-
Notifications
You must be signed in to change notification settings - Fork 4
/
net.h
100 lines (87 loc) · 5.38 KB
/
net.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
//-----Richard Luis Martin, Lawrence Berkeley National Laboratory, 2013
/* this file contains classes and functions required for handling topology (net) information */
#ifndef NET_H
#define NET_H
#include <string>
#include <vector>
#include <sstream>
using namespace std;
#include "geometry.h"
/* defines and consts */
#define MAX_DUPE_CON_ANGLE_DIFF PI/36.0
#define MAX_DUPE_CON_MAG_DIFF 5
#define MIN_UNIT_ATOM_NETWORK_SIDE_LENGTH 0.5
#define NEARLY_PARALLEL_ANGLE_DEGREES 10.0
#define GENERAL_BOND_DISTANCE 1.9 //if two atoms are within this distance, they are considered to be bonded
#define IS_PART_OF_SITE_DISTANCE 2.5 //if an atom and a site marker are within this distance, the atom is considered to be part of the site - if two atoms are both part of some site, then they will not be counted as collisions (because they may be forming a legitimate bond)
#define TOLERANCE_PROPORTION 1.05 //5% tolerance in distance measurements etc.
#define SAME_POSITION_DISTANCE 0.1 //how far apart sites should be in distinct aligned molecules in order to the alignments to be considered unique (note: setting the tolerance too high can cause the correct alignment to be discarded ...)
#define DISTANCE_TOLERANCE 0.01 //used for distances etc. when an absolute difference between things is calculated
#define SITE_DEVIATION_WARNING 1.5 //1.0 //if sites are further apart than this in the best framework, issue a warning
/* class to store vertex position and connectivity information */
class VERTEX {
public:
XYZ abc; //the fractional position of this VERTEX
int expected_edges;
std::vector<XYZ> edges; //data on the edges for this vertex
std::vector<XYZ> dummy_edges; //a single dummy edge is used only for 2-c vertices, as a means of providing an orthogonal direction to use when fitting 2-c molecules (which also have a corresponding dummy site) - it is stored as a vector to enable easy checking of whether it is declared
std::string name;
/* constructors */
VERTEX(double a0, double b0, double c0); //fractional constructor
VERTEX();
};
/* class to store vertex connection information */
class CONNECTION{
public:
int v1, v2;
int e1, e2;
int a, b, c; //the periodicity of this connection
//constructor
CONNECTION(int v1_, int v2_, int e1_, int a_, int b_, int c_);
};
/* class to store a non-periodic collection of atoms, i.e. a molecule, including the position of connection sites to attach to other molecules, and the order of sites used w.r.t. the underlying net */
class MOLECULE {
public:
vector<XYZ> atoms_xyz;
vector<string> atoms_type;
vector<string> atoms_label;
vector<int> sites;
vector<int> dummy_sites;
vector<int> permutation; //stores the order in which the sites correspond to the edges of a vertex in the net, i.e. edge[i] corresponds to site permutation[i]
XYZ com; //centre of mass, or just centroid, of site positions
};
/* class to store possible orientations of a molecule to some reference points */
class FIT{
public:
MOLECULE fit;
double rmsd;
int perm_ID;
};
/* method declarations */
XYZ get_mol_site_CoM(MOLECULE *mol);
bool bonded_xyz(XYZ xyz1, XYZ xyz2);
bool bonded_xyz(XYZ xyz1, XYZ xyz2, double threshold);
bool matches(CONNECTION ci, CONNECTION cj);
void swap(vector<int> *vec, int a, int b);
void recursive_visit_vertices(int this_v, vector<CONNECTION> *two_way_connections, vector<bool> *visited_vertex);
bool recursive_find_loops(int this_v, int a, int b, int c, XYZ xyz, vector<CONNECTION> *two_way_connections, vector<MOLECULE> *assembled_molecules, vector<bool> *edge_traversed, vector<int> *vertex_visit_a, vector<int> *vertex_visit_b, vector<int> *vertex_visit_c, vector<XYZ> *vertex_visit_xyz, vector<bool> *vertex_visited, vector<int> *loops_a, vector<int> *loops_b, vector<int> *loops_c, vector<XYZ> *loops_xyz, vector<int> *unit_cell_vector_IDs, vector<XYZ> *unit_cell_vectors, int dimensionality);
bool try_unit_cell_vector_assign(int a, int b, int c, XYZ xyz, vector<int> *loops_a, vector<int> *loops_b, vector<int> *loops_c, vector<XYZ> *loops_xyz, vector<int> *unit_cell_vector_IDs, vector<XYZ> *unit_cell_vectors, int num_uc_vectors_required);
bool loop_is_unique(int a, int b, int c, vector<int> *loops_a, vector<int> *loops_b, vector<int> *loops_c);
MOLECULE translate(MOLECULE m, XYZ t);
MOLECULE rotate(MOLECULE orig, double mat[3][3]);
bool molecule_alignment_chemistry_is_unique(MOLECULE *mol, vector<MOLECULE> *existing);
bool overlaps_xyz(XYZ xyz1, XYZ xyz2);
void permute(vector<int> vec, int pos, vector< vector<int> > *out_vec);
int recursive_test_dimensionality(int this_v, int a, int b, int c, vector<CONNECTION> *two_way_connections, vector<bool> *edge_traversed, vector<int> *vertex_visit_a, vector<int> *vertex_visit_b, vector<int> *vertex_visit_c, vector<bool> *vertex_visited, vector<bool> *is_periodic);
void get_com(MOLECULE *m);
int assign_dummy_site(MOLECULE *m);
/* TO_FIX from file_and_string_ops.h - need to sort out any possible redundancies here */
void write_connections(FILE *f, vector<CONNECTION> *two_way_connections, vector<MOLECULE> *assembled_molecules, string name);
void write_molecule(FILE *rotmol, MOLECULE *rotated, string name, int vertex_ID, int sym_op, bool write_out_sites);
void write_framework(FILE *f, MOLECULE *framework, string name);
void search_for_char(FILE *f, char c);
string convertToString(int number);
string toLowerCase(string s);
/* TO_FIX - REDUNDANT RESOLVE THIS */
vector<XYZ> get_periodic_images_of_uc_abc_position(XYZ e_abc);
#endif