Try to merge

.gitignore

@@ -0,0 +1,3 @@
+.DS_Store
+*.pyc
+template_errors

README.md

@@ -9,11 +9,27 @@
 Our Topologically Based Crystal Constructor (ToBaCCo) was developed to rapidly produce molecular representations of porous crystals as crystallographic information (.cif) files, which can then be used for molecular simulation or for materials characterization. 
 
 # Installation and Dependencies
-To install dependencies:
+ToBaCCo has been tested for Python 2.7 and Python 3.7. We recommend building a Python 2.7/3.7 environment using Anaconda. You will need the following packages:
+- numpy
+- networkx
+- scipy
+
+To set up a Python X.7 environment first install Anaconda. After installing Anaconda, run:
+```
+conda create --name my_tobacco python=X.7
+```
+where my_tobacco is the name of the environment and X is 2 or 3, which can be changed to whatever you like. Next, load your new environment:
+```
+conda activate my_tobacco
+```
+(this command changes for Windows, see https://docs.anaconda.com/anaconda/user-guide/tasks/switch-environment/)
+Finally, install the above packages, thus:
 ```
-pip install -r tobacco_requirements.txt
+conda install numpy
+conda install networkx
+conda install scipy
 ```
-Once the required modules are installed, simply clone the repository and ToBaCCo is ready to run. 
+Once these are installed you can clone or download the repository and start running ToBaCCo.
 
 # Usage
 Execute the tobacco.py file to run ToBaCCo:

SBU_geometry.py

@@ -1,4 +1,4 @@
-from bbcif_properties import X_vecs, calc_edge_len
+from bbcif_properties import calc_edge_len
 import numpy as np
 
 def SBU_coords(augTG, ea_dict, csbl):
@@ -27,7 +27,7 @@ def SBU_coords(augTG, ea_dict, csbl):
 				else:
 					direction = -1
 					ov = positive_direction[0]
-
+					
 				xvecname,dx_v,xvec = ea_dict[vertex][ind]
 				dx_ov = ea_dict[ov][ind][1]
 

adjust_edges.py

@@ -51,7 +51,7 @@ def adjust_edges(placed_edges, placed_nodes, sc_unit_cell):
 
 	edge_dict = dict((k,[]) for k in edge_labels)
 
-	node_connection_points = [map(float,i[1:4]) for i in placed_nodes if re.sub('[0-9]','',i[5]) == 'X']
+	node_connection_points = [list(map(float,i[1:4])) for i in placed_nodes if re.sub('[0-9]','',i[5]) == 'X']
 
 	for edge in placed_edges:
 		ty = int(edge[-1])
@@ -61,12 +61,12 @@ def adjust_edges(placed_edges, placed_nodes, sc_unit_cell):
 
 		edge = np.asarray(edge_dict[k])
 		elems = edge[:,0]
-		evecs = [map(float,i) for i in edge[:,1:4]]
+		evecs = [list(map(float,i)) for i in edge[:,1:4]]
 		charges = edge[:,4]
 		cp = edge[:,5]
 		ty = edge[:,6]
 
-		xvecs = [map(float,i) for (i,j) in zip(evecs,cp) if re.sub('[0-9]','',j) == 'X']
+		xvecs = [list(map(float,i)) for (i,j) in zip(evecs,cp) if re.sub('[0-9]','',j) == 'X']
 		relavent_node_xvecs = []
 		relavent_node_xvecs_append = relavent_node_xvecs.append
 

bbcif_properties.py

@@ -1,7 +1,5 @@
 import re
-import sys
 import numpy as np
-import networkx as nx
 import os
 
 PT = ['H' , 'He', 'Li', 'Be', 'B' , 'C' , 'N' , 'O' , 'F' , 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P' , 'S' , 'Cl', 'Ar',
@@ -11,6 +9,12 @@
 	  'Ra', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Ac', 'Th', 
 	  'Pa', 'U' , 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'FG', 'X' ]
 
