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molecule_to_abstract.cc
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molecule_to_abstract.cc
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//Richard L Martin 2013/05/16
//C code to read an xyz file and convert it to an abstract linker - it can handle carboxy or Br sites, with the appropriate flag
//Arguments: real_molecule.xyz site_type output_abstract_molecule.xyz
/*------------------------------
INCLUDES, CONSTS
------------------------------*/
#include <algorithm>
#include <stdlib.h>
#include <vector>
#include <string>
#include <cstring>
#include <cstdio>
using namespace std;
#include "geometry.h"
#include "mindist.h"
#include "networkinfo.h"
#include "rmsd.h"
#include "networkstorage.h"
#include "net.h"
#include "symmetry.h"
#include "string_additions.h"
#include "zeo_consts.h"
const int CARBOXY = 0, BROMINE = 1, DIALCOHOL = 2, A_P_CATECHOL = 3, ALDEHYDE = 4;
const int MAX_CHAR_ARRAY_LENGTH = 500;
const double CARBON_CARBON_BOND_LENGTH = 1.43; //Angstroms
const double MAX_HYDROGEN_BOND_LENGTH = 1.2; //Angstroms
//const double MAX_CARBOXY_BOND_LENGTH = 1.5; //Angstroms
const double MAX_CARBOXY_BOND_LENGTH = 1.6; //Angstroms
const double MAX_BROMINE_BOND_LENGTH = 2.1; //Angstroms
const double MAX_SITE_DISTANCE_DEVIATION = 2.0; //Angstroms
const double MAX_SITE_ANGLE_DEVIATION = 30.0; //degrees
const int NUM_MC = 100000;
const double DEFAULT_RADIUS = 1.35; //Angstroms
const double GRID_RES = 0.25; //Angstroms
/*------------------------------
CLASSES
------------------------------*/
//int3
class INT3 {
public:
int x, y, z;
//constructor
INT3();
};
/*------------------------------
METHOD DECLARATIONS
------------------------------*/
/*
void search_for_char(FILE *f, char c);
*/
void read_molecule(string filename, vector<ATOM> *atom_vector);
void read_incon(string filename, vector<ATOM> *atom_vector);
void read_xyz(string filename, vector<ATOM> *atom_vector);
void write_xyz(FILE *outfile, vector<ATOM> *atom_vector, string input_name);
void find_sites(vector<ATOM> *molecule, vector<INT3> *indices, int site_type);
void replace_sites_with_abstract(vector<ATOM> *molecule, vector<INT3> *indices, int site_type, string name);
bool bonded(ATOM a, ATOM b, double d);
double dist(ATOM a, ATOM b);
vector<ATOM> rotate(vector<ATOM> *orig, double mat[3][3]);
double get_rad(string s);
double dist(double x, double y, double z, ATOM b);
XYZ get_vector_from_to(XYZ start, XYZ end);
XYZ midpoint(XYZ a, XYZ b);
XYZ project_onto_line(XYZ initial, XYZ line_start, XYZ line_end);
double radians_to_degrees(double r);
/*
vector<string> split(string line, string delims);
*/
//sorting functions
bool increasing_double (double i, double j) { return (i<j); }
/*------------------------------
MAIN
------------------------------*/
int main(int argc, char *argv[]) {
//-----hardcoded settings
bool verbose = false;
//-----check arguments
int num_args = 4;
if(argc!=num_args) {
printf("%d arguments were provided but %d are required:\n", argc, num_args);
printf("a.out\n");
printf("real_molecule.xyz\n");
printf("site_type\n");
printf("abstract_molecule_output.xyz\n");
printf("Where site_type is one of:\n\t0 (carboxy)\n\t1 (Br)\n\t2 (dialcohol)\n\t3 (acetenol-protected catechol)\n\t4 (aldehyde)\n");
printf("Please try again.\n");
exit(EXIT_FAILURE);
}
//by default, we want to populate the table with radii and masses, even if later we will not reference them
initializeRadTable();
initializeMassTable();
initializeCovRadTable();
//-----parse arguments
string real_mol_name, out_name;
real_mol_name = argv[1];
int site_type = atoi(argv[2]);
out_name = argv[3];
//read input, saving a vector of atoms found
vector<ATOM> real_molecule;
read_molecule(real_mol_name, &real_molecule);
int num_real_atoms = real_molecule.size();
if(verbose) printf("real molecule contains %d atoms\n", num_real_atoms);
//find the connection sites
vector<INT3> real_site_indices;
find_sites(&real_molecule, &real_site_indices, site_type);
int num_real_sites = real_site_indices.size();
if(verbose) printf("real molecule contains %d sites\n", num_real_sites);
//replace the site atoms with an abstract site
replace_sites_with_abstract(&real_molecule, &real_site_indices, site_type, real_mol_name);
//-----write out the molecule to output
FILE *outfile = fopen(out_name.c_str(), "w");
if(outfile==NULL) {
printf("ERROR: could not open output molecule file with name %s\n", out_name.c_str());
exit(EXIT_FAILURE);
}
write_xyz(outfile, &real_molecule, real_mol_name);
//printf("Program complete\n\n");
