4182 1.000
H14 H 0.14 0.7691 0.9182 1.000
H15 H 0.1466 0.5519 0.0702 1.000
H16 H 0.1466 0.9481 0.5702 1.000
H17 H 0.1801 0.186 0.4613 1.000
H18 H 0.1801 0.314 0.9613 1.000
H19 H 0.1889 0.7105 0.2476 1.000
H20 H 0.1889 0.7895 0.7476 1.000
H21 H 0.1925 0.667 0.6749 1.000
H22 H 0.1925 0.833 0.1749 1.000
H23 H 0.1966 0.5474 0.4405 1.000
H24 H 0.1966 0.9526 0.9405 1.000
H25 H 0.2211 0.1294 0.3674 1.000
H26 H 0.2211 0.3706 0.8674 1.000
H27 H 0.2315 0.1107 0.6467 1.000
H28 H 0.2315 0.3893 0.1467 1.000
H29 H 0.2353 0.5897 0.9618 1.000
H30 H 0.2353 0.9103 0.4618 1.000
H31 H 0.2647 0.0897 0.9618 1.000
H32 H 0.2647 0.4103 0.4618 1.000
H33 H 0.2685 0.6107 0.6467 1.000
H34 H 0.2685 0.8893 0.1467 1.000
H35 H 0.2789 0.6294 0.3674 1.000
H36 H 0.2789 0.8706 0.8674 1.000
H37 H 0.3034 0.0474 0.4405 1.000
H38 H 0.3034 0.4526 0.9405 1.000
H39 H 0.3075 0.167 0.6749 1.000
H40 H 0.3075 0.333 0.1749 1.000
H41 H 0.3111 0.2105 0.2476 1.000
H42 H 0.3111 0.2895 0.7476 1.000
H43 H 0.3199 0.686 0.4613 1.000
H44 H 0.3199 0.814 0.9613 1.000
H45 H 0.3534 0.0519 0.0702 1.000
H46 H 0.3534 0.4481 0.5702 1.000
H47 H 0.36 0.2309 0.4182 1.000
H48 H 0.36 0.2691 0.9182 1.000
H49 H 0.4204 0.1484 0.884 1.000
H50 H 0.4204 0.3516 0.384 1.000
H51 H 0.4304 0.1283 0.2485 1.000
H52 H 0.4304 0.3717 0.7485 1.000
H53 H 0.4429 0.6046 0.048 1.000
H54 H 0.4429 0.8954 0.548 1.000
H55 H 0.4476 0.5116 0.8466 1.000
H56 H 0.4476 0.9884 0.3466 1.000
H57 H 0.4893 0.6042 0.5324 1.000
H58 H 0.4893 0.8958 0.0324 1.000
H59 H 0.4914 0.6839 0.2238 1.000
H60 H 0.4914 0.8161 0.7238 1.000
H61 H 0.5086 0.1839 0.2762 1.000
H62 H 0.5086 0.3161 0.7762 1.000
H63 H 0.5107 0.1042 0.9676 1.000
H64 H 0.5107 0.3958 0.4676 1.000
H65 H 0.5524 0.0116 0.6534 1.000
H66 H 0.5524 0.4884 0.1534 1.000
H67 H 0.5571 0.1046 0.452 1.000
H68 H 0.5571 0.3954 0.952 1.000
H69 H 0.5696 0.6283 0.2515 1.000
H70 H 0.5696 0.8717 0.7515 1.000
H71 H 0.5796 0.6484 0.616 1.000
H72 H 0.5796 0.8516 0.116 1.000
H73 H 0.64 0.7309 0.0818 1.000
H74 H 0.64 0.7691 0.5818 1.000
H75 H 0.6466 0.5519 0.4298 1.000
H76 H 0.6466 0.9481 0.9298 1.000
H77 H 0.6801 0.186 0.0387 1.000
H78 H 0.6801 0.314 0.5387 1.000
H79 H 0.6889 0.7105 0.2524 1.000
H80 H 0.6889 0.7895 0.7524 1.000
H81 H 0.6925 0.667 0.8251 1.000
H82 H 0.6925 0.833 0.3251 1.000
H83 H 0.6966 0.5474 0.0595 1.000
H84 H 0.6966 0.9526 0.5595 1.000
H85 H 0.7211 0.1294 0.1326 1.000
H86 H 0.7211 0.3706 0.6326 1.000
H87 H 0.7315 0.1107 0.8533 1.000
H88 H 0.7315 0.3893 0.3533 1.000
H89 H 0.7353 0.5897 0.5382 1.000
H90 H 0.7353 0.9103 0.0382 1.000
H91 H 0.7647 0.0897 0.5382 1.000
H92 H 0.7647 0.4103 0.0382 1.000
H93 H 0.7685 0.6107 0.8533 1.000
H94 H 0.7685 0.8893 0.3533 1.000
H95 H 0.7789 0.6294 0.1326 1.000
H96 H 0.7789 0.8706 0.6326 1.000
H97 H 0.8034 0.0474 0.0595 1.000
H98 H 0.8034 0.4526 0.5595 1.000
H99 H 0.8075 0.167 0.8251 1.000
H100 H 0.8075 0.333 0.3251 1.000
H101 H 0.8111 0.2105 0.2524 1.000
H102 H 0.8111 0.2895 0.7524 1.000
H103 H 0.8199 0.686 0.0387 1.000
H104 H 0.8199 0.814 0.5387 1.000
H105 H 0.8534 0.0519 0.4298 1.000
H106 H 0.8534 0.4481 0.9298 1.000
H107 H 0.86 0.2309 0.0818 1.000
H108 H 0.86 0.2691 0.5818 1.000
H109 H 0.9204 0.1484 0.616 1.000
H110 H 0.9204 0.3516 0.116 1.000
H111 H 0.9304 0.1283 0.2515 1.000
H112 H 0.9304 0.3717 0.7515 1.000
H113 H 0.9429 0.6046 0.452 1.000
H114 H 0.9429 0.8954 0.952 1.000
H115 H 0.9476 0.5116 0.6534 1.000
H116 H 0.9476 0.9884 0.1534 1.000
H117 H 0.9893 0.6042 0.9676 1.000
H118 H 0.9893 0.8958 0.4676 1.000
H119 H 0.9914 0.6839 0.2762 1.000
H120 H 0.9914 0.8161 0.7762 1.000
O1 O 0.0571 0.04482 0.7805 1.000
O2 O 0.0571 0.45518 0.2805 1.000
O3 O 0.1199 0.54806 0.4732 1.000
O4 O 0.1199 0.95194 0.9732 1.000
O5 O 0.1689 0.02088 0.2969 1.000
O6 O 0.1689 0.47912 0.7969 1.000
O7 O 0.3311 0.52088 0.2969 1.000
O8 O 0.3311 0.97912 0.7969 1.000
O9 O 0.3801 0.04806 0.4732 1.000
O10 O 0.3801 0.45194 0.9732 1.000
O11 O 0.4429 0.54482 0.7805 1.000
O12 O 0.4429 0.95518 0.2805 1.000
O13 O 0.5571 0.04482 0.7195 1.000
O14 O 0.5571 0.45518 0.2195 1.000
O15 O 0.6199 0.54806 0.0268 1.000