+def nn(string):
+	return re.sub('[^a-zA-Z]','', string)
+
+def nl(string):
+	return re.sub('[^0-9]','', string)
+
 def isfloat(value):
 	"""
 		determines if a value is a float
@@ -25,11 +29,7 @@ def iscoord(line):
 	"""
 		identifies coordinates in CIFs
 	"""
-	if (re.sub('[^a-zA-Z]','', line[0]) in PT and
-	line[1] in PT and
-	isfloat(line[2]) and
-	isfloat(line[3]) and
-	isfloat(line[4])):
+	if nn(line[0]) in PT and line[1] in PT and False not in map(isfloat,line[2:5]):
 		return True
 	else:
 		return False
@@ -38,11 +38,7 @@ def isbond(line):
 	"""
 		identifies bonding in cifs
 	"""
-	if (re.sub('[^a-zA-Z]','', line[0]) in PT and
-	re.sub('[^a-zA-Z]','', line[1]) in PT and
-	isfloat(line[2]) and
-	not isfloat(line[3]) and
-	not isfloat(line[4])):
+	if nn(line[0]) in PT and nn(line[1]) in PT and isfloat(line[2]) and line[-1] in ('S', 'D', 'T', 'A'):
 		return True
 	else:
 		return False
@@ -126,11 +122,11 @@ def bb2array(cifname, direc):
 		if '_cell_angle_gamma' in line:
 			gamma = s[1]
 		if iscoord(s):
-			fvec = np.array(map(float, s[2:5]))
+			fvec = np.array([float(q) for q	 in s[2:5]])
 			fcoords_append([s[0],fvec])
 
 	pi = np.pi
-	a,b,c,alpha,beta,gamma = map(float, (a,b,c,alpha,beta,gamma))
+	a,b,c,alpha,beta,gamma = list(map(float, (a,b,c,alpha,beta,gamma)))
 	ax = a
 	ay = 0.0
 	az = 0.0
@@ -177,6 +173,7 @@ def X_vecs(cifname, direc, label):
 
 	fcoords = []
 	fcoords_append = fcoords.append
+
 	for line in cif:
 		s = line.split()
 		if '_cell_length_a' in line:
@@ -192,10 +189,11 @@ def X_vecs(cifname, direc, label):
 		if '_cell_angle_gamma' in line:
 			gamma = s[1]
 		if iscoord(s) and 'X' in s[0]:
-			fcoords_append([s[0],np.array(map(float, s[2:5]))])
+			fvec = np.array([float(q) for q in s[2:5]])
+			fcoords_append([s[0],fvec])
 
 	pi = np.pi
-	a,b,c,alpha,beta,gamma = map(float, (a,b,c,alpha,beta,gamma))
+	a,b,c,alpha,beta,gamma = list(map(float, (a,b,c,alpha,beta,gamma)))
 	ax = a
 	ay = 0.0
 	az = 0.0
@@ -265,10 +263,11 @@ def calc_edge_len(cifname, direc):
 		if '_cell_angle_gamma' in line:
 			gamma = s[1]
 		if iscoord(s) and 'X' in s[0]:
-			fcoords_append([s[0],np.array(map(float, s[2:5]))])
+			fvec = np.array([float(q) for q in s[2:5]])
+			fcoords_append([s[0],fvec])
 
 	pi = np.pi
-	a,b,c,alpha,beta,gamma = map(float, (a,b,c,alpha,beta,gamma))
+	a,b,c,alpha,beta,gamma = list(map(float, (a,b,c,alpha,beta,gamma)))
 	ax = a
 	ay = 0.0
 	az = 0.0
@@ -282,7 +281,7 @@ def calc_edge_len(cifname, direc):
 
 	mic_fcoords = [PBC3DF(fcoords[0][1],vec[1]) for vec in fcoords]
 	ccoords = [np.dot(unit_cell,vec) for vec in mic_fcoords]
-	
+
 	return np.linalg.norm(ccoords[0] - ccoords[1])
 
 def cncalc(cifname, direc, cn1):