}
/*------------------------------
OTHER METHODS
------------------------------*/
void replace_sites_with_abstract(vector<ATOM> *molecule, vector<INT3> *indices, int site_type, string name) {
bool verbose = true;
int num_sites = indices->size();
int num_atoms = molecule->size();
if(site_type==CARBOXY) { //replace the C atom with Q, and remove the O atoms; also remove any H atoms near to the O
for(int i=0; i<num_sites; i++) {
INT3 site = indices->at(i);
molecule->at(site.y).type = "Q"; //replace the C
molecule->at(site.y).label = "Q";
molecule->at(site.x).keep = false;
molecule->at(site.z).keep = false; //remove the Os
//now find H atoms
for(int j=0; j<num_atoms; j++) { //find H atoms bonded to this O
if(molecule->at(j).type=="H" && molecule->at(j).keep) {
if(bonded(molecule->at(site.x), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH) || bonded(molecule->at(site.z), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH)) {
molecule->at(j).keep = false;
}
}
}
}
} else if(site_type==BROMINE) { //else remove the Br atom and replace it with Q positioned so as to be a carbon bond length away from the adjacent atom
if(num_sites!=2) {
/*
printf("ERROR: >2 Br sites (%d) in structure %s so cannot align them - not writing out\n", num_sites, name.c_str());
exit(EXIT_FAILURE);
*/
printf("WARNING: >2 Br sites (%d) in structure %s so cannot align them - will write out abstract molecule as it is\n", num_sites, name.c_str());
for(int i=0; i<num_sites; i++) {
INT3 site = indices->at(i);
molecule->at(site.x).type = "Q"; //replace the Br with Q
molecule->at(site.x).label = "Q";
molecule->at(site.x).set_xyz(molecule->at(site.y).xyz() + get_vector_from_to(molecule->at(site.y).xyz(), molecule->at(site.x).xyz()).unit().scale(MAX_CARBOXY_BOND_LENGTH)); //shift the Q
}
} else { //if dibromo, we can also orient them so that the structure has a chance to be built with nonlinear molecules
INT3 site_0 = indices->at(0);
INT3 site_1 = indices->at(1);
molecule->at(site_0.x).type = "Q"; //replace the Br with Q
molecule->at(site_0.x).label = "Q";
molecule->at(site_1.x).type = "Q";
molecule->at(site_1.x).label = "Q";
//now, if both Br are anchored to the same atom, we have a problem - we will have to handle it separately:
if(site_0.y==site_1.y) {
XYZ site_0_1 = get_vector_from_to(molecule->at(site_0.x).xyz(), molecule->at(site_1.x).xyz()).unit().scale(MAX_CARBOXY_BOND_LENGTH);
molecule->at(site_1.x).set_xyz(molecule->at(site_1.y).xyz() + site_0_1);
molecule->at(site_0.x).set_xyz(molecule->at(site_0.y).xyz() + site_0_1.scale(-1));
} else {
XYZ anchor_anchor = get_vector_from_to(molecule->at(site_0.y).xyz(), molecule->at(site_1.y).xyz()).unit().scale(MAX_CARBOXY_BOND_LENGTH);
molecule->at(site_1.x).set_xyz(molecule->at(site_1.y).xyz() + anchor_anchor);
molecule->at(site_0.x).set_xyz(molecule->at(site_0.y).xyz() + anchor_anchor.scale(-1));
}
}
} else if(site_type==ALDEHYDE) { //replace the O (x) atom with Q only
for(int i=0; i<num_sites; i++) {
INT3 site = indices->at(i);
molecule->at(site.x).type = "Q"; //replace the O
molecule->at(site.x).label = "Q";
}
} else if(site_type==A_P_CATECHOL) { //replace the C (x) atom with Q, and remove the CH3 groups (y/z and surrounding H)
for(int i=0; i<num_sites; i++) {
INT3 site = indices->at(i);
molecule->at(site.x).type = "Q"; //replace the C
molecule->at(site.x).label = "Q";
//now find H atoms
for(int j=0; j<num_atoms; j++) { //find H atoms bonded to this O
if(molecule->at(j).type=="H" && molecule->at(j).keep) {
if(bonded(molecule->at(site.y), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH) || bonded(molecule->at(site.z), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH)) {
molecule->at(j).keep = false;
}
}
}
//finally, remove the C of CH3
molecule->at(site.y).keep = false;
molecule->at(site.z).keep = false;
}
} else if(site_type==DIALCOHOL) { //replace the dummy Z (z) atom with Q, and remove the H on y/x
for(int i=0; i<num_sites; i++) {
INT3 site = indices->at(i);
molecule->at(site.z).type = "Q"; //replace the dummy Z
molecule->at(site.z).label = "Q";
//now find H atoms
for(int j=0; j<num_atoms; j++) { //find H atoms bonded to this O
if(molecule->at(j).type=="H" && molecule->at(j).keep) {
if(bonded(molecule->at(site.y), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH) || bonded(molecule->at(site.x), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH)) {
molecule->at(j).keep = false;
}
}
}
}
} else {
printf("ERROR: did not recognize site type %d\n", site_type);
exit(EXIT_FAILURE);
}
}
