Prepare for beta launch (#43)

* Change the name Radical to funcGroups * Add creation of CJSON structure * Add cjson in save_dict * FIx error on cjson structure * Remove print * Separete the IO tools from tools * Update * Add the source from the atoms (core:C, connector:Q, functionalization:R) * Save building block is False by default * Fix wrong index on cif file * Split the core in C1 and C2 * Update * Improve the net staking creation * Improve stacking creation and add FXT and FXT_A nets * Change the logotype * Add nitrone group * Add the beta-ketenamine connection group * Create pylint.yml * Delete .github/workflows/pylint.yml * Fix problem with HDZN on the order of replace X * Fix the S4 building blocks * Add new S4 building blocks * Add COOH as connection group to form the amide condensation * Add COOH as building block * improve documentation in tools * Update tools * Rename Building_Block to BuildingBlock * Small changes * Small fixes * Add BRZN and TOTB tritopic building blocks * Add new functions to create building blocks from xyz and gjf files * Add two new S4 building blocks * Fix building block creation * Add new H6 building blocks * Fix new building blocks * Fix building blocks * Add example of how to create building blocks * Small fix * Fix smiles for HEXB and PORP * Fix smiles for TPCA * Add BB images * Fix PORP code * Upload image of S4 buiding blocks * Update the readme section * Update Readme.md
lipelopesoliveira · Oct 23, 2023 · 4a8fcc3 · 4a8fcc3
1 parent 0e8d57b
commit 4a8fcc3
Show file tree

Hide file tree

Showing 126 changed files with 380,123 additions and 3,853 deletions.
diff --git a/README.md b/README.md
@@ -2,7 +2,9 @@
 
 ![puCOFBuilder](docs/header.png)
 
-**pyCOFBuilder** is a simple and powerful python package to automatically assembly COF structures with specifics building blocks, topologies, and functionalizations. The project was developed to address the need for generation of COFs structures in a high-throughput style, based on a nomenclature tha allows direct sctructural feature interpretation from a simple name. The package uses[pymatgen](https://pymatgen.org/) to create the structures. The package is still under development, but it is already possible to create a large number of COFs structures.
+**pyCOFBuilder** is a simple and powerful python package to automatically assembly COF structures with specifics building blocks, topologies, and functionalizations. The project was developed to address the need for generation of COFs structures in a high-throughput style, based on a nomenclature tha allows direct sctructural feature interpretation from a simple name. The package uses [pymatgen](https://pymatgen.org/) to create the structures. 
+
+This package is still under development and currently on beta version, but it is already possible to create a large number of COFs structures.
 
 Learn more at [ToNano&Beyond](https://tonanoandbeyondblog.wordpress.com/)
 
@@ -11,18 +13,27 @@ Learn more at [ToNano&Beyond](https://tonanoandbeyondblog.wordpress.com/)
 For detailed instructions see the [installation instructions](https://tonanoandbeyondblog.wordpress.com/).
 If the requirements are already satisfied `[WILL BE UPDATED!!!!]`
 
-```bash
-pip install pycofbuilder
+Currently the best way to use pyCOFBuilder is to manually import it using the `sys` module, as exemplified below:
+
+```python
+# importing module
+import sys
+
+# appending a path
+sys.path.append('{PATH_TO_PYCOFBUILDER}/pyCOFBuilder/src')
+
+import pycofbuilder as pcb
 ```
 
+Just remember to change the `{PATH_TO_PYCOFBUILDER}` to the directory where you download the pyCOFBuilder package. 
+
 ### Requirements
 
-0. Python >= 3.7
+0. Python >= 3.10
 1. pymatgen >= 2022.0.0
 2. numpy >= 1.2
 3. scipy >= 1.6.3
 4. simplejson
-5. tqdm
 
 The Python dependencies are most easily satisfied using a conda
 ([anaconda](https://www.anaconda.com/distribution)/[miniconda](https://docs.conda.io/en/latest/miniconda.html))
@@ -34,14 +45,14 @@ conda env create --file environment.yml
 
 ## Basic Usage
 
-To create a specific COF, like `T3_BENZ_NH2_OH-L2_BENZ_CHO_H-HCB_A-AA`:
+To create a specific COF, such as `T3_BENZ_NH2_OH-L2_BENZ_CHO_H-HCB_A-AA`:
 
 ```python
 >>> import pycofbuilder as cof
 
 >>> cof.Framework('T3_BENZ_CHO_OH-L2_BENZ_NH2_H-HCB_A-AA')
 T3_BENZ_NH2_OH-L2_BENZ_CHO_H_H-HCB_A-AA                       hexagonal   P    P6/m # 175    12 sym. op.
->>> cof.save(fmt='cif', supercell = [1, 1, 2])
+>>> cof.save(fmt='cif', supercell = [1, 1, 2], save_dir = '.')
 ```
 
 A `.cif` file (the default save format is CIF, but it can be easily changed by setting other value on the `fmt` option) will be created in the `out` folder. The code will print out some information about the structure created.
@@ -63,72 +74,6 @@ array([[ 22.49540055,   0.        ,   0.        ],
 'P6/m'
 ```
 