O16 O 0.6199 0.95194 0.5268 1.000
O17 O 0.6689 0.02088 0.2031 1.000
O18 O 0.6689 0.47912 0.7031 1.000
O19 O 0.8311 0.52088 0.2031 1.000
O20 O 0.8311 0.97912 0.7031 1.000
O21 O 0.8801 0.04806 0.0268 1.000
O22 O 0.8801 0.45194 0.5268 1.000
O23 O 0.9429 0.54482 0.7195 1.000
O24 O 0.9429 0.95518 0.2195 1.000
#END
The program classifies ICSD cif files and removes duplicate files.
classification rules - component/element type/space group/
usage: ./bin/ICSD_classify --input_dir=string --output_dir=string [options] ...
options:
-i, --input_dir icsd folder location (string)
-o, --output_dir classification result export location (string)
-l, --log print the detail log, no log by default
-?, --help print this message
$ ./bin/ICSD_classify -i ./examples/icsd -o ./examples/icsd_classify
This program is used to remove files containing metal elements, disorder molecules and known solvents from the CSD database. You can specify to exclude only certain metal elements. The result may contain two folders, the folder csd_warning indicates that the atoms in the structure are bonded to two or more parts, and the folder csd_normal indicates that the atoms in the structure will only be bonded to one part.
usage: ./bin/csd_classify --input_dir=string --output_dir=string [options] ...
options:
-i, --input_dir csd folder location (string)
-o, --output_dir classification result export location (string)
-r, --remove only remove the cif which contains special elements or special bonds(the input form likes special meatal/special bonds(Fe|Cu/Fe-O|C-O&C-H) or only input one of them, please use '/' as separators for elements and bonds) (string [=])
-k, --keep only keep the cif which contains special elements and special bond(the input form likes special meatal/special bonds(Fe|Cu/Fe-O|C-O&C-H) or only input one of them, please use '/' as separators for elements and bonds (string [=])
-l, --log print the detail log, no log by default
-u, --unique remove duplicate files
-?, --help print this message
./bin/CSD_classify -i ./examples/csd -o ./examples/csd_classify
The program is used to convert the cif file into a file of another format. It supports customizing the atomic coordinates (atomic fractional coordinates / cartesian coordinates) in the conversion result and converting the molecular structure to in-cell or asymmetric mode.
usage: ./bin/format --input=string --output=string --type=string [options] ...
options:
-i, --input input file (string)
-o, --output output path of the conversion result (string)
-m, --mode the mode of the format conversion(in-cell/asymmetric) (string [=asymmetric])
-t, --type the type of the result format(gjf/vasp), convert format to vasp file format or gaussion format (string)
-c, --coord_type the type of the coordinate(fract/cart), the coordinates of the atom in the conversion result are fractional coordinates or cartesian coordinates (string [=fract])
-?, --help print this message
convert to gaussion file
$ ./bin/format -i ./examples/cod/WAJZUE.cif -o ./examples/result -t gjf
convert to vasp file
$ ./bin/format -i ./examples/cod/WAJZUE.cif -o ./examples/result -t vasp
The program is used to splice A and B molecules according to specified atoms.
usage: ./bin/splice_molecule --molecule_a=string --molecule_b=string --output=string --type=string --connect_a=int --connect_b=int [options] ...
options:
-a, --molecule_a path of the molecule A (string)
-b, --molecule_b path of the molecule B (string)
-o, --output the output path (string)
-t, --type the type of the result format(gjf/xyz), convert format to gaussion format or xyz format (string)
-i, --connect_a the serial number of connect site in molecule A (int)
-j, --connect_b the serial number of connect site in molecule B (int)
-?, --help print this message
$ ./bin/splice_molecule -a ./examples/mol/molecule-A-label.mol -b ./examples/mol/molecule-B-label.mol -i 31 -j 7 -t gjf -o ./examples/mol
the red box represents the specified spliced atom
Molecule A
Molecule B
Splice Result