void find_sites(vector<ATOM> *molecule, vector<INT3> *indices, int site_type) {
bool verbose = true;
int num_atoms = molecule->size();
vector<bool> already_checked;
for(int i=0; i<num_atoms; i++) already_checked.push_back(false);
if(site_type==CARBOXY) { //CARBOXY SITES
for(int i=0; i<num_atoms; i++) {
if(molecule->at(i).type=="O" && !already_checked.at(i)) { //found a new oxygen; potentially a connection site
if(verbose) printf("found an O atom\n");
INT3 trial_site;
trial_site.x = i;
already_checked.at(trial_site.x) = true;
//is this a connection site? we need to find if there is one bond only (carbon - ignore hydrogens), and if that carbon is bonded to an oxygen with only one bond (that carbon - ignore hydrogens)
bool cannot_be_site_first_O = false;
int num_non_H_bonds_first_O = 0;
for(int j=0; j<num_atoms && !cannot_be_site_first_O; j++) { //find how many non-H atoms are bonded to this O
if(molecule->at(j).type!="H" && j!=trial_site.x) {
if(bonded(molecule->at(trial_site.x), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)) {
if(verbose) printf("first O is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(trial_site.x), molecule->at(j)));
num_non_H_bonds_first_O++;
if(num_non_H_bonds_first_O>1 || molecule->at(j).type!="C") cannot_be_site_first_O = true;
else if(molecule->at(j).type=="C" && !already_checked.at(j)) { //this is a potential C from a carboxy
trial_site.y = j;
}
}
}
}
if(verbose) printf("the first O atom has %d non-H bonds (exactly one required)\n", num_non_H_bonds_first_O);
//at this point, if we did not find too many bonds, this is still a potential site, and we need to find the other oxygen - otherwise, bypass the rest and move on to test the next oxygen
bool site_completed = false;
for(int j=0; j<num_atoms && !cannot_be_site_first_O && !site_completed; j++) {
if(molecule->at(j).type!="H" && j!=trial_site.y) {
if(bonded(molecule->at(trial_site.y), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)) {
if(molecule->at(j).type=="O" && !already_checked.at(j)) { //this is a potential other O from a carboxy
if(verbose) printf("found a second O atom that is bonded to this C\n");
trial_site.z = j;
already_checked.at(trial_site.z) = true;
bool cannot_be_site_second_O = false;
int num_non_H_bonds_second_O = 0;
for(int k=0; k<num_atoms && !cannot_be_site_second_O; k++) { //find how many non-H atoms are bonded to this O
if(molecule->at(k).type!="H" && k!=trial_site.z) {
if(bonded(molecule->at(trial_site.z), molecule->at(k), MAX_CARBOXY_BOND_LENGTH)) {
if(verbose) printf("second O is bonded to %s with distance %.3f\n", molecule->at(k).type.c_str(), dist(molecule->at(trial_site.z), molecule->at(k)));
num_non_H_bonds_second_O++;
if(num_non_H_bonds_second_O>1 || k!=trial_site.y) cannot_be_site_second_O = true;
}
}
}
if(verbose) printf("the second O atom has %d non-H bonds (exactly one required)\n", num_non_H_bonds_second_O);
if(!cannot_be_site_second_O) {
//at this point, if we did not find too many bonds, this is a site!
indices->push_back(trial_site);
already_checked.at(trial_site.y) = true; //now safe to flag this carbon as having been checked already
site_completed = true;
}
}
}
}
}
if(verbose) {
if(!site_completed) printf("this O atom did not constitute part of a carboxy group\n"); else printf("site found!\n");
}
}
}
} else if(site_type==BROMINE) { //BROMINE sites
for(int i=0; i<num_atoms; i++) {
if(molecule->at(i).type=="Br" && !already_checked.at(i)) { //found a new bromine; potentially a connection site
if(verbose) printf("found a Br atom\n");
bool site_completed = false;
INT3 trial_site;
trial_site.x = i;
trial_site.z = -1; //this site is only one atom, and the one it is bonded to (y) - we don't need this third position - this output will be parsed appropriately later
already_checked.at(trial_site.x) = true;
//is this a connection site? we need to find if there is one bond only (doesn't matter what element)
bool cannot_be_site_Br = false;
int num_bonds_Br = 0;
for(int j=0; j<num_atoms && !cannot_be_site_Br; j++) { //find how many non-H atoms are bonded to this Br
if(molecule->at(j).type!="H" && j!=trial_site.x) {
if(bonded(molecule->at(trial_site.x), molecule->at(j), MAX_BROMINE_BOND_LENGTH)) {
if(verbose) printf("this Br is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(trial_site.x), molecule->at(j)));
num_bonds_Br++;
trial_site.y = j;
if(num_bonds_Br>1) cannot_be_site_Br = true;
}
}
}
if(verbose) printf("the Br atom has %d bonds (exactly one required)\n", num_bonds_Br);
if(!cannot_be_site_Br) {
//at this point, if we did not find too many bonds, this is a site!