-## Creating multiple COFs
-
-You can also create multiple building blocks and then construct all available COFs from the connection of those blocks.
-
-```python
-import pycofbuilder as COF
-
-for BB1 in ['C3_BENZ_CHO_H', 'C3_BENZ_CHO_OH', 'C3_BENZ_CHO_CH3', 'C3_BENZ_CHO_F']:
-    COF.Building_Block(BB1)
-
-for BB2 in ['C2_BENZ_NH2_H', 'C2_BENZ_NH2_OH', 'C2_BENZ_NH2_CH3', 'C2_BENZ_NH2_F']:
-    COF.Building_Block(BB2)
-
-COF.build_all_available_COFs()
-
-```
-
-You should see this output, where the code will calculate how many COFs will be created and ask for confirmation. Once you type `y` to confirm, a progress bar will indicate the creation of the structures as well as the estimated time for concluding the task. After the creation, the code will print some information about the COFs created, how many of the structures were created successfully, and the elapsed time.
-
-```python
->>> 20 COFs will be created. Do you want to proceed? Type [y] to continue.
-y
-                      COF Name                              |    Lattice    | Point Group | N° of symmetry op. |
-C3_BENZ_CHO_CH3-C2_BENZ_NH2_CH3_H-HCB_A-AA                    hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_CH3-C2_BENZ_NH2_F_H-HCB_A-AA                      hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_CH3-C2_BENZ_NH2_H_H-HCB_A-AA                      hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_CH3-C2_BENZ_NH2_OH_H-HCB_A-AA                     hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_CH3-C2_HDZ_NH2-HCB_A-AA                           hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_F-C2_BENZ_NH2_CH3_H-HCB_A-AA                      hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_F-C2_BENZ_NH2_F_H-HCB_A-AA                        hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_F-C2_BENZ_NH2_H_H-HCB_A-AA                        hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_F-C2_BENZ_NH2_OH_H-HCB_A-AA                       hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_F-C2_HDZ_NH2-HCB_A-AA                             hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_H-C2_BENZ_NH2_CH3_H-HCB_A-AA                      hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_H-C2_BENZ_NH2_F_H-HCB_A-AA                        hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_H-C2_BENZ_NH2_H_H-HCB_A-AA                        hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_H-C2_BENZ_NH2_OH_H-HCB_A-AA                       hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_H-C2_HDZ_NH2-HCB_A-AA                             hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_OH-C2_BENZ_NH2_CH3_H-HCB_A-AA                     hexagonal   P     P6  # 168    6  sym. op.
-C3_BENZ_CHO_OH-C2_BENZ_NH2_F_H-HCB_A-AA                       hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_OH-C2_BENZ_NH2_H_H-HCB_A-AA                       hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_OH-C2_BENZ_NH2_OH_H-HCB_A-AA                      hexagonal   P    P6/m # 175    12 sym. op.
-C3_BENZ_CHO_OH-C2_HDZ_NH2-HCB_A-AA                            hexagonal   P    P6/m # 175    12 sym. op.
-20 sucessful. 0 failled (100.0 % success rate)
-Enlapsed time: 1.476 s
-```
-
-All the structures created will be saved as `.cif` file on the `out`folder.  
-Finally, it is possible to clean all the building blocks created
-
-```python
->>> COF.clean_bb_list()
-Deleted data\bb_lib\C2_BENZ_NH2_CH3_H.xyz
-Deleted data\bb_lib\C2_BENZ_NH2_F_H.xyz
-Deleted data\bb_lib\C2_BENZ_NH2_H_H.xyz
-Deleted data\bb_lib\C2_BENZ_NH2_OH_H.xyz
-Deleted data\bb_lib\C2_HDZ_NH2.xyz
-Deleted data\bb_lib\C3_BENZ_CHO_CH3.xyz
-Deleted data\bb_lib\C3_BENZ_CHO_F.xyz
-Deleted data\bb_lib\C3_BENZ_CHO_H.xyz
-Deleted data\bb_lib\C3_BENZ_CHO_OH.xyz
-```
-
-For more examples see _examples/_ and the [docs](https://github.com/lipelopesoliveira/pyCOFBuilder/examples.html)
-for the complete explanation of implementation and functionalities.
-
 ## COFs and Building Blocks nomenclature
 
 In order to ensure greater reproducibility as well as quickly and easily access to relevant information from the COFs, I've developed a simple nomenclature to name the structure. Generally speaking, a COF can be described as
@@ -157,24 +102,25 @@ Note that every "card" for the building block name is separated by an underline
 
 ## Current available Building Blocks
 
-![Bipodal](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/BB_C2.png)
-![Tripodal](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/BB_C3.png)
-![Tetrapodal_2D](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/BB_C4.png)
+![Ditopic](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/L2_1.png)
+![Ditopic](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/L2_2.png)
+![Tritopic](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/T3.png)
+![Tetratopic](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/S4.png)
+![Hexatopic](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/H6.png)
 
 ## Current available Connector Groups
 
-- NH2
-- CHO
+![Connection groups](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/Q_GROUPS.png)
 
 ## Current available R Groups
 
-![R_groups](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/R_GROUPS.png)
+![Functional Groups](https://github.com/lipelopesoliveira/pyCOFBuilder/blob/master/docs/R_GROUPS.png)
 
 ## Citation
 
 If you find **pyCOFBuilder** useful in your research please consider citing the following papers:
 
 > F. L. Oliveira and P. M. Esteves,
-> _pyCOFBuilder: A Python Module for Automated Assembly of Covalent Organic Frameworks_
+> _pyCOFBuilder: A python package for automated assembly of Covalent Organic Framework structures_
 >
-> _Manuscript in preparation._ [DOI](https://doi.org/)
+> _arxiv.org/abs/2210.09456._ [DOI](https://arxiv.org/abs/XXXX)
diff --git a/docs/BB_C2.png b/docs/BB_C2.png
diff --git a/docs/BB_C3.png b/docs/BB_C3.png
diff --git a/docs/BB_C4.png b/docs/BB_C4.png
diff --git a/docs/Blocos_de_constru.pptx b/docs/Blocos_de_constru.pptx
diff --git a/docs/H6.pdf b/docs/H6.pdf
diff --git a/docs/H6.png b/docs/H6.png