indices->push_back(trial_site);
site_completed = true;
}
if(verbose) {
if(!site_completed) printf("this Br atom did not constitute a connection site\n"); else printf("site found!\n");
}
}
}
} else if(site_type==ALDEHYDE) { //ALDEHYDE SITES
for(int i=0; i<num_atoms; i++) {
if(molecule->at(i).type=="O" && !already_checked.at(i)) { //found a new oxygen; potentially a connection site
if(verbose) printf("found an O atom\n");
INT3 trial_site;
trial_site.x = i;
already_checked.at(trial_site.x) = true;
//is this a connection site? we need to find if there is one bond only (carbon - CHECK FOR hydrogens), and if that carbon is bonded to a hydrogen
bool cannot_be_site_first_O = false;
int num_bonds_first_O = 0;
for(int j=0; j<num_atoms && !cannot_be_site_first_O; j++) { //find how many atoms are bonded to this O
if(
( molecule->at(j).type!="H" && j!=trial_site.x && bonded(molecule->at(trial_site.x), molecule->at(j), MAX_CARBOXY_BOND_LENGTH) )
||
( molecule->at(j).type=="H" && j!=trial_site.x && bonded(molecule->at(trial_site.x), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH) )
) {
if(verbose) printf("first O is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(trial_site.x), molecule->at(j)));
num_bonds_first_O++;
if(num_bonds_first_O!=1) cannot_be_site_first_O = true;
else if(molecule->at(j).type=="C" && !already_checked.at(j)) { //this is a potential C from an aldehyde
trial_site.y = j;
}
}
}
if(verbose) printf("the first O atom has %d bonds (exactly one required)\n", num_bonds_first_O);
//at this point, if we did not find too many bonds, this is still a potential site, and we need to find the hydrogen AND EXACTLY ONE OTHER
bool site_completed = false;
int num_H = 0, num_non_H = 0;
int id_H = -1;
for(int j=0; j<num_atoms && !cannot_be_site_first_O && !site_completed; j++) {
if(molecule->at(j).type=="H" && !already_checked.at(j) && j!=trial_site.x && j!=trial_site.y && bonded(molecule->at(trial_site.y), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH)) {
//this is a potential H to complete the aldehyde
if(verbose) printf("found an H atom that is bonded to this C\n");
num_H++;
id_H = j;
} else if(molecule->at(j).type!="H" && j!=trial_site.x && j!=trial_site.y && bonded(molecule->at(trial_site.y), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)) {
//this is a potential non-H to complete the aldehyde
if(verbose) printf("found a non-H atom that is bonded to this C\n");
num_non_H++;
}
}
//it's only an aldehyde if both num_H and num_non_H are 1
if(num_H==1 && num_non_H==1) {
trial_site.z = id_H;
already_checked.at(trial_site.z) = true;
//at this point, this is a site!
already_checked.at(trial_site.y) = true; //now safe to flag this carbon as having been checked already
indices->push_back(trial_site);
site_completed = true;
}
if(verbose) {
if(!site_completed) printf("this O atom did not constitute part of an aldehyde group\n"); else printf("site found!\n");
}
}
}
} else if(site_type==A_P_CATECHOL) { //A_P_CATECHOL SITES
for(int i=0; i<num_atoms; i++) {
if(molecule->at(i).type=="C" && !already_checked.at(i)) { //found a new carbon; potentially a connection site
if(verbose) printf("found a C atom\n");
INT3 trial_site;
trial_site.x = i;
already_checked.at(trial_site.x) = true;
//is this a connection site? we need to find if there are four bonds: two to CH3 and two to OC
bool cannot_be_site_first_C = false;
int num_non_H_bonds_first_C = 0;
vector<int> bonded_ids;
for(int j=0; j<num_atoms && !cannot_be_site_first_C; j++) { //find how many non-H atoms are bonded to this O
if(
molecule->at(j).type!="H" && j!=trial_site.x && bonded(molecule->at(trial_site.x), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)
) {
if(verbose) printf("first C (%d) is bonded to %s (%d) with distance %.3f\n", trial_site.x, molecule->at(j).type.c_str(), j, dist(molecule->at(trial_site.x), molecule->at(j)));
num_non_H_bonds_first_C++;
bonded_ids.push_back(j);
}
}
if(num_non_H_bonds_first_C!=4) cannot_be_site_first_C = true;
else { //find out if those 4 bonds are the 4 we are expecting
int num_bonds_to_CH3_first_C = 0;
int num_bonds_to_OC_first_C = 0;
vector<int> bonded_CH3_ids;
vector<int> OC_C_ids;
bool fail = false;
for(int j=0; j<num_non_H_bonds_first_C; j++) {
int id = bonded_ids.at(j);
if(molecule->at(id).type=="O" && (!already_checked.at(id))) { //test for OC
int num_other_bonds = 0;
int other_bond_id = -1;
for(int k=0; k<num_atoms; k++) {
if(
( k!=id && k!=trial_site.x && molecule->at(k).type=="H" && bonded(molecule->at(id), molecule->at(k), MAX_HYDROGEN_BOND_LENGTH) )
||
( k!=id && k!=trial_site.x && molecule->at(k).type!="H" && bonded(molecule->at(id), molecule->at(k), MAX_CARBOXY_BOND_LENGTH) )
) {
if(verbose) printf("an O on this first C is bonded to %s with distance %.3f\n", molecule->at(k).type.c_str(), dist(molecule->at(id), molecule->at(k)));
other_bond_id = k;
num_other_bonds++;
}
}
if(num_other_bonds!=1) fail=true; else {OC_C_ids.push_back(other_bond_id); num_bonds_to_OC_first_C++;}
} else if(molecule->at(id).type=="C") { //test for CH3
int num_H = 0;
for(int k=0; k<num_atoms; k++) {
if(
k!=id && k!=trial_site.x && molecule->at(k).type=="H" && bonded(molecule->at(id), molecule->at(k), MAX_HYDROGEN_BOND_LENGTH)
) {
if(verbose) printf("a C on this first C is bonded to %s with distance %.3f\n", molecule->at(k).type.c_str(), dist(molecule->at(id), molecule->at(k)));
num_H++;
}
}
if(num_H!=3) fail=true; else {bonded_CH3_ids.push_back(bonded_ids.at(j)); num_bonds_to_CH3_first_C++;}
}
}
if(num_bonds_to_OC_first_C!=2 || num_bonds_to_CH3_first_C!=2 || fail) {
printf("NOTE: this first C fails here with %d bonds to OC and %d bonds to CH3 groups\n", num_bonds_to_OC_first_C, num_bonds_to_CH3_first_C);
cannot_be_site_first_C = true;
} else if(!bonded(molecule->at(OC_C_ids.at(0)), molecule->at(OC_C_ids.at(1)), MAX_CARBOXY_BOND_LENGTH)) cannot_be_site_first_C = true;
else { //this is a C from an a_p_catechol group
trial_site.y = bonded_CH3_ids.at(0);
trial_site.z = bonded_CH3_ids.at(1);
already_checked.at(trial_site.y) = true;
already_checked.at(trial_site.z) = true;
//at this point, this is a site!
indices->push_back(trial_site);
}
}
if(verbose) {
if(cannot_be_site_first_C) printf("this C atom did not constitute part of an a_p_catechol group\n"); else printf("site found!\n");
}
}
}
} else if(site_type==DIALCOHOL) { //DIALCOHOL SITES
for(int i=0; i<num_atoms; i++) {
if(molecule->at(i).type=="O" && !already_checked.at(i)) { //found a new oxygen; potentially a connection site
if(verbose) printf("found an O atom\n");
INT3 trial_site;
trial_site.x = i;
already_checked.at(trial_site.x) = true;
//is this a connection site? we need to find if it is an OH, bonded to a C, which is bonded to another C-O-H
bool cannot_be_site_first_O = false;
int num_C_bonds_first_O = 0;
int num_H_bonds_first_O = 0;
int first_C_id = -1;
for(int j=0; j<num_atoms && !cannot_be_site_first_O; j++) { //find bonds
if(
(!already_checked.at(j)) && molecule->at(j).type=="C" && j!=trial_site.x && bonded(molecule->at(trial_site.x), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)
) {
if(verbose) printf("first O is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(trial_site.x), molecule->at(j)));
num_C_bonds_first_O++;
first_C_id = j;
} else if(
(!already_checked.at(j)) && molecule->at(j).type=="H" && j!=trial_site.x && bonded(molecule->at(trial_site.x), molecule->at(j), MAX_HYDROGEN_BOND_LENGTH)
) {
if(verbose) printf("first O is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(trial_site.x), molecule->at(j)));
num_H_bonds_first_O++;
}
}
if(num_C_bonds_first_O!=1 || num_H_bonds_first_O!=1) cannot_be_site_first_O = true;
else { //we know this is an H-O-C, but does the C connect us to another C-O-H? check bonding environment of first C
already_checked.at(first_C_id) = true; //we can flag this first C as being considered, since no other C-O-H group will contain it
vector<int> second_C_id_possibilities;
for(int j=0; j<num_atoms && !cannot_be_site_first_O; j++) { //find bonds
if(
(!already_checked.at(j)) && molecule->at(j).type=="C" && j!=first_C_id && bonded(molecule->at(first_C_id), molecule->at(j), MAX_CARBOXY_BOND_LENGTH)
) {
if(verbose) printf("first C is bonded to %s with distance %.3f\n", molecule->at(j).type.c_str(), dist(molecule->at(first_C_id), molecule->at(j)));
second_C_id_possibilities.push_back(j);
}
}
if(second_C_id_possibilities.size()<1) cannot_be_site_first_O = true;
else { //there are some second C choices to consider
bool site_found = false; //allow to quit these loops early as soon as a site is found
for(int j=0; j<second_C_id_possibilities.size() && !site_found; j++) {
//this second C must be bonded to an OH
int candidate_second_C_id = second_C_id_possibilities.at(j);
for(int k=0; k<num_atoms && !cannot_be_site_first_O && !site_found; k++) { //find bonds
if(
(!already_checked.at(k)) && molecule->at(k).type=="O" && bonded(molecule->at(candidate_second_C_id), molecule->at(k), MAX_CARBOXY_BOND_LENGTH)
) {
if(verbose) printf("candidate second C is bonded to %s with distance %.3f\n", molecule->at(k).type.c_str(), dist(molecule->at(candidate_second_C_id), molecule->at(k)));
//if this k O is an OH, we are good to go
int num_H = 0;
for(int l=0; l<num_atoms && !cannot_be_site_first_O && !site_found; l++) { //find bonds
if( molecule->at(l).type=="H" && bonded(molecule->at(k), molecule->at(l), MAX_HYDROGEN_BOND_LENGTH) ) {
num_H++;
if(verbose) printf("candidate second C's O is bonded to %s with distance %.3f\n", molecule->at(l).type.c_str(), dist(molecule->at(l), molecule->at(k)));
}
}
if(num_H==1) { //satisfied that this is a site
trial_site.y = k;
//we need to find where the z site is, because it is not an atom!
//first find the centroid of site.x, site.y and the two carbons, first_C_id and candidate_second_C_id
XYZ site_centroid = ( molecule->at(candidate_second_C_id).xyz() + molecule->at(first_C_id).xyz() + molecule->at(trial_site.y).xyz() + molecule->at(trial_site.x).xyz() ).scale(0.25);
double atom_centroid_distance = dist(site_centroid.x,site_centroid.y,site_centroid.z,molecule->at(trial_site.x));
XYZ projection_of_centroid = project_onto_line(site_centroid, molecule->at(trial_site.x).xyz(), molecule->at(trial_site.y).xyz());
XYZ new_atom_vector = (projection_of_centroid-site_centroid).unit();
XYZ new_atom_pos = site_centroid+(new_atom_vector.scale(atom_centroid_distance));
//make a new atom at this position
ATOM new_atom(new_atom_pos,"Z",0.0);
molecule->push_back(new_atom);
already_checked.push_back(true);
trial_site.z = num_atoms;
num_atoms++;
already_checked.at(trial_site.y) = true;
site_found = true;
//at this point, this is a site!
indices->push_back(trial_site);
}
}
}
}
//at this stage, this is a dead end
if(!site_found) cannot_be_site_first_O = true;
}
}
if(verbose) {
if(cannot_be_site_first_O) printf("this O atom did not constitute part of a dialcohol group\n"); else printf("site found!\n");
}
}
}
} else {
printf("ERROR: did not recognize site type %d\n", site_type);
exit(EXIT_FAILURE);
}
}
void read_molecule(string filename, vector<ATOM> *atom_vector) {
//this function inspects the filename, and decides which read function to call - for xyz or incon format
string extension_start = ".";
unsigned pos = filename.rfind(extension_start);
if(pos==-1) {
printf("ERROR: could not identify extension for the input file named \"%s\"\n", filename.c_str());
exit(EXIT_FAILURE);
}
string xyz_format = "xyz";
unsigned pos2 = filename.find(xyz_format, pos);
if(pos2!=-1) {
//we found xyz in the file extension - treat it as an xyz format file
read_xyz(filename, atom_vector);
} else {
//not xyz .. is it incon?
string incon_format = "incon";
unsigned pos3 = filename.find(incon_format, pos);
if(pos3!=-1) {
//we found incon in the file extension - treat it as an incon format file
read_incon(filename, atom_vector);
} else {
printf("ERROR: could not parse either \"%s\" or \"%s\" in the extension for the input file named \"%s\"\n", xyz_format.c_str(), incon_format.c_str(), filename.c_str());
exit(EXIT_FAILURE);
}
}
}
void read_incon(string filename, vector<ATOM> *atom_vector) {
bool verbose = false;
int status = 0;
//open input
FILE *input;
input = fopen(filename.c_str(), "r");
if(input==NULL) {
printf("ERROR: could not open file with name %s. Please try again.\n", filename.c_str());
exit(EXIT_FAILURE);
}
//read input
int num_atoms_read = 0;
char ch1[MAX_CHAR_ARRAY_LENGTH] = "";
bool done_reading_atoms = false;
bool started_reading_atoms = false;
// char *atom_line_second_column = new char[MAX_CHAR_ARRAY_LENGTH];
// atom_line_second_column = "core";
char atom_line_second_column[MAX_CHAR_ARRAY_LENGTH] = "core";
while(fgets(ch1, MAX_CHAR_ARRAY_LENGTH, input)!=NULL && !done_reading_atoms) {
// vector<string> token;
// token = split(ch1," \r\t");
double x=0,y=0,z=0;
char *name = new char[MAX_CHAR_ARRAY_LENGTH];
char *dummy = new char[MAX_CHAR_ARRAY_LENGTH];
status = sscanf(ch1, "%s %s %lf %lf %lf", name, dummy, &x, &y, &z);
// if(token.size()==5) { //a line comprising an atom name, a string, and three coords
if(strcmp(atom_line_second_column,dummy)==0) { //line contains an atom in incon format!
started_reading_atoms = true;
ATOM a;
// char *name = new char[MAX_CHAR_ARRAY_LENGTH];
// char *dummy = new char[MAX_CHAR_ARRAY_LENGTH];
// status = sscanf(ch1, "%s %s %lf %lf %lf", name, dummy, &a.x, &a.y, &a.z);
a.x = x; a.y = y; a.z = z;
string name_string(name);
a.label = name_string;
//parse out any digits from the name of the element
int name_length = name_string.length();
int digit_pos = -1;
for(int i=0; i<name_length && digit_pos==-1; i++) {
if(isdigit(name_string[i])) digit_pos = i;
}
if(digit_pos==0) { //first character was a digit - this is no good
if(started_reading_atoms) done_reading_atoms = true; //if we have already started parsing atom data, and encounter a line without a valid atom name, then we should stop
} else {
if(digit_pos>0) {
a.type = name_string.substr(0,digit_pos);
} else a.type = name_string;
//good to go - store in vector
a.radius = get_rad(a.type);
if(verbose) printf("atom %s assigned radius %.3f\n", a.type.c_str(), a.radius);
delete[] name;
delete[] dummy;
atom_vector->push_back(a);
}
} else {
//printf("DEBUG: line did not have 5 tokens (%d tokens): %s\n", num_tokens, ch1);
//printf("DEBUG: line did not have %s as the second component: %s\n", atom_line_second_column, ch1);
if(started_reading_atoms) done_reading_atoms = true; //if we have already started parsing atom data, and encounter a line without atom data, then we should stop
}
}
if(!done_reading_atoms) {
printf("ERROR: finished reading data but did not finishing parsing atom info correctly - managed to read %d atoms\n", (int)(atom_vector->size()));
exit(EXIT_FAILURE);
}
}
void read_xyz(string filename, vector<ATOM> *atom_vector) {
bool verbose = false;
int status = 0;
//open input
FILE *input;
input = fopen(filename.c_str(), "r");
if(input==NULL) {
printf("ERROR: could not open file with name %s. Please try again.\n", filename.c_str());
exit(EXIT_FAILURE);
}
//read input
char ch1[MAX_CHAR_ARRAY_LENGTH] = "";
int num_input_atoms = -1;
if(fgets(ch1, MAX_CHAR_ARRAY_LENGTH, input)!=NULL) {
string str = string(ch1);
int pos=0;
char c = str[pos];
while(c<=0) { //for some reason, xyz files from marvinsketch have three characters at the beginning with ascii codes <0 - very strange, but we need to remove these to succesfully parse any data
pos++;
c = str[pos];
}
char ch2[MAX_CHAR_ARRAY_LENGTH] = "";
str.copy(ch2, str.size()-pos, pos);
status = sscanf(ch2, "%d", &num_input_atoms);
if(num_input_atoms<=0) {
printf("ERROR: number of atoms to be read from file is %d<=0\n", num_input_atoms);
exit(EXIT_FAILURE);
}
} else {
printf("ERROR: could not read string\n");
exit(EXIT_FAILURE);
}
search_for_char(input, '\n'); //now we are on a line containing an atom
for(int i=0; i<num_input_atoms; i++) {
ATOM a;
char ch[MAX_CHAR_ARRAY_LENGTH];
if(fgets(ch, MAX_CHAR_ARRAY_LENGTH, input)!=NULL) {
string str = string(ch);
int pos=0;
char c = str[pos];
while(c<=0) { //for some reason, xyz files from marvinsketch have three characters at the beginning with ascii codes <0 - very strange, but we need to remove these to succesfully parse any data
pos++;
c = str[pos];
}
char ch2[MAX_CHAR_ARRAY_LENGTH] = "";
str.copy(ch2, str.size()-pos, pos);
char *name = new char[MAX_CHAR_ARRAY_LENGTH];
status = sscanf(ch2, "%s %lf %lf %lf", name, &a.x, &a.y, &a.z);
string name_string = string(name);
a.label = name_string;
//parse out any digits from the name of the element
int name_length = name_string.length();
int digit_pos = -1;
for(int i=0; i<name_length && digit_pos==-1; i++) {
if(isdigit(name_string[i])) digit_pos = i;
}
if(digit_pos==0) { //first character was a digit - this is no good
printf("ERROR: could not parse label from atom beginning with a digit in read_xyz: %s: %s\n", filename.c_str(), name_string.c_str());
exit(EXIT_FAILURE);
} else {
if(digit_pos>0) {
a.type = name_string.substr(0,digit_pos);
} else a.type = name_string;
//printf("DEBUG: with name_string=%s, digit_pos=%d, therefore a.type=%s\n", name_string.c_str(), digit_pos, a.type.c_str());
}
a.radius = get_rad(a.type);
if(verbose) printf("atom %s assigned radius %.3f\n", a.type.c_str(), a.radius);
delete[] name;
} else {
printf("ERROR: could not read expected atom coord string from %s - %d out of %d atom coords were read\n", filename.c_str(), i, num_input_atoms);
exit(EXIT_FAILURE);
}
char match = 0;
atom_vector->push_back(a);
}
fclose(input);
}
void write_xyz(FILE *outfile, vector<ATOM> *atom_vector, string input_name) {
int num_atoms_total = atom_vector->size();
int num_atoms_to_print = 0;
for(int i=0; i<num_atoms_total; i++) {
if(atom_vector->at(i).keep) num_atoms_to_print++;
}
fprintf(outfile, "%d\nabstract molecule created from input %s\n", num_atoms_to_print, input_name.c_str());
for(int i=0; i<num_atoms_total; i++) {
if(atom_vector->at(i).keep) {
ATOM a = atom_vector->at(i);
fprintf(outfile, "%s %.6f %.6f %.6f\n", a.label.c_str(), a.x, a.y, a.z);
// fprintf(outfile, "%s %.6f %.6f %.6f\n", a.type.c_str(), a.x, a.y, a.z);
}
}
fclose(outfile);
}
/*
void search_for_char(FILE *f, char target) {
char c = getc(f);
while(c!=target && c!=EOF) {
c = getc(f);
}
if(c==EOF) {
printf("ERROR: The required character (%c, with int value %d) was not found in this file.\n", target, (int)target);
exit(EXIT_FAILURE);
}
}
*/
bool bonded(ATOM a, ATOM b, double d) {
if(dist(a,b)<d) return true; else return false;
}
double dist(ATOM a, ATOM b) {
XYZ a_xyz(a.x,a.y,a.z);
XYZ b_xyz(b.x,b.y,b.z);
return (a_xyz-b_xyz).magnitude();
/*
double dx = a.xyz.x-b.xyz.x;
double dy = a.xyz.y-b.xyz.y;
double dz = a.xyz.z-b.xyz.z;
return sqrt((dx*dx)+(dy*dy)+(dz*dz));
*/
}
double dist(double x, double y, double z, ATOM b) {
XYZ a_xyz(x,y,z);
XYZ b_xyz(b.x,b.y,b.z);
return (a_xyz-b_xyz).magnitude();
/*
double dx = x-b.xyz.x;
double dy = y-b.xyz.y;
double dz = z-b.xyz.z;
return sqrt((dx*dx)+(dy*dy)+(dz*dz));
*/
}
double get_rad(string s) { //CCDC radii
if(s=="H") return 1.09;
else if(s=="He") return 1.4;
else if(s=="Li") return 1.82;
else if(s=="Be") return 2;
else if(s=="B") return 2;
else if(s=="C") return 1.7;
else if(s=="N") return 1.55;
else if(s=="O") return 1.52;
else if(s=="F") return 1.47;
else if(s=="Ne") return 1.54;
else if(s=="Na") return 2.27;
else if(s=="Mg") return 1.73;
else if(s=="Al") return 2;
else if(s=="Si") return 2.1;
else if(s=="P") return 1.8;
else if(s=="S") return 1.8;
else if(s=="Cl") return 1.75;
else if(s=="Ar") return 1.88;
else if(s=="K") return 2.75;
else if(s=="Ca") return 2;
else if(s=="Sc") return 2;
else if(s=="Ti") return 2;
else if(s=="V") return 2;
else if(s=="Cr") return 2;
else if(s=="Mn") return 2;
else if(s=="Fe") return 2;
else if(s=="Co") return 2;
else if(s=="Ni") return 1.63;
else if(s=="Cu") return 1.4;
else if(s=="Zn") return 1.39;
else if(s=="Ga") return 1.87;
else if(s=="Ge") return 2;
else if(s=="As") return 1.85;
else if(s=="Se") return 1.9;
else if(s=="Br") return 1.85;
else if(s=="Kr") return 2.02;
else if(s=="Rb") return 2;
else if(s=="Sr") return 2;
else if(s=="Y") return 2;
else if(s=="Zr") return 2;
else if(s=="Nb") return 2;
else if(s=="Mo") return 2;
else if(s=="Tc") return 2;
else if(s=="Ru") return 2;
else if(s=="Rh") return 2;
else if(s=="Pd") return 1.63;
else if(s=="Ag") return 1.72;
else if(s=="Cd") return 1.58;
else if(s=="In") return 1.93;
else if(s=="Sn") return 2.17;
else if(s=="Sb") return 2;
else if(s=="Te") return 2.06;
else if(s=="I") return 1.98;
else if(s=="Xe") return 2.16;
else if(s=="Cs") return 2;
else if(s=="Ba") return 2;
else if(s=="La") return 2;
else if(s=="Ce") return 2;
else if(s=="Pr") return 2;
else if(s=="Nd") return 2;
else if(s=="Pm") return 2;
else if(s=="Sm") return 2;
else if(s=="Eu") return 2;
else if(s=="Gd") return 2;
else if(s=="Tb") return 2;
else if(s=="Dy") return 2;
else if(s=="Ho") return 2;
else if(s=="Er") return 2;
else if(s=="Tm") return 2;
else if(s=="Yb") return 2;
else if(s=="Lu") return 2;
else if(s=="Hf") return 2;
else if(s=="Ta") return 2;
else if(s=="W") return 2;
else if(s=="Re") return 2;
else if(s=="Os") return 2;
else if(s=="Ir") return 2;
else if(s=="Pt") return 1.72;
else if(s=="Au") return 1.66;
else if(s=="Hg") return 1.55;
else if(s=="Tl") return 1.96;
else if(s=="Pb") return 2.02;
else if(s=="Bi") return 2;
else if(s=="Po") return 2;
else if(s=="At") return 2;
else if(s=="Rn") return 2;
else if(s=="Fr") return 2;
else if(s=="Ra") return 2;
else if(s=="Ac") return 2;
else if(s=="Th") return 2;
else if(s=="Pa") return 2;
else if(s=="U") return 1.86;
else if(s=="Np") return 2;
else if(s=="Pu") return 2;
else if(s=="Am") return 2;
else if(s=="Cm") return 2;
else if(s=="Bk") return 2;
else if(s=="Cf") return 2;
else if(s=="Es") return 2;
else if(s=="Fm") return 2;
else if(s=="Md") return 2;
else if(s=="No") return 2;
else if(s=="Lr") return 2;
else if(s=="Rf") return 2;
else if(s=="Db") return 2;
else if(s=="Sg") return 2;
else if(s=="Bh") return 2;
else if(s=="Hs") return 2;
else if(s=="Mt") return 2;
else if(s=="Ds") return 2;
else {
printf("WARNING: could not find radius for element type %s - using default of %.3f\n", s.c_str(), DEFAULT_RADIUS);
return DEFAULT_RADIUS;
}
}
INT3::INT3() {
x = 0; y = 0; z = 0;
}
double radians_to_degrees(double r) {return 360.0*r/(2.0*PI);}
/*
vector<string> split(string line, string delims) {
vector<string> token;
string temp=line;
int ndx;
while(!temp.empty()) {
ndx = temp.find_first_of(delims);
if(ndx>0) {
token.push_back(temp.substr(0,ndx));
}
else if(ndx ==-1) {
token.push_back(temp);
return token;
}
temp=temp.substr(ndx+1);
}
return token;
}
*/
//OLD CODE BELOW HERE
/*
ATOM::ATOM(double x0, double y0, double z0, string s0, double r0) {
XYZ xyz1(x0,y0,z0);
xyz = xyz1;
name = s0;
rad = r0;
keep = true;
}
ATOM::ATOM(XYZ xyz0, string s0, double r0) {
xyz = xyz0;
name = s0;
rad = r0;
keep = true;
}
ATOM::ATOM() {
name = "";
rad = 0;
keep = true;
}
*/
/*
bool increasing_rmsd (FIT i, FIT j) { return (i.rmsd<j.rmsd); }
*/
//ATOM
/*
class ATOM {
public:
bool keep;
XYZ xyz; //the Cartesian position of this ATOM
double rad;
string name;
//constructor
ATOM(double x0, double y0, double z0, string s0, double r0); //separate Cartesian values constructor
ATOM(XYZ xyz0, string s0, double r0); //XYZ constructor
ATOM();
};
*/
//FIT
/*
class FIT{
public:
vector<ATOM> molecule;
double rmsd;
int perm_ID;
};
*/
/*
//XYZ
class XYZ {
public:
double x, y, z;
//constructor
XYZ(double x0, double y0, double z0);
XYZ();
//methods
double angle_between(XYZ other);
double dot_product(XYZ other);
XYZ cross_product(XYZ other);
double magnitude();
XYZ scale(double factor);
XYZ unit();
XYZ operator-(XYZ other);
XYZ operator+(XYZ other);
};
*/
/*
XYZ::XYZ(double x0, double y0, double z0) {